############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:RefPlus.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings RefPlus_1.72.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/RefPlus.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘RefPlus/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RefPlus’ version ‘1.72.0’ * 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 ‘RefPlus’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘affyPLM’ 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 rma.para: no visible global function definition for ‘rmaPLM’ rma.para: no visible global function definition for ‘coefs.probe’ rma.para: no visible global function definition for ‘coefs’ Undefined global functions or variables: coefs coefs.probe rmaPLM * checking Rd files ... NOTE prepare_Rd: colMedians.Rd:19: Dropping empty section \references prepare_Rd: rmaref.predict.Rd:29-30: Dropping empty section \examples * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘RefPlus-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: RefPlus-package > ### Title: RMA based on reference microarrays: RMA+ and RMA++ methods > ### Aliases: RefPlus-package RefPlus > ### Keywords: package > > ### ** Examples > > if (require(affydata)) { + ## Use Dilution in affydata package + data(Dilution) + + ##Calculate RMA intensities using the rma function. + Ex0<-exprs(rma(Dilution)) + + ## Background correct, estimate the probe effects, and calculate the + ## RMA intensities using rma.para function. + Para<-rma.para(Dilution, bg=TRUE,exp=TRUE) + Ex1<-Para[[3]] + + ## Calculate the RMA+ intensity using rmaplus function. + Ex2<-rmaplus(Dilution, rmapara=Para, bg = TRUE) + } Loading required package: affydata Package LibPath Item [1,] "affydata" "/home/biocbuild/bbs-3.18-bioc/R/site-library" "Dilution" Title [1,] "AffyBatch instance Dilution" also installing the dependencies ‘sys’, ‘cli’, ‘glue’, ‘lifecycle’, ‘fastmap’, ‘askpass’, ‘bit’, ‘vctrs’, ‘cachem’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘R6’, ‘bit64’, ‘blob’, ‘memoise’, ‘pkgconfig’, ‘rlang’, ‘httr’, ‘png’, ‘DBI’, ‘RSQLite’, ‘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/cli_3.6.2.tar.gz' Content type 'application/x-gzip' length 569771 bytes (556 KB) ================================================== downloaded 556 KB trying URL 'https://cloud.r-project.org/src/contrib/glue_1.7.0.tar.gz' Content type 'application/x-gzip' length 105420 bytes (102 KB) ================================================== downloaded 102 KB trying URL 'https://cloud.r-project.org/src/contrib/lifecycle_1.0.4.tar.gz' Content type 'application/x-gzip' length 107656 bytes (105 KB) ================================================== downloaded 105 KB trying URL 'https://cloud.r-project.org/src/contrib/fastmap_1.1.1.tar.gz' Content type 'application/x-gzip' length 46412 bytes (45 KB) ================================================== downloaded 45 KB trying URL 'https://cloud.r-project.org/src/contrib/askpass_1.2.0.tar.gz' Content type 'application/x-gzip' length 6040 bytes ================================================== downloaded 6040 bytes trying URL 'https://cloud.r-project.org/src/contrib/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/vctrs_0.6.5.tar.gz' Content type 'application/x-gzip' length 969066 bytes (946 KB) ================================================== downloaded 946 KB trying URL 'https://cloud.r-project.org/src/contrib/cachem_1.0.8.tar.gz' Content type 'application/x-gzip' length 26510 bytes (25 KB) ================================================== downloaded 25 KB trying URL 'https://cloud.r-project.org/src/contrib/curl_5.2.1.tar.gz' Content type 'application/x-gzip' length 716695 bytes (699 KB) ================================================== downloaded 699 KB trying URL 'https://cloud.r-project.org/src/contrib/jsonlite_1.8.8.tar.gz' Content type 'application/x-gzip' length 1053028 bytes (1.0 MB) ================================================== downloaded 1.0 MB trying URL 'https://cloud.r-project.org/src/contrib/mime_0.12.tar.gz' Content type 'application/x-gzip' length 12562 bytes (12 KB) ================================================== downloaded 12 KB trying URL 'https://cloud.r-project.org/src/contrib/openssl_2.1.1.tar.gz' Content type 'application/x-gzip' length 1206233 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cloud.r-project.org/src/contrib/R6_2.5.1.tar.gz' Content type 'application/x-gzip' length 63422 bytes (61 KB) ================================================== downloaded 61 KB trying URL 'https://cloud.r-project.org/src/contrib/bit64_4.0.5.tar.gz' Content type 'application/x-gzip' length 135091 bytes (131 KB) ================================================== downloaded 131 KB trying URL 'https://cloud.r-project.org/src/contrib/blob_1.2.4.tar.gz' Content type 'application/x-gzip' length 10620 bytes (10 KB) ================================================== downloaded 10 KB trying URL 'https://cloud.r-project.org/src/contrib/memoise_2.0.1.tar.gz' Content type 'application/x-gzip' length 17852 bytes (17 KB) ================================================== downloaded 17 KB trying URL 'https://cloud.r-project.org/src/contrib/pkgconfig_2.0.3.tar.gz' Content type 'application/x-gzip' length 6080 bytes ================================================== downloaded 6080 bytes trying URL 'https://cloud.r-project.org/src/contrib/rlang_1.1.3.tar.gz' Content type 'application/x-gzip' length 763765 bytes (745 KB) ================================================== downloaded 745 KB 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://cloud.r-project.org/src/contrib/DBI_1.2.2.tar.gz' Content type 'application/x-gzip' length 1132818 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.6.tar.gz' Content type 'application/x-gzip' length 4249332 bytes (4.1 MB) ================================================== downloaded 4.1 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/KEGGREST_1.42.0.tar.gz' Content type 'application/x-gzip' length 22412 bytes (21 KB) ================================================== downloaded 21 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/AnnotationDbi_1.64.1.tar.gz' Content type 'application/x-gzip' length 4359564 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://bioconductor.org/packages/3.18/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-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c exec.c -o exec.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o sys.so exec.o init.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-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 ‘cli’ ... ** package ‘cli’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c ansi.c -o ansi.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c cleancall.c -o cleancall.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c diff.c -o diff.o diff.c: In function ‘clic_diff_chr’: diff.c:104:3: warning: ‘sn’ may be used uninitialized [-Wmaybe-uninitialized] 104 | SET_VECTOR_ELT(result, 0, allocVector(INTSXP, sn)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c errors.c -o errors.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c glue.c -o glue.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c inst.c -o inst.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c keypress-unix.c -o keypress-unix.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c keypress-win.c -o keypress-win.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c keypress.c -o keypress.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c md5.c -o md5.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c progress-altrep.c -o progress-altrep.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c progress.c -o progress.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c sha1.c -o sha1.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c sha256.c -o sha256.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c thread.c -o thread.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c tty.c -o tty.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c utf8.c -o utf8.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c vt.c -o vt.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c vtparse.c -o vtparse.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c vtparse_table.c -o vtparse_table.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c win-utf8.c -o win-utf8.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c winfiles.c -o winfiles.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-cli/00new/cli/libs ** R ** exec ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cli) * installing *source* package ‘glue’ ... ** package ‘glue’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c glue.c -o glue.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c trim.c -o trim.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-glue/00new/glue/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (glue) * installing *source* package ‘fastmap’ ... ** package ‘fastmap’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Ilib/ -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -Wall -c fastmap.cpp -o fastmap.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Ilib/ -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o fastmap.so fastmap.o init.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-fastmap/00new/fastmap/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fastmap) * installing *source* package ‘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-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c attrutil.c -o attrutil.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bit.c -o bit.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c chunkutil.c -o chunkutil.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c clone.c -o clone.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c integerutil.c -o integerutil.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c merge.c -o merge.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rle.c -o rle.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sort.c -o sort.o gcc -shared -L/home/biocbuild/bbs-3.18-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-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-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 findport.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-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c callbacks.c -o callbacks.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c curl.c -o curl.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c download.c -o download.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c escape.c -o escape.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c fetch.c -o fetch.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c findport.c -o findport.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c form.c -o form.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c getdate.c -o getdate.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c handle.c -o handle.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ieproxy.c -o ieproxy.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c interrupt.c -o interrupt.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c multi.c -o multi.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c nslookup.c -o nslookup.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c options.c -o options.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c reflist.c -o reflist.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c split.c -o split.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ssl.c -o ssl.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c typechecking.c -o typechecking.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c version.c -o version.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c winidn.c -o winidn.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c writer.c -o writer.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o findport.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-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-curl/00new/curl/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (curl) * installing *source* package ‘jsonlite’ ... ** package ‘jsonlite’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c base64.c -o base64.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c collapse_array.c -o collapse_array.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c collapse_object.c -o collapse_object.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c collapse_pretty.c -o collapse_pretty.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c escape_chars.c -o escape_chars.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c integer64_to_na.c -o integer64_to_na.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c is_datelist.c -o is_datelist.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c is_recordlist.c -o is_recordlist.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c is_scalarlist.c -o is_scalarlist.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c modp_numtoa.c -o modp_numtoa.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c null_to_na.c -o null_to_na.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c num_to_char.c -o num_to_char.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c parse.c -o parse.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c prettify.c -o prettify.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c push_parser.c -o push_parser.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c r-base64.c -o r-base64.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c register.c -o register.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c row_collapse.c -o row_collapse.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c transpose_list.c -o transpose_list.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c validate.c -o validate.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl.c -o yajl/yajl.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_buf.c -o yajl/yajl_buf.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_encode.c -o yajl/yajl_encode.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_gen.c -o yajl/yajl_gen.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_lex.c -o yajl/yajl_lex.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_parser.c -o yajl/yajl_parser.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_tree.c -o yajl/yajl_tree.o ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-jsonlite/00new/jsonlite/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs” in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime” in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms” in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json” in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64” in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist” in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob” in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar” in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf” in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc” in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (jsonlite) * installing *source* package ‘mime’ ... ** package ‘mime’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rawmatch.c -o rawmatch.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o mime.so init.o rawmatch.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-mime/00new/mime/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mime) * installing *source* package ‘R6’ ... ** package ‘R6’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (R6) * installing *source* package ‘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 ‘rlang’ ... ** package ‘rlang’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c capture.c -o capture.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c internal.c -o internal.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rlang.c -o rlang.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c version.c -o version.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o rlang.so capture.o internal.o rlang.o version.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-rlang/00new/rlang/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rlang) * installing *source* package ‘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-3.18-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-3.18-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-3.18-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-3.18-bioc/R/lib -L/usr/local/lib -o png.so dummy.o read.o write.o -lpng16 -lm -lz -lm -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-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 *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DBI) * installing *source* package ‘lifecycle’ ... ** package ‘lifecycle’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lifecycle) * installing *source* package ‘askpass’ ... ** package ‘askpass’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c askpass.c -o askpass.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o askpass.so askpass.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-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 ‘cachem’ ... ** package ‘cachem’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cache.c -o cache.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o cachem.so cache.o init.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-cachem/00new/cachem/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cachem) * installing *source* package ‘bit64’ ... ** package ‘bit64’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bsearch.c -o bsearch.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cache.c -o cache.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash64.c -o hash64.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.18-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-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sort64.c -o sort64.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sortuse64.c -o sortuse64.o gcc -shared -L/home/biocbuild/bbs-3.18-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-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-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 ‘vctrs’ ... ** package ‘vctrs’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c altrep-lazy-character.c -o altrep-lazy-character.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c altrep-rle.c -o altrep-rle.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c altrep.c -o altrep.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c arg-counter.c -o arg-counter.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c arg.c -o arg.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c assert.c -o assert.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c bind.c -o bind.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c c-unchop.c -o c-unchop.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c c.c -o c.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c callables.c -o callables.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c cast-bare.c -o cast-bare.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c cast-dispatch.c -o cast-dispatch.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c cast.c -o cast.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c compare.c -o compare.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c complete.c -o complete.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c conditions.c -o conditions.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c dictionary.c -o dictionary.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c dim.c -o dim.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c empty.c -o empty.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c equal.c -o equal.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c expand.c -o expand.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c fields.c -o fields.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c fill.c -o fill.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c globals.c -o globals.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c group.c -o group.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c growable.c -o growable.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c hash.c -o hash.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c interval.c -o interval.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c match-joint.c -o match-joint.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c match.c -o match.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c missing.c -o missing.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c names.c -o names.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-collate.c -o order-collate.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-groups.c -o order-groups.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-sortedness.c -o order-sortedness.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-truelength.c -o order-truelength.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order.c -o order.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c poly-op.c -o poly-op.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c proxy-restore.c -o proxy-restore.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c proxy.c -o proxy.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype-common.c -o ptype-common.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype.c -o ptype.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype2-dispatch.c -o ptype2-dispatch.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype2.c -o ptype2.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rank.c -o rank.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rep.c -o rep.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rlang-dev.c -o rlang-dev.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rlang.c -o rlang.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c runs.c -o runs.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c set.c -o set.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c shape.c -o shape.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c size-common.c -o size-common.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c size.c -o size.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-array.c -o slice-array.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-assign-array.c -o slice-assign-array.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-assign.c -o slice-assign.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-chop.c -o slice-chop.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-interleave.c -o slice-interleave.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice.c -o slice.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c split.c -o split.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c subscript-loc.c -o subscript-loc.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c subscript.c -o subscript.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c translate.c -o translate.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-data-frame.c -o type-data-frame.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-date-time.c -o type-date-time.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-factor.c -o type-factor.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-info.c -o type-info.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-integer64.c -o type-integer64.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-tibble.c -o type-tibble.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c typeof2-s3.c -o typeof2-s3.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c typeof2.c -o typeof2.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c unspecified.c -o unspecified.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c utils-dispatch.c -o utils-dispatch.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c vctrs-core.c -o vctrs-core.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c version.c -o version.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o vctrs.so altrep-lazy-character.o altrep-rle.o altrep.o arg-counter.o arg.o assert.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o empty.o equal.o expand.o fields.o fill.o globals.o group.o growable.o hash.o init.o interval.o match-joint.o match.o missing.o names.o order-collate.o order-groups.o order-sortedness.o order-truelength.o order.o poly-op.o proxy-restore.o proxy.o ptype-common.o ptype.o ptype2-dispatch.o ptype2.o rank.o rep.o rlang-dev.o rlang.o runs.o set.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice-interleave.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-integer64.o type-tibble.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils.o vctrs-core.o version.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-vctrs/00new/vctrs/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (vctrs) * installing *source* package ‘openssl’ ... ** package ‘openssl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3 ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o gcc -I"/home/biocbuild/bbs-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-bioc/R/lib -lR installing to /tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/00LOCK-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 ‘memoise’ ... ** package ‘memoise’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (memoise) * installing *source* package ‘blob’ ... ** package ‘blob’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (blob) * installing *source* package ‘httr’ ... ** package ‘httr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (httr) ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’ * removing ‘/tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/RSQLite’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘RSQLite’ had non-zero exit status * installing *source* package ‘KEGGREST’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (KEGGREST) ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’ * removing ‘/tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/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/RtmpHw3ALD/RLIBS_16f2451ff49395/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/RtmpI7iDIH/downloaded_packages’ Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'exprs': 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: exprs ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘RefPlus.Rnw’... failed ERROR Errors in running code in vignettes: when running code in ‘RefPlus.Rnw’ ... The downloaded source packages are in ‘/tmp/RtmpmT0zrC/downloaded_packages’ When sourcing ‘RefPlus.R’: Error: error in evaluating the argument 'object' in selecting a method for function 'exprs': Could not obtain CDF environment, problems encountered: Specified environment does not contain HG_U95Av2 Library - package hgu95av2cdf not installed Library - package hgu95av2cdf not installed Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘RefPlus.Rnw’ using Sweave Loading required package: Biobase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: affy Loading required package: affyPLM Loading required package: gcrma Loading required package: preprocessCore also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’ trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.6.tar.gz' Content type 'application/x-gzip' length 4249332 bytes (4.1 MB) ================================================== downloaded 4.1 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/AnnotationDbi_1.64.1.tar.gz' Content type 'application/x-gzip' length 4359564 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://bioconductor.org/packages/3.18/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 ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’ * removing ‘/tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/RSQLite’ Warning in install.packages(cdfname, lib = lib, repos = repositories(), : installation of package ‘RSQLite’ had non-zero exit status ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’ * removing ‘/tmp/RtmpHw3ALD/RLIBS_16f2451ff49395/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/RtmpHw3ALD/RLIBS_16f2451ff49395/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/Rtmpkku7VE/downloaded_packages’ Error: processing vignette 'RefPlus.Rnw' failed with diagnostics: chunk 2 Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'exprs': Could not obtain CDF environment, problems encountered: Specified environment does not contain HG_U95Av2 Library - package hgu95av2cdf not installed Library - package hgu95av2cdf not installed --- failed re-building ‘RefPlus.Rnw’ SUMMARY: processing the following file failed: ‘RefPlus.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 5 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/RefPlus.Rcheck/00check.log’ for details.