############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AffyRNADegradation.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings AffyRNADegradation_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/AffyRNADegradation.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘AffyRNADegradation/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AffyRNADegradation’ version ‘1.46.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘AffyRNADegradation’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ComputeTongs: no visible global function definition for ‘filter’ ComputeTongs: no visible global function definition for ‘na.omit’ EstimateHookParams: no visible global function definition for ‘loess’ EstimateHookParams: no visible global function definition for ‘quantile’ GetTongs: no visible global function definition for ‘ave’ PlotDegradationHooks: no visible global function definition for ‘rainbow’ PlotDegradationHooks: no visible global function definition for ‘lines’ PlotDegradationHooks: no visible global function definition for ‘legend’ PlotDx: no visible global function definition for ‘grid’ PlotDx: no visible global function definition for ‘points’ PlotDx: no visible global function definition for ‘lines’ PlotTongs: no visible global function definition for ‘grid’ PlotTongs: no visible global function definition for ‘lines’ PlotTongs: no visible global function definition for ‘legend’ RNADegradation: no visible global function definition for ‘ave’ RNADegradation: no visible global function definition for ‘loess’ RNADegradation: no visible global function definition for ‘approx’ RNADegradation: no visible global function definition for ‘new’ TryToFitDecayFunction: no visible global function definition for ‘nls’ TryToFitDecayFunction: no visible global function definition for ‘coef’ getProbeInfo.index: no visible global function definition for ‘ave’ Undefined global functions or variables: approx ave coef filter grid legend lines loess na.omit new nls points quantile rainbow Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "grid", "legend", "lines", "points") importFrom("methods", "new") importFrom("stats", "approx", "ave", "coef", "filter", "loess", "na.omit", "nls", "quantile") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘AffyRNADegradation-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: AffyDegradationBatch-class > ### Title: Class AffyDegradationBatch > ### Aliases: AffyDegradationBatch-class AffyDegradationBatch,ANY > ### AffyDegradationBatch d afbatch plotDx d,AffyDegradationBatch-method > ### afbatch,AffyDegradationBatch-method > ### plotDx,AffyDegradationBatch-method > ### Keywords: classes > > ### ** Examples > > if (require(AmpAffyExample)) { + # Get example data + data(AmpData) + + affy.deg <- RNADegradation(AmpData[,4]) + + ## Plot degradation + plotDx(affy.deg) + + ## Get degradation measure + d(affy.deg) + + ## Get AffyBatch object with corrected probe intensities + afbatch(affy.deg) + } Loading required package: AmpAffyExample also installing the dependencies ‘sys’, ‘bitops’, ‘cli’, ‘glue’, ‘lifecycle’, ‘fastmap’, ‘askpass’, ‘RCurl’, ‘GenomeInfoDbData’, ‘bit’, ‘rlang’, ‘vctrs’, ‘cachem’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘R6’, ‘XVector’, ‘GenomeInfoDb’, ‘crayon’, ‘bit64’, ‘blob’, ‘memoise’, ‘pkgconfig’, ‘httr’, ‘png’, ‘Biostrings’, ‘IRanges’, ‘DBI’, ‘RSQLite’, ‘S4Vectors’, ‘KEGGREST’, ‘AnnotationDbi’ trying URL 'https://cloud.r-project.org/src/contrib/sys_3.4.2.tar.gz' Content type 'application/x-gzip' length 20169 bytes (19 KB) ================================================== downloaded 19 KB trying URL 'https://cloud.r-project.org/src/contrib/bitops_1.0-7.tar.gz' Content type 'application/x-gzip' length 10809 bytes (10 KB) ================================================== downloaded 10 KB trying URL 'https://cloud.r-project.org/src/contrib/cli_3.6.1.tar.gz' Content type 'application/x-gzip' length 567293 bytes (553 KB) ================================================== downloaded 553 KB trying URL 'https://cloud.r-project.org/src/contrib/glue_1.6.2.tar.gz' Content type 'application/x-gzip' length 106510 bytes (104 KB) ================================================== downloaded 104 KB trying URL 'https://cloud.r-project.org/src/contrib/lifecycle_1.0.3.tar.gz' Content type 'application/x-gzip' length 106854 bytes (104 KB) ================================================== downloaded 104 KB trying URL 'https://cloud.r-project.org/src/contrib/fastmap_1.1.1.tar.gz' Content type 'application/x-gzip' length 46412 bytes (45 KB) ================================================== downloaded 45 KB trying URL 'https://cloud.r-project.org/src/contrib/askpass_1.2.0.tar.gz' Content type 'application/x-gzip' length 6040 bytes ================================================== downloaded 6040 bytes trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.12.tar.gz' Content type 'application/x-gzip' length 731481 bytes (714 KB) ================================================== downloaded 714 KB trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GenomeInfoDbData_1.2.10.tar.gz' Content type 'application/x-gzip' length 12026674 bytes (11.5 MB) ================================================== downloaded 11.5 MB trying URL 'https://cloud.r-project.org/src/contrib/bit_4.0.5.tar.gz' Content type 'application/x-gzip' length 827745 bytes (808 KB) ================================================== downloaded 808 KB trying URL 'https://cloud.r-project.org/src/contrib/rlang_1.1.1.tar.gz' Content type 'application/x-gzip' length 762533 bytes (744 KB) ================================================== downloaded 744 KB trying URL 'https://cloud.r-project.org/src/contrib/vctrs_0.6.4.tar.gz' Content type 'application/x-gzip' length 968450 bytes (945 KB) ================================================== downloaded 945 KB trying URL 'https://cloud.r-project.org/src/contrib/cachem_1.0.8.tar.gz' Content type 'application/x-gzip' length 26510 bytes (25 KB) ================================================== downloaded 25 KB trying URL 'https://cloud.r-project.org/src/contrib/curl_5.1.0.tar.gz' Content type 'application/x-gzip' length 714157 bytes (697 KB) ================================================== downloaded 697 KB trying URL 'https://cloud.r-project.org/src/contrib/jsonlite_1.8.7.tar.gz' Content type 'application/x-gzip' length 1053075 bytes (1.0 MB) ================================================== downloaded 1.0 MB trying URL 'https://cloud.r-project.org/src/contrib/mime_0.12.tar.gz' Content type 'application/x-gzip' length 12562 bytes (12 KB) ================================================== downloaded 12 KB trying URL 'https://cloud.r-project.org/src/contrib/openssl_2.1.1.tar.gz' Content type 'application/x-gzip' length 1206233 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cloud.r-project.org/src/contrib/R6_2.5.1.tar.gz' Content type 'application/x-gzip' length 63422 bytes (61 KB) ================================================== downloaded 61 KB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/XVector_0.40.0.tar.gz' Content type 'application/x-gzip' length 67818 bytes (66 KB) ================================================== downloaded 66 KB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/GenomeInfoDb_1.36.4.tar.gz' Content type 'application/x-gzip' length 3579119 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://cloud.r-project.org/src/contrib/crayon_1.5.2.tar.gz' Content type 'application/x-gzip' length 40567 bytes (39 KB) ================================================== downloaded 39 KB trying URL 'https://cloud.r-project.org/src/contrib/bit64_4.0.5.tar.gz' Content type 'application/x-gzip' length 135091 bytes (131 KB) ================================================== downloaded 131 KB trying URL 'https://cloud.r-project.org/src/contrib/blob_1.2.4.tar.gz' Content type 'application/x-gzip' length 10620 bytes (10 KB) ================================================== downloaded 10 KB trying URL 'https://cloud.r-project.org/src/contrib/memoise_2.0.1.tar.gz' Content type 'application/x-gzip' length 17852 bytes (17 KB) ================================================== downloaded 17 KB trying URL 'https://cloud.r-project.org/src/contrib/pkgconfig_2.0.3.tar.gz' Content type 'application/x-gzip' length 6080 bytes ================================================== downloaded 6080 bytes trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.7.tar.gz' Content type 'application/x-gzip' length 118500 bytes (115 KB) ================================================== downloaded 115 KB trying URL 'https://cloud.r-project.org/src/contrib/png_0.1-8.tar.gz' Content type 'application/x-gzip' length 24880 bytes (24 KB) ================================================== downloaded 24 KB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/Biostrings_2.68.1.tar.gz' Content type 'application/x-gzip' length 12446699 bytes (11.9 MB) ================================================== downloaded 11.9 MB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/IRanges_2.34.1.tar.gz' Content type 'application/x-gzip' length 480919 bytes (469 KB) ================================================== downloaded 469 KB trying URL 'https://cloud.r-project.org/src/contrib/DBI_1.1.3.tar.gz' Content type 'application/x-gzip' length 730243 bytes (713 KB) ================================================== downloaded 713 KB trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.1.tar.gz' Content type 'application/x-gzip' length 4149793 bytes (4.0 MB) ================================================== downloaded 4.0 MB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/S4Vectors_0.38.2.tar.gz' Content type 'application/x-gzip' length 836628 bytes (817 KB) ================================================== downloaded 817 KB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/KEGGREST_1.40.1.tar.gz' Content type 'application/x-gzip' length 21902 bytes (21 KB) ================================================== downloaded 21 KB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.62.2.tar.gz' Content type 'application/x-gzip' length 4359178 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz' Content type 'application/x-gzip' length 1732200 bytes (1.7 MB) ================================================== downloaded 1.7 MB * installing *source* package ‘sys’ ... ** package ‘sys’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c exec.c -o exec.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o sys.so exec.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-sys/00new/sys/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sys) * installing *source* package ‘bitops’ ... ** package ‘bitops’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bit-ops.c -o bit-ops.o bit-ops.c: In function ‘bitShiftL’: bit-ops.c:125:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 125 | else *(xaAb++)=(double) (_2_UINT_(xa[i]) __OP__ I_2_UINT(xb[j] & 31 ) ) ; \ | ^ bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’ 6 | #define I_2_UINT(I) (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I)) | ^ bit-ops.c:145:5: note: in expansion of macro ‘bitshift_BODY’ 145 | bitshift_BODY( << ); | ^~~~~~~~~~~~~ bit-ops.c:136:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 136 | else *(xaAb++)=(double) (_2_UINT_(xa[j]) __OP__ I_2_UINT(xb[i] & 31 )) ; \ | ^ bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’ 6 | #define I_2_UINT(I) (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I)) | ^ bit-ops.c:145:5: note: in expansion of macro ‘bitshift_BODY’ 145 | bitshift_BODY( << ); | ^~~~~~~~~~~~~ bit-ops.c: In function ‘bitShiftR’: bit-ops.c:125:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 125 | else *(xaAb++)=(double) (_2_UINT_(xa[i]) __OP__ I_2_UINT(xb[j] & 31 ) ) ; \ | ^ bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’ 6 | #define I_2_UINT(I) (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I)) | ^ bit-ops.c:149:5: note: in expansion of macro ‘bitshift_BODY’ 149 | bitshift_BODY( >> ); | ^~~~~~~~~~~~~ bit-ops.c:136:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 136 | else *(xaAb++)=(double) (_2_UINT_(xa[j]) __OP__ I_2_UINT(xb[i] & 31 )) ; \ | ^ bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’ 6 | #define I_2_UINT(I) (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I)) | ^ bit-ops.c:149:5: note: in expansion of macro ‘bitshift_BODY’ 149 | bitshift_BODY( >> ); | ^~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cksum.c -o cksum.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o bitops.so bit-ops.o cksum.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-bitops/00new/bitops/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bitops) * installing *source* package ‘cli’ ... ** package ‘cli’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c ansi.c -o ansi.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c cleancall.c -o cleancall.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c diff.c -o diff.o diff.c: In function ‘clic_diff_chr’: diff.c:104:3: warning: ‘sn’ may be used uninitialized [-Wmaybe-uninitialized] 104 | SET_VECTOR_ELT(result, 0, allocVector(INTSXP, sn)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c errors.c -o errors.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c glue.c -o glue.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c inst.c -o inst.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c keypress-unix.c -o keypress-unix.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c keypress-win.c -o keypress-win.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c keypress.c -o keypress.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c md5.c -o md5.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c progress-altrep.c -o progress-altrep.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c progress.c -o progress.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c sha1.c -o sha1.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c sha256.c -o sha256.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c thread.c -o thread.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c tty.c -o tty.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c utf8.c -o utf8.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c vt.c -o vt.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c vtparse.c -o vtparse.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c vtparse_table.c -o vtparse_table.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c win-utf8.c -o win-utf8.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c winfiles.c -o winfiles.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-cli/00new/cli/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cli) * installing *source* package ‘glue’ ... ** package ‘glue’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glue.c -o glue.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c trim.c -o trim.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-glue/00new/glue/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (glue) * installing *source* package ‘fastmap’ ... ** package ‘fastmap’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ilib/ -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -Wall -c fastmap.cpp -o fastmap.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ilib/ -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o fastmap.so fastmap.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-fastmap/00new/fastmap/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fastmap) * installing *source* package ‘GenomeInfoDbData’ ... ** using staged installation ** data ** inst ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomeInfoDbData) * installing *source* package ‘bit’ ... ** package ‘bit’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c attrutil.c -o attrutil.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bit.c -o bit.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c chunkutil.c -o chunkutil.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c clone.c -o clone.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c integerutil.c -o integerutil.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c merge.c -o merge.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rle.c -o rle.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sort.c -o sort.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o bit.so attrutil.o bit.o chunkutil.o clone.o init.o integerutil.o merge.o rle.o sort.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-bit/00new/bit/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bit) * installing *source* package ‘rlang’ ... ** package ‘rlang’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c capture.c -o capture.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c internal.c -o internal.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rlang.c -o rlang.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c version.c -o version.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o rlang.so capture.o internal.o rlang.o version.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-rlang/00new/rlang/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rlang) * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu Using PKG_LIBS=-lcurl ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c callbacks.c -o callbacks.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c curl.c -o curl.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c download.c -o download.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c escape.c -o escape.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c fetch.c -o fetch.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c form.c -o form.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c getdate.c -o getdate.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c handle.c -o handle.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ieproxy.c -o ieproxy.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c interrupt.c -o interrupt.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c multi.c -o multi.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c nslookup.c -o nslookup.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c options.c -o options.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c reflist.c -o reflist.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c split.c -o split.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ssl.c -o ssl.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c typechecking.c -o typechecking.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c version.c -o version.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c winidn.c -o winidn.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c writer.c -o writer.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-curl/00new/curl/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (curl) * installing *source* package ‘jsonlite’ ... ** package ‘jsonlite’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c base64.c -o base64.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c collapse_array.c -o collapse_array.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c collapse_object.c -o collapse_object.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c collapse_pretty.c -o collapse_pretty.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c escape_chars.c -o escape_chars.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c integer64_to_na.c -o integer64_to_na.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c is_datelist.c -o is_datelist.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c is_recordlist.c -o is_recordlist.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c is_scalarlist.c -o is_scalarlist.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c modp_numtoa.c -o modp_numtoa.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c null_to_na.c -o null_to_na.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c num_to_char.c -o num_to_char.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c parse.c -o parse.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c prettify.c -o prettify.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c push_parser.c -o push_parser.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c r-base64.c -o r-base64.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c register.c -o register.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c row_collapse.c -o row_collapse.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c transpose_list.c -o transpose_list.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c validate.c -o validate.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl.c -o yajl/yajl.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_buf.c -o yajl/yajl_buf.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_encode.c -o yajl/yajl_encode.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_gen.c -o yajl/yajl_gen.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_lex.c -o yajl/yajl_lex.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_parser.c -o yajl/yajl_parser.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_tree.c -o yajl/yajl_tree.o ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-jsonlite/00new/jsonlite/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs” in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime” in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms” in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json” in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64” in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist” in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob” in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar” in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf” in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc” in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (jsonlite) * installing *source* package ‘mime’ ... ** package ‘mime’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rawmatch.c -o rawmatch.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o mime.so init.o rawmatch.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-mime/00new/mime/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mime) * installing *source* package ‘R6’ ... ** package ‘R6’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (R6) * installing *source* package ‘crayon’ ... ** package ‘crayon’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (crayon) * installing *source* package ‘pkgconfig’ ... ** package ‘pkgconfig’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pkgconfig) * installing *source* package ‘png’ ... ** package ‘png’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -Wall -c dummy.c -o dummy.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -Wall -c read.c -o read.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -Wall -c write.c -o write.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o png.so dummy.o read.o write.o -lpng16 -lm -lz -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-png/00new/png/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (png) * installing *source* package ‘DBI’ ... ** package ‘DBI’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DBI) * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c AEbufs.c -o AEbufs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c DataFrame_class.c -o DataFrame_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Hits_class.c -o Hits_class.o In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41, from ../inst/include/S4Vectors_defines.h:18, from S4Vectors.h:1, from Hits_class.c:4: Hits_class.c: In function ‘Hits_new’: /home/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:886:33: warning: ‘revmap’ may be used uninitialized in this function [-Wmaybe-uninitialized] 886 | #define defineVar Rf_defineVar | ^~~~~~~~~~~~ Hits_class.c:216:19: note: ‘revmap’ was declared here 216 | SEXP ans, revmap, symbol; | ^~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c LLint_class.c -o LLint_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c List_class.c -o List_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rle_class.c -o Rle_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rle_utils.c -o Rle_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c SEXP_utils.c -o SEXP_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c SimpleList_class.c -o SimpleList_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c anyMissing.c -o anyMissing.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c character_utils.c -o character_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c eval_utils.c -o eval_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash_utils.c -o hash_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c integer_utils.c -o integer_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c logical_utils.c -o logical_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c raw_utils.c -o raw_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c safe_arithm.c -o safe_arithm.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sort_utils.c -o sort_utils.o sort_utils.c:263:13: warning: ‘sort_uchar_array’ defined but not used [-Wunused-function] 263 | static void sort_uchar_array(unsigned char *x, int nelt, int desc) | ^~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c subsetting_utils.c -o subsetting_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c vector_utils.c -o vector_utils.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-S4Vectors/00new/S4Vectors/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List” Creating a new generic function for ‘unname’ in package ‘S4Vectors’ Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’ Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’ Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame” Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table” Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (S4Vectors) * installing *source* package ‘lifecycle’ ... ** package ‘lifecycle’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lifecycle) * installing *source* package ‘askpass’ ... ** package ‘askpass’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c askpass.c -o askpass.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o askpass.so askpass.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-askpass/00new/askpass/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (askpass) * installing *source* package ‘RCurl’ ... ** package ‘RCurl’ successfully unpacked and MD5 sums checked ** using staged installation checking for curl-config... /usr/bin/curl-config checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking how to run the C preprocessor... gcc -E Version has a libidn field Version has CURLOPT_URL Version has CURLINFO_EFFECTIVE_URL Version has CURLINFO_RESPONSE_CODE Version has CURLINFO_TOTAL_TIME Version has CURLINFO_NAMELOOKUP_TIME Version has CURLINFO_CONNECT_TIME Version has CURLINFO_PRETRANSFER_TIME Version has CURLINFO_SIZE_UPLOAD Version has CURLINFO_SIZE_DOWNLOAD Version has CURLINFO_SPEED_DOWNLOAD Version has CURLINFO_SPEED_UPLOAD Version has CURLINFO_HEADER_SIZE Version has CURLINFO_REQUEST_SIZE Version has CURLINFO_SSL_VERIFYRESULT Version has CURLINFO_FILETIME Version has CURLINFO_CONTENT_LENGTH_DOWNLOAD Version has CURLINFO_CONTENT_LENGTH_UPLOAD Version has CURLINFO_STARTTRANSFER_TIME Version has CURLINFO_CONTENT_TYPE Version has CURLINFO_REDIRECT_TIME Version has CURLINFO_REDIRECT_COUNT Version has CURLINFO_PRIVATE Version has CURLINFO_HTTP_CONNECTCODE Version has CURLINFO_HTTPAUTH_AVAIL Version has CURLINFO_PROXYAUTH_AVAIL Version has CURLINFO_OS_ERRNO Version has CURLINFO_NUM_CONNECTS Version has CURLINFO_SSL_ENGINES Version has CURLINFO_COOKIELIST Version has CURLINFO_LASTSOCKET Version has CURLINFO_FTP_ENTRY_PATH Version has CURLINFO_REDIRECT_URL Version has CURLINFO_PRIMARY_IP Version has CURLINFO_APPCONNECT_TIME Version has CURLINFO_CERTINFO Version has CURLINFO_CONDITION_UNMET Version has CURLOPT_WRITEDATA Version has CURLOPT_KEYPASSWD Version has CURLOPT_DIRLISTONLY Version has CURLOPT_APPEND Version has CURLOPT_KRBLEVEL Version has CURLOPT_USE_SSL Version has CURLOPT_TIMEOUT_MS Version has CURLOPT_CONNECTTIMEOUT_MS Version has CURLOPT_HTTP_TRANSFER_DECODING Version has CURLOPT_HTTP_CONTENT_DECODING Version has CURLOPT_NEW_FILE_PERMS Version has CURLOPT_NEW_DIRECTORY_PERMS Version has CURLOPT_POSTREDIR Version has CURLOPT_OPENSOCKETFUNCTION Version has CURLOPT_OPENSOCKETDATA Version has CURLOPT_COPYPOSTFIELDS Version has CURLOPT_PROXY_TRANSFER_MODE Version has CURLOPT_SEEKFUNCTION Version has CURLOPT_SEEKDATA Version has CURLOPT_CRLFILE Version has CURLOPT_ISSUERCERT Version has CURLOPT_ADDRESS_SCOPE Version has CURLOPT_CERTINFO Version has CURLOPT_USERNAME Version has CURLOPT_PASSWORD Version has CURLOPT_PROXYUSERNAME Version has CURLOPT_PROXYPASSWORD Version has CURLOPT_SSH_HOST_PUBLIC_KEY_MD5 Version has CURLOPT_NOPROXY Version has CURLOPT_TFTP_BLKSIZE Version has CURLOPT_SOCKS5_GSSAPI_SERVICE Version has CURLOPT_SOCKS5_GSSAPI_NEC Version has CURLOPT_PROTOCOLS Version has CURLOPT_REDIR_PROTOCOLS Version has CURLOPT_SSH_AUTH_TYPES Version has CURLOPT_SSH_PUBLIC_KEYFILE Version has CURLOPT_SSH_PRIVATE_KEYFILE Version has CURLOPT_FTP_SSL_CCC Version has CURLOPT_COOKIELIST Version has CURLOPT_IGNORE_CONTENT_LENGTH Version has CURLOPT_FTP_SKIP_PASV_IP Version has CURLOPT_FTP_FILEMETHOD Version has CURLOPT_LOCALPORT Version has CURLOPT_LOCALPORTRANGE Version has CURLOPT_CONNECT_ONLY Version has CURLOPT_CONV_FROM_NETWORK_FUNCTION Version has CURLOPT_CONV_TO_NETWORK_FUNCTION Version has CURLOPT_CONV_FROM_UTF8_FUNCTION Version has CURLOPT_MAX_SEND_SPEED_LARGE Version has CURLOPT_MAX_RECV_SPEED_LARGE Version has CURLOPT_FTP_ALTERNATIVE_TO_USER Version has CURLOPT_SOCKOPTFUNCTION Version has CURLOPT_SOCKOPTDATA Version has CURLOPT_SSL_SESSIONID_CACHE libcurl version: libcurl 7.81.0 configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c base64.c -o base64.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c curl.c -o curl.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c curlInit.c -o curlInit.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c curl_base64.c -o curl_base64.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c enums.c -o enums.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c json.c -o json.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c memoryManagement.c -o memoryManagement.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c myUTF8.c -o myUTF8.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -lcurl -lxml2 -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-RCurl/00new/RCurl/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RCurl) * installing *source* package ‘cachem’ ... ** package ‘cachem’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cache.c -o cache.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o cachem.so cache.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-cachem/00new/cachem/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cachem) * installing *source* package ‘bit64’ ... ** package ‘bit64’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bsearch.c -o bsearch.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cache.c -o cache.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash64.c -o hash64.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c integer64.c -o integer64.o integer64.c: In function ‘runif_integer64’: integer64.c:998:15: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 998 | while( (*((long long *) &ii)) == NA_INTEGER64){ | ~^~~~~~~~~~~~~~~~~~ integer64.c:1006:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 1006 | ret[i] = min + ( (long long)(*((unsigned long long *)(&ii))) % d); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sort64.c -o sort64.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sortuse64.c -o sortuse64.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o bit64.so bsearch.o cache.o hash64.o init.o integer64.o sort64.o sortuse64.o -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-bit64/00new/bit64/libs ** R ** data ** exec ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bit64) * installing *source* package ‘IRanges’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c CompressedList_class.c -o CompressedList_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Grouping_class.c -o Grouping_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c IPosRanges_comparison.c -o IPosRanges_comparison.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_class.c -o IRanges_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_constructor.c -o IRanges_constructor.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c NCList.c -o NCList.o NCList.c:1173:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function] 1173 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist, | ^~~~~~~~~~~~~~~~~~~~~~~~~ NCList.c:202:22: warning: ‘next_top_down’ defined but not used [-Wunused-function] 202 | static const NCList *next_top_down(const NCList *nclist) | ^~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_IRanges.c -o R_init_IRanges.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Ranges_class.c -o Ranges_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c RleViews_utils.c -o RleViews_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c coverage_methods.c -o coverage_methods.o coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’: coverage_methods.c:579:35: warning: ‘x_end’ may be used uninitialized in this function [-Wmaybe-uninitialized] 579 | if (*out_ranges_are_tiles && x_end != cvg_len) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ coverage_methods.c:495:28: note: ‘x_end’ was declared here 495 | i, j, x_start, x_end, shift_elt, tmp; | ^~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractListFragments.c -o extractListFragments.o extractListFragments.c: In function ‘C_find_partition_overlaps’: extractListFragments.c:66:33: warning: ‘split_partitions_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized] 66 | IntAE_insert_at(split_partitions_buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 | IntAE_get_nelt(split_partitions_buf), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | q_prev_end); | ~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c inter_range_methods.c -o inter_range_methods.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-IRanges/00new/IRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (IRanges) * installing *source* package ‘vctrs’ ... ** package ‘vctrs’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c altrep-lazy-character.c -o altrep-lazy-character.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c altrep-rle.c -o altrep-rle.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c altrep.c -o altrep.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c arg-counter.c -o arg-counter.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c arg.c -o arg.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c assert.c -o assert.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c bind.c -o bind.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c c-unchop.c -o c-unchop.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c c.c -o c.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c callables.c -o callables.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c cast-bare.c -o cast-bare.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c cast-dispatch.c -o cast-dispatch.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c cast.c -o cast.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c compare.c -o compare.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c complete.c -o complete.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c conditions.c -o conditions.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c dictionary.c -o dictionary.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c dim.c -o dim.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c empty.c -o empty.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c equal.c -o equal.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c expand.c -o expand.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c fields.c -o fields.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c fill.c -o fill.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c globals.c -o globals.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c group.c -o group.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c growable.c -o growable.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c hash.c -o hash.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c interval.c -o interval.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c match-joint.c -o match-joint.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c match.c -o match.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c missing.c -o missing.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c names.c -o names.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-collate.c -o order-collate.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-groups.c -o order-groups.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-sortedness.c -o order-sortedness.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-truelength.c -o order-truelength.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order.c -o order.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c poly-op.c -o poly-op.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c proxy-restore.c -o proxy-restore.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c proxy.c -o proxy.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype-common.c -o ptype-common.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype.c -o ptype.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype2-dispatch.c -o ptype2-dispatch.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype2.c -o ptype2.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rank.c -o rank.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rep.c -o rep.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rlang-dev.c -o rlang-dev.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rlang.c -o rlang.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c runs.c -o runs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c set.c -o set.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c shape.c -o shape.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c size-common.c -o size-common.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c size.c -o size.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-array.c -o slice-array.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-assign-array.c -o slice-assign-array.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-assign.c -o slice-assign.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-chop.c -o slice-chop.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-interleave.c -o slice-interleave.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice.c -o slice.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c split.c -o split.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c subscript-loc.c -o subscript-loc.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c subscript.c -o subscript.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c translate.c -o translate.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-data-frame.c -o type-data-frame.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-date-time.c -o type-date-time.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-factor.c -o type-factor.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-info.c -o type-info.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-integer64.c -o type-integer64.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-tibble.c -o type-tibble.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c typeof2-s3.c -o typeof2-s3.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c typeof2.c -o typeof2.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c unspecified.c -o unspecified.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c utils-dispatch.c -o utils-dispatch.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c vctrs-core.c -o vctrs-core.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c version.c -o version.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o vctrs.so altrep-lazy-character.o altrep-rle.o altrep.o arg-counter.o arg.o assert.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o empty.o equal.o expand.o fields.o fill.o globals.o group.o growable.o hash.o init.o interval.o match-joint.o match.o missing.o names.o order-collate.o order-groups.o order-sortedness.o order-truelength.o order.o poly-op.o proxy-restore.o proxy.o ptype-common.o ptype.o ptype2-dispatch.o ptype2.o rank.o rep.o rlang-dev.o rlang.o runs.o set.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice-interleave.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-integer64.o type-tibble.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils.o vctrs-core.o version.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-vctrs/00new/vctrs/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (vctrs) * installing *source* package ‘openssl’ ... ** package ‘openssl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3 ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c aes.c -o aes.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c base64.c -o base64.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c bignum.c -o bignum.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c cert.c -o cert.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c compatibility.c -o compatibility.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c diffie.c -o diffie.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c envelope.c -o envelope.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c error.c -o error.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c hash.c -o hash.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c info.c -o info.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c keygen.c -o keygen.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c keys.c -o keys.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c onload.c -o onload.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c openssh.c -o openssh.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c password.c -o password.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c pbkdf.c -o pbkdf.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c pem.c -o pem.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c pkcs12.c -o pkcs12.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c pkcs7.c -o pkcs7.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c rand.c -o rand.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c rsa.c -o rsa.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c signing.c -o signing.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c ssl.c -o ssl.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c stream.c -o stream.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c write.c -o write.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c x25519.c -o x25519.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c bcrypt/blowfish.c -o bcrypt/blowfish.o ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -l:libssl.so.3 -l:libcrypto.so.3 -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-openssl/00new/openssl/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (openssl) * installing *source* package ‘XVector’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c RDS_random_access.c -o RDS_random_access.o RDS_random_access.c: In function ‘RDS_extract_subarray’: RDS_random_access.c:796:25: warning: unused variable ‘ans’ [-Wunused-variable] 796 | SEXP subscript, ans; | ^~~ RDS_random_access.c:793:18: warning: variable ‘x_type’ set but not used [-Wunused-but-set-variable] 793 | SEXPTYPE x_type; | ^~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_XVector.c -o R_init_XVector.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedDouble_class.c -o SharedDouble_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedInteger_class.c -o SharedInteger_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedRaw_class.c -o SharedRaw_class.o SharedRaw_class.c: In function ‘SharedRaw_read_complexes_from_subscript’: SharedRaw_class.c:396:20: warning: variable ‘src_tag’ set but not used [-Wunused-but-set-variable] 396 | SEXP dest, src_tag; | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedVector_class.c -o SharedVector_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XDouble_class.c -o XDouble_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XInteger_class.c -o XInteger_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XRawList_comparison.c -o XRawList_comparison.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XRaw_class.c -o XRaw_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVectorList_class.c -o XVectorList_class.o XVectorList_class.c: In function ‘_new_XRawList_from_CharAEAE’: XVectorList_class.c:459:17: warning: ‘lkup_length’ may be used uninitialized in this function [-Wmaybe-uninitialized] 459 | _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 460 | (char *) dest.ptr, dest.length, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 461 | src->elts, CharAE_get_nelt(src), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 462 | lkup0, lkup_length); | ~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_class.c -o XVector_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c io_utils.c -o io_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c slice_methods.c -o slice_methods.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c vector_copy.c -o vector_copy.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c view_summarization_methods.c -o view_summarization_methods.o view_summarization_methods.c: In function ‘get_which_min_from_Ints_holder’: view_summarization_methods.c:219:45: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized] 219 | if (which_min == NA_INTEGER || x < cur_min) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c: In function ‘get_which_min_from_Doubles_holder’: view_summarization_methods.c:246:45: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized] 246 | if (which_min == NA_INTEGER || x < cur_min) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c: In function ‘get_which_max_from_Ints_holder’: view_summarization_methods.c:269:45: warning: ‘cur_max’ may be used uninitialized in this function [-Wmaybe-uninitialized] 269 | if (which_max == NA_INTEGER || x > cur_max) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c: In function ‘get_which_max_from_Doubles_holder’: view_summarization_methods.c:296:45: warning: ‘cur_max’ may be used uninitialized in this function [-Wmaybe-uninitialized] 296 | if (which_max == NA_INTEGER || x > cur_max) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-XVector/00new/XVector/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (XVector) * installing *source* package ‘GenomeInfoDb’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomeInfoDb) * installing *source* package ‘memoise’ ... ** package ‘memoise’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (memoise) * installing *source* package ‘blob’ ... ** package ‘blob’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (blob) * installing *source* package ‘httr’ ... ** package ‘httr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (httr) * installing *source* package ‘Biostrings’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c BAB_class.c -o BAB_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c BitMatrix.c -o BitMatrix.o BitMatrix.c:299:13: warning: ‘BitMatrix_print’ defined but not used [-Wunused-function] 299 | static void BitMatrix_print(BitMatrix *bitmat) | ^~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c MIndex_class.c -o MIndex_class.o MIndex_class.c: In function ‘SparseMIndex_endIndex’: MIndex_class.c:184:27: warning: unused variable ‘poffsets_order’ [-Wunused-variable] 184 | IntAE *poffsets, *poffsets_order; | ^~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XStringSet_class.c -o XStringSet_class.o XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’: XStringSet_class.c:124:17: warning: ‘lkup_len’ may be used uninitialized in this function [-Wmaybe-uninitialized] 124 | _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | INTEGER(start)[i], lkup0, lkup_len); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XString_class.c -o XString_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c align_needwunsQS.c -o align_needwunsQS.o align_needwunsQS.c: In function ‘align_needwunsQS’: align_needwunsQS.c:155:29: warning: ‘sc’ may be used uninitialized in this function [-Wmaybe-uninitialized] 155 | INTEGER(ans_elt)[0] = score; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c align_utils.c -o align_utils.o align_utils.c: In function ‘PairwiseAlignmentsSingleSubject_align_aligned’: align_utils.c:250:42: warning: ‘indelWidthSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized] 250 | jPattern += indelWidthSubject; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:231:63: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized] 231 | if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) { | ~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:239:72: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized] 239 | mappedStringPtr[index] = gapCodeValue; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ align_utils.c:232:78: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized] 232 | if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c gtestsim.c -o gtestsim.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c inject_code.c -o inject_code.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c letter_frequency.c -o letter_frequency.o letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’: letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable] 957 | int x_width, y_width, x_length, *ans_mat, i, x_pos; | ^~~~~ letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable] 956 | SEXP ans, ans_dimnames; | ^~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_PWM.c -o match_PWM.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern.c -o match_pattern.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern_indels.c -o match_pattern_indels.o match_pattern_indels.c:7:13: warning: ‘test_match_pattern_indels’ defined but not used [-Wunused-function] 7 | static void test_match_pattern_indels(const char *p, const char *s, | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict.c -o match_pdict.o match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’: match_pdict.c:419:33: warning: ‘ans_col’ may be used uninitialized in this function [-Wmaybe-uninitialized] 419 | ans_col += tb_length; | ~~~~~~~~^~~~~~~~~~~~ match_pdict.c:392:65: note: ‘ans_col’ was declared here 392 | int tb_length, S_length, collapse0, i, j, match_count, *ans_col; | ^~~~~~~ match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’: match_pdict.c:470:41: warning: ‘ans_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized] 470 | ans_elt += P_length; | ~~~~~~~~^~~~~~~~~~~ match_pdict.c:441:64: note: ‘ans_elt’ was declared here 441 | int P_length, S_length, collapse0, i, j, match_count, *ans_elt; | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o match_pdict_ACtree2.c: In function ‘split_and_move_pointers’: match_pdict_ACtree2.c:1031:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable] 1031 | ACnode *node0, *node1, *node2; | ^~~~~ match_pdict_ACtree2.c: In function ‘merge_pointers’: match_pdict_ACtree2.c:1076:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable] 1076 | ACnode *node0, *node1, *node2; | ^~~~~ At top level: match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function] 602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function] 139 | static void debug_node_counting_functions(int maxdepth) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o match_pdict_Twobit.c: In function ‘build_Twobit’: match_pdict_Twobit.c:75:27: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized] 75 | PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos)); | ^~~~~~~~~~~~~~~~~~~~~ match_pdict_Twobit.c:110:19: note: ‘twobit_sign2pos’ was declared here 110 | SEXP ans, twobit_sign2pos; | ^~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict_utils.c -o match_pdict_utils.o match_pdict_utils.c: In function ‘match_ppheadtail0’: match_pdict_utils.c:653:56: warning: unused variable ‘ncol’ [-Wunused-variable] 653 | int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol; | ^~~~ match_pdict_utils.c: In function ‘match_ppheadtail’: match_pdict_utils.c:713:13: warning: unused variable ‘nelt’ [-Wunused-variable] 713 | int nelt, nkey0, nkey1, nkey2, i, key; | ^~~~ match_pdict_utils.c: In function ‘_match_pdict_all_flanks’: match_pdict_utils.c:820:51: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~~~~ match_pdict_utils.c:820:34: warning: unused variable ‘total_NFC’ [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~ match_pdict_utils.c:819:40: warning: unused variable ‘NFC’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~ match_pdict_utils.c:819:33: warning: unused variable ‘nloci’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~~ match_pdict_utils.c:819:27: warning: unused variable ‘ndup’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~ At top level: match_pdict_utils.c:820:34: warning: ‘total_NFC’ defined but not used [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~ match_pdict_utils.c:820:51: warning: ‘subtotal_NFC’ defined but not used [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~~~~ match_pdict_utils.c:261:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function] 261 | static void match_headtail_by_loc(const HeadTail *headtail, | ^~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_reporting.c -o match_reporting.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c matchprobes.c -o matchprobes.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c read_fasta_files.c -o read_fasta_files.o In function ‘new_FASTAloaderExt’, inlined from ‘read_fasta_files’ at read_fasta_files.c:430:15: read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 186 | return loader_ext; | ^~~~~~~~~~ read_fasta_files.c: In function ‘read_fasta_files’: read_fasta_files.c:182:24: note: ‘loader_ext’ declared here 182 | FASTAloaderExt loader_ext; | ^~~~~~~~~~ In function ‘new_FASTAloaderExt’, inlined from ‘read_fasta_files’ at read_fasta_files.c:430:15: read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.length’ may be used uninitialized [-Wmaybe-uninitialized] 186 | return loader_ext; | ^~~~~~~~~~ read_fasta_files.c: In function ‘read_fasta_files’: read_fasta_files.c:182:24: note: ‘loader_ext’ declared here 182 | FASTAloaderExt loader_ext; | ^~~~~~~~~~ In function ‘new_FASTAloaderExt’, inlined from ‘read_fasta_blocks’ at read_fasta_files.c:596:15: read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.ptr’ is used uninitialized [-Wuninitialized] 186 | return loader_ext; | ^~~~~~~~~~ read_fasta_files.c: In function ‘read_fasta_blocks’: read_fasta_files.c:182:24: note: ‘loader_ext’ declared here 182 | FASTAloaderExt loader_ext; | ^~~~~~~~~~ In function ‘new_FASTAloaderExt’, inlined from ‘read_fasta_blocks’ at read_fasta_files.c:596:15: read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.length’ is used uninitialized [-Wuninitialized] 186 | return loader_ext; | ^~~~~~~~~~ read_fasta_files.c: In function ‘read_fasta_blocks’: read_fasta_files.c:182:24: note: ‘loader_ext’ declared here 182 | FASTAloaderExt loader_ext; | ^~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c read_fastq_files.c -o read_fastq_files.o read_fastq_files.c: In function ‘parse_FASTQ_file’: read_fastq_files.c:392:28: warning: ‘dont_load’ may be used uninitialized in this function [-Wmaybe-uninitialized] 392 | if (dont_load || loader->new_empty_seq_hook == NULL) | ^ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c replaceAt.c -o replaceAt.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c replace_letter_at.c -o replace_letter_at.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c strutils.c -o strutils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c translate.c -o translate.o translate.c: In function ‘DNAStringSet_translate’: translate.c:110:36: warning: ‘if_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized] 110 | if (if_ambig == TRANSLATE_ERROR) { | ^ translate.c:136:36: note: ‘if_ambig0’ was declared here 136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode; | ^~~~~~~~~ translate.c:106:36: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized] 106 | if (if_non_ambig == TRANSLATE_TO_X) | ^ translate.c:136:21: note: ‘if_non_ambig0’ was declared here 136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode; | ^~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o utils.c: In function ‘_get_twobit_signature’: utils.c:157:16: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized] 157 | return twobit_sign; | ^~~~~~~~~~~ utils.c: In function ‘_get_twobit_signature_at’: utils.c:164:19: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized] 164 | int i, j, twobit_sign; | ^~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include' -I'/tmp/RtmpkVk01s/RLIBS_310b25799169c2/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c xscat.c -o xscat.o In file included from /tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include/S4Vectors_defines.h:18, from /tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include/IRanges_defines.h:18, from ../inst/include/Biostrings_defines.h:18, from Biostrings.h:1, from xscat.c:1: xscat.c: In function ‘XString_xscat’: /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:91:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized] 91 | #define NEW_RAW(n) Rf_allocVector(RAWSXP,n) | ^~~~~~~~~~~~~~ xscat.c:18:20: note: ‘ans_length’ was declared here 18 | int nargs, ans_length, tag_offset, j; | ^~~~~~~~~~ xscat.c:52:23: warning: ‘ans_classname’ may be used uninitialized in this function [-Wmaybe-uninitialized] 52 | PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag)); | ^~~~~~~~~~~~~~~~~ In file included from /tmp/RtmpkVk01s/RLIBS_310b25799169c2/S4Vectors/include/S4Vectors_defines.h:18, from /tmp/RtmpkVk01s/RLIBS_310b25799169c2/IRanges/include/IRanges_defines.h:18, from ../inst/include/Biostrings_defines.h:18, from Biostrings.h:1, from xscat.c:1: xscat.c: In function ‘XStringSet_xscat’: /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:85:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized] 85 | #define NEW_INTEGER(n) Rf_allocVector(INTSXP,n) | ^~~~~~~~~~~~~~ xscat.c:66:39: note: ‘ans_length’ was declared here 66 | int nargs, *arg_lengths, *ii, ans_length, i, j, *width; | ^~~~~~~~~~ xscat.c:108:23: warning: ‘ans_element_type’ may be used uninitialized in this function [-Wmaybe-uninitialized] 108 | PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width)); | ^~~~~~~~~~~~~~~~~ gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /tmp/RtmpkVk01s/RLIBS_310b25799169c2/00LOCK-Biostrings/00new/Biostrings/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet” Creating a new generic function for ‘strsplit’ in package ‘Biostrings’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’ Creating a new generic function for ‘pattern’ in package ‘Biostrings’ Creating a new generic function for ‘offset’ in package ‘Biostrings’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Biostrings) ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’ * removing ‘/tmp/RtmpkVk01s/RLIBS_310b25799169c2/RSQLite’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘RSQLite’ had non-zero exit status * installing *source* package ‘KEGGREST’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (KEGGREST) ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’ * removing ‘/tmp/RtmpkVk01s/RLIBS_310b25799169c2/AnnotationDbi’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘AnnotationDbi’ had non-zero exit status ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu133acdf’ * removing ‘/tmp/RtmpkVk01s/RLIBS_310b25799169c2/hgu133acdf’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘hgu133acdf’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmpOXzneF/downloaded_packages’ Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HG-U133A Library - package hgu133acdf not installed Library - package hgu133acdf not installed Calls: RNADegradation ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘vignette.Rnw’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘vignette.Rnw’ ... The downloaded source packages are in ‘/tmp/RtmpfSkhaU/downloaded_packages’ When sourcing ‘vignette.R’: Error: Could not obtain CDF environment, problems encountered: Specified environment does not contain HG-U133A Library - package hgu133acdf not installed Library - package hgu133acdf not installed Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘vignette.Rnw’ using Sweave Loading required package: affy Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’ trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.1.tar.gz' Content type 'application/x-gzip' length 4149793 bytes (4.0 MB) ================================================== downloaded 4.0 MB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.62.2.tar.gz' Content type 'application/x-gzip' length 4359178 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz' Content type 'application/x-gzip' length 1732200 bytes (1.7 MB) ================================================== downloaded 1.7 MB ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’ * removing ‘/tmp/RtmpkVk01s/RLIBS_310b25799169c2/RSQLite’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘RSQLite’ had non-zero exit status ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’ * removing ‘/tmp/RtmpkVk01s/RLIBS_310b25799169c2/AnnotationDbi’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘AnnotationDbi’ had non-zero exit status ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu133acdf’ * removing ‘/tmp/RtmpkVk01s/RLIBS_310b25799169c2/hgu133acdf’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘hgu133acdf’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmpvVih79/downloaded_packages’ Warning: missing cdf environment! in show(AffyBatch) also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’ trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.1.tar.gz' Content type 'application/x-gzip' length 4149793 bytes (4.0 MB) ================================================== downloaded 4.0 MB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.62.2.tar.gz' Content type 'application/x-gzip' length 4359178 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz' Content type 'application/x-gzip' length 1732200 bytes (1.7 MB) ================================================== downloaded 1.7 MB ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’ * removing ‘/tmp/RtmpkVk01s/RLIBS_310b25799169c2/RSQLite’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘RSQLite’ had non-zero exit status ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’ * removing ‘/tmp/RtmpkVk01s/RLIBS_310b25799169c2/AnnotationDbi’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘AnnotationDbi’ had non-zero exit status ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu133acdf’ * removing ‘/tmp/RtmpkVk01s/RLIBS_310b25799169c2/hgu133acdf’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘hgu133acdf’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmpvVih79/downloaded_packages’ Error: processing vignette 'vignette.Rnw' failed with diagnostics: Could not obtain CDF environment, problems encountered: Specified environment does not contain HG-U133A Library - package hgu133acdf not installed Library - package hgu133acdf not installed --- failed re-building ‘vignette.Rnw’ SUMMARY: processing the following file failed: ‘vignette.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/AffyRNADegradation.Rcheck/00check.log’ for details.