##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RefPlus.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings RefPlus_1.70.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RefPlus.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 ‘RefPlus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RefPlus’ version ‘1.70.0’
* 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-3.17-bioc/R/site-library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
also installing the dependencies ‘sys’, ‘cli’, ‘glue’, ‘lifecycle’, ‘fastmap’, ‘askpass’, ‘bit’, ‘rlang’, ‘vctrs’, ‘cachem’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘R6’, ‘bit64’, ‘blob’, ‘memoise’, ‘pkgconfig’, ‘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_3.6.1.tar.gz'
Content type 'application/x-gzip' length 567293 bytes (553 KB)
==================================================
downloaded 553 KB

trying URL 'https://cloud.r-project.org/src/contrib/glue_1.6.2.tar.gz'
Content type 'application/x-gzip' length 106510 bytes (104 KB)
==================================================
downloaded 104 KB

trying URL 'https://cloud.r-project.org/src/contrib/lifecycle_1.0.3.tar.gz'
Content type 'application/x-gzip' length 106854 bytes (104 KB)
==================================================
downloaded 104 KB

trying URL 'https://cloud.r-project.org/src/contrib/fastmap_1.1.1.tar.gz'
Content type 'application/x-gzip' length 46412 bytes (45 KB)
==================================================
downloaded 45 KB

trying URL 'https://cloud.r-project.org/src/contrib/askpass_1.2.0.tar.gz'
Content type 'application/x-gzip' length 6040 bytes
==================================================
downloaded 6040 bytes

trying URL 'https://cloud.r-project.org/src/contrib/bit_4.0.5.tar.gz'
Content type 'application/x-gzip' length 827745 bytes (808 KB)
==================================================
downloaded 808 KB

trying URL 'https://cloud.r-project.org/src/contrib/rlang_1.1.1.tar.gz'
Content type 'application/x-gzip' length 762533 bytes (744 KB)
==================================================
downloaded 744 KB

trying URL 'https://cloud.r-project.org/src/contrib/vctrs_0.6.4.tar.gz'
Content type 'application/x-gzip' length 968450 bytes (945 KB)
==================================================
downloaded 945 KB

trying URL 'https://cloud.r-project.org/src/contrib/cachem_1.0.8.tar.gz'
Content type 'application/x-gzip' length 26510 bytes (25 KB)
==================================================
downloaded 25 KB

trying URL 'https://cloud.r-project.org/src/contrib/curl_5.1.0.tar.gz'
Content type 'application/x-gzip' length 714157 bytes (697 KB)
==================================================
downloaded 697 KB

trying URL 'https://cloud.r-project.org/src/contrib/jsonlite_1.8.7.tar.gz'
Content type 'application/x-gzip' length 1053075 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cloud.r-project.org/src/contrib/mime_0.12.tar.gz'
Content type 'application/x-gzip' length 12562 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://cloud.r-project.org/src/contrib/openssl_2.1.1.tar.gz'
Content type 'application/x-gzip' length 1206233 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/R6_2.5.1.tar.gz'
Content type 'application/x-gzip' length 63422 bytes (61 KB)
==================================================
downloaded 61 KB

trying URL 'https://cloud.r-project.org/src/contrib/bit64_4.0.5.tar.gz'
Content type 'application/x-gzip' length 135091 bytes (131 KB)
==================================================
downloaded 131 KB

trying URL 'https://cloud.r-project.org/src/contrib/blob_1.2.4.tar.gz'
Content type 'application/x-gzip' length 10620 bytes (10 KB)
==================================================
downloaded 10 KB

trying URL 'https://cloud.r-project.org/src/contrib/memoise_2.0.1.tar.gz'
Content type 'application/x-gzip' length 17852 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'https://cloud.r-project.org/src/contrib/pkgconfig_2.0.3.tar.gz'
Content type 'application/x-gzip' length 6080 bytes
==================================================
downloaded 6080 bytes

trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.7.tar.gz'
Content type 'application/x-gzip' length 118500 bytes (115 KB)
==================================================
downloaded 115 KB

trying URL 'https://cloud.r-project.org/src/contrib/png_0.1-8.tar.gz'
Content type 'application/x-gzip' length 24880 bytes (24 KB)
==================================================
downloaded 24 KB

trying URL 'https://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/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/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-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-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c ansi.c -o ansi.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c cleancall.c -o cleancall.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c diff.c -o diff.o
diff.c: In function ‘clic_diff_chr’:
diff.c:104:3: warning: ‘sn’ may be used uninitialized [-Wmaybe-uninitialized]
  104 |   SET_VECTOR_ELT(result, 0, allocVector(INTSXP, sn));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c errors.c -o errors.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c glue.c -o glue.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c inst.c -o inst.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c keypress-unix.c -o keypress-unix.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c keypress-win.c -o keypress-win.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c keypress.c -o keypress.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c md5.c -o md5.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c progress-altrep.c -o progress-altrep.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c progress.c -o progress.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c sha1.c -o sha1.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c sha256.c -o sha256.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c thread.c -o thread.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c tty.c -o tty.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c utf8.c -o utf8.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c vt.c -o vt.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c vtparse.c -o vtparse.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c vtparse_table.c -o vtparse_table.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c win-utf8.c -o win-utf8.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c winfiles.c -o winfiles.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-cli/00new/cli/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cli)
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c glue.c -o glue.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c trim.c -o trim.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-glue/00new/glue/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (glue)
* installing *source* package ‘fastmap’ ...
** package ‘fastmap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ilib/  -I/usr/local/include   -DR_NO_REMAP -fpic  -g -O2  -Wall -c fastmap.cpp -o fastmap.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ilib/  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o fastmap.so fastmap.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-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-3.17-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/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-bit/00new/bit/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bit)
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c capture.c -o capture.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c internal.c -o internal.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rlang.c -o rlang.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c version.c -o version.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o rlang.so capture.o internal.o rlang.o version.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-rlang/00new/rlang/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rlang)
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu
Using PKG_LIBS=-lcurl
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c callbacks.c -o callbacks.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c curl.c -o curl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c download.c -o download.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c escape.c -o escape.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c fetch.c -o fetch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c form.c -o form.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c getdate.c -o getdate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c handle.c -o handle.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ieproxy.c -o ieproxy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c interrupt.c -o interrupt.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c multi.c -o multi.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c nslookup.c -o nslookup.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c options.c -o options.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c reflist.c -o reflist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c split.c -o split.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ssl.c -o ssl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c typechecking.c -o typechecking.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c version.c -o version.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c winidn.c -o winidn.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c writer.c -o writer.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-curl/00new/curl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (curl)
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c collapse_array.c -o collapse_array.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c collapse_object.c -o collapse_object.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c collapse_pretty.c -o collapse_pretty.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c escape_chars.c -o escape_chars.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c integer64_to_na.c -o integer64_to_na.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c is_datelist.c -o is_datelist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c is_recordlist.c -o is_recordlist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c is_scalarlist.c -o is_scalarlist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c modp_numtoa.c -o modp_numtoa.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c null_to_na.c -o null_to_na.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c num_to_char.c -o num_to_char.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c parse.c -o parse.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c prettify.c -o prettify.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c push_parser.c -o push_parser.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c r-base64.c -o r-base64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c row_collapse.c -o row_collapse.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c transpose_list.c -o transpose_list.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c validate.c -o validate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl.c -o yajl/yajl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_buf.c -o yajl/yajl_buf.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_encode.c -o yajl/yajl_encode.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_gen.c -o yajl/yajl_gen.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_lex.c -o yajl/yajl_lex.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_parser.c -o yajl/yajl_parser.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-jsonlite/00new/jsonlite/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime”
in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms”
in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json”
in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64”
in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist”
in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob”
in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar”
in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf”
in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc”
in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (jsonlite)
* installing *source* package ‘mime’ ...
** package ‘mime’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c rawmatch.c -o rawmatch.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o mime.so init.o rawmatch.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-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 ‘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/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-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 ‘lifecycle’ ...
** package ‘lifecycle’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lifecycle)
* installing *source* package ‘askpass’ ...
** package ‘askpass’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c askpass.c -o askpass.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o askpass.so askpass.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-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-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o cachem.so cache.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-cachem/00new/cachem/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cachem)
* installing *source* package ‘bit64’ ...
** package ‘bit64’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c bsearch.c -o bsearch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c hash64.c -o hash64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c integer64.c -o integer64.o
integer64.c: In function ‘runif_integer64’:
integer64.c:998:15: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  998 |     while( (*((long long *) &ii)) == NA_INTEGER64){
      |              ~^~~~~~~~~~~~~~~~~~
integer64.c:1006:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
 1006 |     ret[i] = min + ( (long long)(*((unsigned long long *)(&ii))) % d);
      |                                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sort64.c -o sort64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sortuse64.c -o sortuse64.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o bit64.so bsearch.o cache.o hash64.o init.o integer64.o sort64.o sortuse64.o -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-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-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c altrep-lazy-character.c -o altrep-lazy-character.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c altrep-rle.c -o altrep-rle.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c altrep.c -o altrep.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c arg-counter.c -o arg-counter.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c arg.c -o arg.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c assert.c -o assert.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c bind.c -o bind.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c c-unchop.c -o c-unchop.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c c.c -o c.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c callables.c -o callables.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cast-bare.c -o cast-bare.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cast-dispatch.c -o cast-dispatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cast.c -o cast.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c compare.c -o compare.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c complete.c -o complete.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c conditions.c -o conditions.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c dictionary.c -o dictionary.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c dim.c -o dim.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c empty.c -o empty.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c equal.c -o equal.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c expand.c -o expand.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c fields.c -o fields.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c fill.c -o fill.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c globals.c -o globals.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c group.c -o group.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c growable.c -o growable.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c interval.c -o interval.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c match-joint.c -o match-joint.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c match.c -o match.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c missing.c -o missing.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c names.c -o names.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-collate.c -o order-collate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-groups.c -o order-groups.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-sortedness.c -o order-sortedness.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-truelength.c -o order-truelength.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order.c -o order.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c poly-op.c -o poly-op.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c proxy-restore.c -o proxy-restore.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c proxy.c -o proxy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype-common.c -o ptype-common.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype.c -o ptype.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype2-dispatch.c -o ptype2-dispatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype2.c -o ptype2.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rank.c -o rank.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rep.c -o rep.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rlang-dev.c -o rlang-dev.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rlang.c -o rlang.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c runs.c -o runs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c set.c -o set.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c shape.c -o shape.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c size-common.c -o size-common.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c size.c -o size.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-array.c -o slice-array.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-assign-array.c -o slice-assign-array.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-assign.c -o slice-assign.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-chop.c -o slice-chop.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-interleave.c -o slice-interleave.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice.c -o slice.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c split.c -o split.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c subscript-loc.c -o subscript-loc.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c subscript.c -o subscript.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c translate.c -o translate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-data-frame.c -o type-data-frame.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-date-time.c -o type-date-time.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-factor.c -o type-factor.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-info.c -o type-info.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-integer64.c -o type-integer64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-tibble.c -o type-tibble.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c typeof2-s3.c -o typeof2-s3.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c typeof2.c -o typeof2.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c unspecified.c -o unspecified.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c utils-dispatch.c -o utils-dispatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c vctrs-core.c -o vctrs-core.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c version.c -o version.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o vctrs.so altrep-lazy-character.o altrep-rle.o altrep.o arg-counter.o arg.o assert.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o empty.o equal.o expand.o fields.o fill.o globals.o group.o growable.o hash.o init.o interval.o match-joint.o match.o missing.o names.o order-collate.o order-groups.o order-sortedness.o order-truelength.o order.o poly-op.o proxy-restore.o proxy.o ptype-common.o ptype.o ptype2-dispatch.o ptype2.o rank.o rep.o rlang-dev.o rlang.o runs.o set.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice-interleave.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-integer64.o type-tibble.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils.o vctrs-core.o version.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-vctrs/00new/vctrs/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (vctrs)
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c aes.c -o aes.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c bignum.c -o bignum.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c cert.c -o cert.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c compatibility.c -o compatibility.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c diffie.c -o diffie.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c envelope.c -o envelope.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c error.c -o error.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c info.c -o info.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c keygen.c -o keygen.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c keys.c -o keys.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c onload.c -o onload.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c openssh.c -o openssh.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c password.c -o password.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pbkdf.c -o pbkdf.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pem.c -o pem.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pkcs12.c -o pkcs12.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pkcs7.c -o pkcs7.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c rand.c -o rand.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c rsa.c -o rsa.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c signing.c -o signing.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c ssl.c -o ssl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c stream.c -o stream.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c write.c -o write.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c x25519.c -o x25519.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c bcrypt/blowfish.c -o bcrypt/blowfish.o
ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -l:libssl.so.3 -l:libcrypto.so.3 -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpTKg7U9/RLIBS_2cad403020f524/00LOCK-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/RtmpTKg7U9/RLIBS_2cad403020f524/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/RtmpTKg7U9/RLIBS_2cad403020f524/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/RtmpTKg7U9/RLIBS_2cad403020f524/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/Rtmp4ok1Qt/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/RtmpaBTh41/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_2.3.1.tar.gz'
Content type 'application/x-gzip' length 4149793 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.62.2.tar.gz'
Content type 'application/x-gzip' length 4359178 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/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/RtmpTKg7U9/RLIBS_2cad403020f524/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/RtmpTKg7U9/RLIBS_2cad403020f524/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/RtmpTKg7U9/RLIBS_2cad403020f524/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/RtmpXRdujN/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-3.17-bioc/meat/RefPlus.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RefPlus
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘RefPlus’ ...
** using staged installation
** R
** 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 (RefPlus)