Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2212/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
twilight 1.82.0 (landing page) Stefanie Scheid
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the twilight package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/twilight.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: twilight |
Version: 1.82.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:twilight.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings twilight_1.82.0.tar.gz |
StartedAt: 2024-12-21 12:44:07 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 12:44:47 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 39.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: twilight.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:twilight.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings twilight_1.82.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/twilight.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘twilight/DESCRIPTION’ ... OK * this is package ‘twilight’ version ‘1.82.0’ * 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 ‘twilight’ can be installed ... WARNING Found the following significant warnings: sep.c:70:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] sep.c:97:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] sep.c:116:19: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] sep.c:143:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/twilight.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ ‘stats’ A package should be listed in only one of these fields. * 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 ... NOTE Package in Depends field not imported from: ‘splines’ 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 NB: .First.lib is obsolete and will not be used in R >= 3.0.0 twilight: no visible global function definition for ‘makeCluster’ twilight: no visible global function definition for ‘clusterEvalQ’ twilight: no visible binding for '<<-' assignment to ‘.twilight.lambda.xxx’ twilight: no visible binding for '<<-' assignment to ‘.twilight.pval.xxx’ twilight: no visible binding for '<<-' assignment to ‘.twilight.score.xxx’ twilight: no visible global function definition for ‘clusterExport’ twilight: no visible global function definition for ‘parCapply’ twilight: no visible binding for global variable ‘.twilight.lambda.xxx’ twilight: no visible binding for global variable ‘.twilight.pval.xxx’ twilight: no visible binding for global variable ‘.twilight.score.xxx’ twilight: no visible global function definition for ‘stopCluster’ Undefined global functions or variables: .twilight.lambda.xxx .twilight.pval.xxx .twilight.score.xxx clusterEvalQ clusterExport makeCluster parCapply stopCluster * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/twilight/libs/twilight.so’: Found ‘_rand’, possibly from ‘rand’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... NOTE The following files look like leftovers/mistakes: ‘Rplots.pdf’ Please remove them from your package. * checking examples ... OK * 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, 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/twilight.Rcheck/00check.log’ for details.
twilight.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL twilight ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘twilight’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c confidence.line.c -o confidence.line.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c correlation.c -o correlation.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kstest.c -o kstest.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sep.c -o sep.o sep.c:70:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] ix[randnum]=fabs(1-ix[randnum]); ^ sep.c:70:16: note: use function 'abs' instead ix[randnum]=fabs(1-ix[randnum]); ^~~~ abs sep.c:97:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] ix[randnum]=fabs(1-ix[randnum]); ^ sep.c:97:20: note: use function 'abs' instead ix[randnum]=fabs(1-ix[randnum]); ^~~~ abs sep.c:116:19: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] ix[randnum]=fabs(1-ix[randnum]); ^ sep.c:116:19: note: use function 'abs' instead ix[randnum]=fabs(1-ix[randnum]); ^~~~ abs sep.c:143:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] ix[randnum]=fabs(1-ix[randnum]); ^ sep.c:143:16: note: use function 'abs' instead ix[randnum]=fabs(1-ix[randnum]); ^~~~ abs 4 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c twosample.perm.c -o twosample.perm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c twosample.single.c -o twosample.single.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o twilight.so confidence.line.o correlation.o kstest.o sep.o twosample.perm.o twosample.single.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-twilight/00new/twilight/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 (twilight)
twilight.Rcheck/twilight-Ex.timings
name | user | system | elapsed | |
plot.twilight | 0.284 | 0.022 | 0.307 | |
print.twilight | 0.062 | 0.003 | 0.065 | |
twilight | 0.506 | 0.024 | 0.534 | |
twilight.combi | 0.002 | 0.001 | 0.003 | |
twilight.filtering | 0 | 0 | 0 | |
twilight.pval | 0.415 | 0.014 | 0.432 | |
twilight.teststat | 0.004 | 0.001 | 0.005 | |