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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:RefPlus.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings RefPlus_1.72.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/RefPlus.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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/R/R-4.3.1/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’

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* installing *source* package ‘sys’ ...
** package ‘sys’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c exec.c -o exec.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o sys.so exec.o init.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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 in this function [-Wmaybe-uninitialized]
  104 |   SET_VECTOR_ELT(result, 0, allocVector(INTSXP, sn));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c glue.c -o glue.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c trim.c -o trim.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -Ilib/  -I/usr/local/include   -DR_NO_REMAP -fPIC  -g -O2  -Wall -c fastmap.cpp -o fastmap.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/lib -L/usr/local/lib -o fastmap.so fastmap.o init.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c attrutil.c -o attrutil.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c bit.c -o bit.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c chunkutil.c -o chunkutil.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c clone.c -o clone.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c integerutil.c -o integerutil.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c merge.c -o merge.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c rle.c -o rle.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c sort.c -o sort.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c capture.c -o capture.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c internal.c -o internal.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c rlang.c -o rlang.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/lib -L/usr/local/lib -o rlang.so capture.o internal.o rlang.o version.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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=
Using PKG_LIBS=-lcurl 
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
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/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c callbacks.c -o callbacks.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c curl.c -o curl.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c download.c -o download.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c escape.c -o escape.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c fetch.c -o fetch.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c form.c -o form.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c getdate.c -o getdate.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c handle.c -o handle.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c ieproxy.c -o ieproxy.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c interrupt.c -o interrupt.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c multi.c -o multi.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c nslookup.c -o nslookup.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c options.c -o options.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c reflist.c -o reflist.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c split.c -o split.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c ssl.c -o ssl.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c typechecking.c -o typechecking.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c version.c -o version.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c winidn.c -o winidn.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c writer.c -o writer.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fPIC  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fPIC  -g -O2  -Wall -c parse.c -o parse.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fPIC  -g -O2  -Wall -c prettify.c -o prettify.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fPIC  -g -O2  -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fPIC  -g -O2  -Wall -c validate.c -o validate.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c rawmatch.c -o rawmatch.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o mime.so init.o rawmatch.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    `libpng-config --cflags` -fPIC  -g -O2  -Wall -c dummy.c -o dummy.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    `libpng-config --cflags` -fPIC  -g -O2  -Wall -c read.c -o read.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    `libpng-config --cflags` -fPIC  -g -O2  -Wall -c write.c -o write.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o png.so dummy.o read.o write.o -L/usr/lib64 -lpng16 -lm -lz -lm -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c askpass.c -o askpass.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o askpass.so askpass.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o cachem.so cache.o init.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c bsearch.c -o bsearch.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c hash64.c -o hash64.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c sort64.c -o sort64.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c sortuse64.c -o sortuse64.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c altrep.c -o altrep.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c arg.c -o arg.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c assert.c -o assert.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c bind.c -o bind.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c c.c -o c.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c callables.c -o callables.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cast.c -o cast.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c compare.c -o compare.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c complete.c -o complete.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c conditions.c -o conditions.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c dictionary.c -o dictionary.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c dim.c -o dim.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c empty.c -o empty.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c equal.c -o equal.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c expand.c -o expand.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c fields.c -o fields.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c fill.c -o fill.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c globals.c -o globals.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c group.c -o group.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c growable.c -o growable.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c interval.c -o interval.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c match.c -o match.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c missing.c -o missing.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c names.c -o names.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c order.c -o order.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c proxy.c -o proxy.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c ptype.c -o ptype.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c ptype2.c -o ptype2.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c rank.c -o rank.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c rep.c -o rep.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c rlang.c -o rlang.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c runs.c -o runs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c set.c -o set.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c shape.c -o shape.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c size.c -o size.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c slice.c -o slice.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c split.c -o split.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c subscript.c -o subscript.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c translate.c -o translate.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c typeof2.c -o typeof2.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c unspecified.c -o unspecified.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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.1.1 -l:libcrypto.so.1.1 
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
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/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c aes.c -o aes.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c bignum.c -o bignum.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c cert.c -o cert.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c compatibility.c -o compatibility.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c diffie.c -o diffie.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c envelope.c -o envelope.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c error.c -o error.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c info.c -o info.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c keygen.c -o keygen.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c keys.c -o keys.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c onload.c -o onload.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c openssh.c -o openssh.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c password.c -o password.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c pbkdf.c -o pbkdf.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c pem.c -o pem.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c pkcs12.c -o pkcs12.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c pkcs7.c -o pkcs7.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c rand.c -o rand.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c rsa.c -o rsa.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c signing.c -o signing.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c ssl.c -o ssl.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c stream.c -o stream.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c write.c -o write.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c x25519.c -o x25519.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -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/R/R-4.3.1/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.1.1 -l:libcrypto.so.1.1 -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/00LOCK-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 ‘/home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/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 ‘/home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/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 ‘/home/biocbuild/tmp/RtmpZGjoim/RLIBS_1f202e4c455777/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
	‘/home/biocbuild/tmp/RtmpYWRW5s/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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/RefPlus.Rcheck/00check.log’
for details.