Justin Lee
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/CGEN |
| git_branch: devel |
| git_last_commit: 6a4ae24 |
| git_last_commit_date: 2025-04-15 12:27:38 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:04 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 330/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CGEN 3.45.0 (landing page) Justin Lee
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - 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. |
| Package: CGEN |
| Version: 3.45.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CGEN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CGEN_3.45.0.tar.gz |
| StartedAt: 2025-10-23 20:00:40 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 20:03:25 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 164.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CGEN.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CGEN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CGEN_3.45.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CGEN.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGEN/DESCRIPTION’ ... OK
* this is package ‘CGEN’ version ‘3.45.0’
* 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 ‘CGEN’ can be installed ... WARNING
Found the following significant warnings:
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/CGEN.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 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 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 ... NOTE
checkRd: (-1) snp.effects.plot.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
* 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 usage of KIND in Fortran files ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
additive.test 38.345 7.876 46.628
getMatchedSets 9.309 0.195 9.553
snp.matched 7.654 0.047 7.756
* 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 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/CGEN.Rcheck/00check.log’
for details.
CGEN.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CGEN
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘CGEN’ ...
** this is package ‘CGEN’ version ‘3.45.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Additive.c -o Additive.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CML.c -o CML.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ccl.c -o ccl.o
ccl.c:430:16: warning: variable 'det' set but not used [-Wunused-but-set-variable]
double temp , det = 1.0 ;
^
1 warning generated.
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c csclust.f -o csclust.o
f951: Warning: Nonconforming tab character in column 1 of line 46 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 83 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 203 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 205 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 207 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 270 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 271 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 275 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 276 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 277 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 278 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 282 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 283 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 286 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 287 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 288 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 289 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 290 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 291 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 292 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 293 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 294 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 295 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 296 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 306 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 307 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 309 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 310 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 311 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 312 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 313 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 314 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 315 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 316 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 317 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 319 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 320 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 321 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 329 [-Wtabs]
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)
csclust.f:222:3:
222 | 650 RETURN
| 1
Warning: Label 650 at (1) defined but not used [-Wunused-label]
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fsclust.c -o fsclust.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hcl.c -o hcl.o
hcl.c:419:16: warning: variable 'det' set but not used [-Wunused-but-set-variable]
double temp , det = 1.0 ;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pmatch.c -o pmatch.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c score.c -o score.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 | 0.001 | 0.002 | 0.004 | |
| GxE.scan.combine | 0.000 | 0.001 | 0.000 | |
| GxE.scan.partition | 0.002 | 0.002 | 0.003 | |
| LocusMapData | 0.019 | 0.006 | 0.025 | |
| QQ.plot | 0.011 | 0.003 | 0.014 | |
| Xdata | 0.010 | 0.002 | 0.013 | |
| Xdata2 | 0.030 | 0.002 | 0.033 | |
| additive.test | 38.345 | 7.876 | 46.628 | |
| chromosome.plot | 0.430 | 0.008 | 0.441 | |
| getMatchedSets | 9.309 | 0.195 | 9.553 | |
| getSummary | 0.003 | 0.000 | 0.004 | |
| getWaldTest | 0.003 | 0.000 | 0.003 | |
| printEffects | 0.205 | 0.009 | 0.215 | |
| snp.effects | 0.183 | 0.009 | 0.193 | |
| snp.effects.plot | 0.690 | 0.010 | 0.707 | |
| snp.list | 0.000 | 0.000 | 0.001 | |
| snp.logistic | 0.386 | 0.010 | 0.398 | |
| snp.matched | 7.654 | 0.047 | 7.756 | |
| snp.score | 0.019 | 0.001 | 0.020 | |