| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:27 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 | ||||
|
To the developers/maintainers of the CGEN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CGEN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 306/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CGEN 3.37.1 (landing page) Justin Lee
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: CGEN |
| Version: 3.37.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CGEN.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CGEN_3.37.1.tar.gz |
| StartedAt: 2023-05-09 11:18:19 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 11:23:22 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 303.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CGEN.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CGEN.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CGEN_3.37.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CGEN.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘CGEN/DESCRIPTION’ ... OK
* this is package ‘CGEN’ version ‘3.37.1’
* 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 ‘CGEN’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used Fortran compiler: ‘GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
GPL-2 + file LICENSE
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
additive.test 85.972 0.552 86.532
snp.matched 24.353 0.039 24.394
getMatchedSets 20.723 0.164 20.888
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘vignette.Rnw’... OK
‘vignette_GxE.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/CGEN.Rcheck/00check.log’
for details.
CGEN.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CGEN
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘CGEN’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Additive.c -o Additive.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c CML.c -o CML.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ccl.c -o ccl.o
gfortran -fPIC -g -O2 -c csclust.f -o csclust.o
csclust.f:72:72:
72 | 10 FLAG(I)=.TRUE.
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fsclust.c -o fsclust.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c hcl.c -o hcl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c pmatch.c -o pmatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c score.c -o score.o
gcc -shared -L/usr/local/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -lgfortran -lm
installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-CGEN/00new/CGEN/libs
** R
** data
** 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 (CGEN)
CGEN.Rcheck/CGEN-Ex.timings
| name | user | system | elapsed | |
| GxE.scan | 0.003 | 0.000 | 0.002 | |
| GxE.scan.combine | 0 | 0 | 0 | |
| GxE.scan.partition | 0.003 | 0.000 | 0.003 | |
| LocusMapData | 0.019 | 0.004 | 0.023 | |
| QQ.plot | 0.016 | 0.000 | 0.017 | |
| Xdata | 0.007 | 0.004 | 0.011 | |
| Xdata2 | 0.036 | 0.004 | 0.041 | |
| additive.test | 85.972 | 0.552 | 86.532 | |
| chromosome.plot | 0.547 | 0.008 | 0.556 | |
| getMatchedSets | 20.723 | 0.164 | 20.888 | |
| getSummary | 0.004 | 0.000 | 0.004 | |
| getWaldTest | 0.004 | 0.000 | 0.004 | |
| printEffects | 0.236 | 0.012 | 0.248 | |
| snp.effects | 0.231 | 0.000 | 0.231 | |
| snp.effects.plot | 0.889 | 0.000 | 0.889 | |
| snp.list | 0 | 0 | 0 | |
| snp.logistic | 0.491 | 0.000 | 0.491 | |
| snp.matched | 24.353 | 0.039 | 24.394 | |
| snp.score | 0.032 | 0.000 | 0.032 | |