############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TurboNorm.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings TurboNorm_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TurboNorm.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 ‘TurboNorm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TurboNorm’ version ‘1.48.0’ * 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 ‘TurboNorm’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 Packages in Depends field not imported from: ‘convert’ ‘limma’ ‘marray’ 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 normalize.AffyBatch.pspline: no visible global function definition for ‘intensity<-’ pspline: no visible global function definition for ‘as’ pspline: no visible global function definition for ‘maRb<-’ pspline: no visible global function definition for ‘maGb<-’ pspline: no visible global function definition for ‘maA’ pspline: no visible global function definition for ‘maM’ pspline: no visible global function definition for ‘layout’ pspline: no visible global function definition for ‘maM<-’ pspline: no visible global function definition for ‘lines’ turbotrend: no visible global function definition for ‘median’ Undefined global functions or variables: as intensity<- layout lines maA maGb<- maM maM<- maRb<- median Consider adding importFrom("graphics", "layout", "lines") importFrom("methods", "as") importFrom("stats", "median") 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘TurboNorm-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: normalize.pspline > ### Title: Functions for single-colour microarray data normalization using > ### the P-splines > ### Aliases: normalize.pspline normalize.AffyBatch.pspline > ### Keywords: smooth > > ### ** Examples > > > library(affydata) Loading required package: affy Package LibPath Item [1,] "affydata" "/home/biocbuild/bbs-3.17-bioc/R/site-library" "Dilution" Title [1,] "AffyBatch instance Dilution" > data(Dilution) > PM <- log2(pm(Dilution[,c(1,3)])) also installing the dependencies ‘sys’, ‘bitops’, ‘askpass’, ‘RCurl’, ‘GenomeInfoDbData’, ‘bit’, ‘curl’, ‘openssl’, ‘XVector’, ‘GenomeInfoDb’, ‘crayon’, ‘bit64’, ‘blob’, ‘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/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/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/openssl_2.1.1.tar.gz' Content type 'application/x-gzip' length 1206233 bytes (1.2 MB) ================================================== downloaded 1.2 MB 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/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/hgu95av2cdf_2.18.0.tar.gz' Content type 'application/x-gzip' length 1331391 bytes (1.3 MB) ================================================== downloaded 1.3 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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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 ‘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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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 ‘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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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 ‘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 ‘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 ‘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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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 ‘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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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 ‘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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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 ‘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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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) ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’ * removing ‘/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/RSQLite’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘RSQLite’ had non-zero exit status * 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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/IRanges/include' -I'/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c xscat.c -o xscat.o In file included from /tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include/S4Vectors_defines.h:18, from /tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/S4Vectors/include/S4Vectors_defines.h:18, from /tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/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/RtmpGFt18V/RLIBS_57a0622a33bd0/00LOCK-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) * 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/RtmpGFt18V/RLIBS_57a0622a33bd0/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 ‘hgu95av2cdf’ * removing ‘/tmp/RtmpGFt18V/RLIBS_57a0622a33bd0/hgu95av2cdf’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘hgu95av2cdf’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmpCcaVOT/downloaded_packages’ Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HG_U95Av2 Library - package hgu95av2cdf not installed Library - package hgu95av2cdf not installed Calls: pm -> pm -> .local -> getCdfInfo Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘turbonorm.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/TurboNorm.Rcheck/00check.log’ for details.