Kai-Ming Chang
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024) |
| git_url: https://git.bioconductor.org/packages/RefPlus |
| git_branch: RELEASE_3_19 |
| git_last_commit: b01bf68 |
| git_last_commit_date: 2024-04-30 10:16:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:41:20 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1727/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Kai-Ming Chang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the RefPlus package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RefPlus.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: RefPlus |
| Version: 1.74.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:RefPlus.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings RefPlus_1.74.0.tar.gz |
| StartedAt: 2024-05-09 11:04:17 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 11:08:05 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 228.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RefPlus.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:RefPlus.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings RefPlus_1.74.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RefPlus.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘1.74.0’
* 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 code 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 whether startup messages can be suppressed ... 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
[1,] "affydata" "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library"
Item Title
[1,] "Dilution" "AffyBatch instance Dilution"
also installing the dependencies ‘cli’, ‘glue’, ‘lifecycle’, ‘fastmap’, ‘bit’, ‘vctrs’, ‘cachem’, ‘bit64’, ‘blob’, ‘memoise’, ‘pkgconfig’, ‘rlang’, ‘png’, ‘DBI’, ‘RSQLite’, ‘KEGGREST’, ‘AnnotationDbi’
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trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/KEGGREST_1.44.0.tar.gz'
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* 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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/tmp/RtmpPrHrZD/RLIBS_513ed5b21beab/00LOCK-cli/00new/cli/libs
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cli)
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -c glue.c -o glue.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -c trim.c -o trim.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/tmp/RtmpPrHrZD/RLIBS_513ed5b21beab/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -L/usr/local/lib -o fastmap.so fastmap.o init.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/tmp/RtmpPrHrZD/RLIBS_513ed5b21beab/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-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c attrutil.c -o attrutil.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c bit.c -o bit.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c chunkutil.c -o chunkutil.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c clone.c -o clone.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c integerutil.c -o integerutil.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c merge.c -o merge.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c rle.c -o rle.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c sort.c -o sort.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/tmp/RtmpPrHrZD/RLIBS_513ed5b21beab/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 ‘pkgconfig’ ...
** package ‘pkgconfig’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pkgconfig)
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -L/usr/local/lib -o rlang.so capture.o internal.o rlang.o version.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/tmp/RtmpPrHrZD/RLIBS_513ed5b21beab/00LOCK-rlang/00new/rlang/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rlang)
* installing *source* package ‘png’ ...
** package ‘png’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/tmp/RtmpPrHrZD/RLIBS_513ed5b21beab/00LOCK-png/00new/png/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (png)
* installing *source* package ‘DBI’ ...
** package ‘DBI’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DBI)
* installing *source* package ‘lifecycle’ ...
** package ‘lifecycle’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lifecycle)
* installing *source* package ‘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-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o cachem.so cache.o init.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/tmp/RtmpPrHrZD/RLIBS_513ed5b21beab/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-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c bsearch.c -o bsearch.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c hash64.c -o hash64.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c sort64.c -o sort64.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c sortuse64.c -o sortuse64.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/tmp/RtmpPrHrZD/RLIBS_513ed5b21beab/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 ‘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)
* 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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/tmp/RtmpPrHrZD/RLIBS_513ed5b21beab/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 ‘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)
ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/home/biocbuild/tmp/RtmpPrHrZD/RLIBS_513ed5b21beab/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 ‘/home/biocbuild/tmp/RtmpPrHrZD/RLIBS_513ed5b21beab/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/RtmpPrHrZD/RLIBS_513ed5b21beab/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/RtmpU41cbN/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 ... 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-3.19-bioc/meat/RefPlus.Rcheck/00check.log’
for details.
RefPlus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL RefPlus ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 Warning in fun(libname, pkgname) : Package 'RefPlus' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'RefPlus' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (RefPlus)
RefPlus.Rcheck/RefPlus-Ex.timings
| name | user | system | elapsed |