Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:44 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the multtest package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/multtest.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1230/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
multtest 2.48.0 (landing page) Katherine S. Pollard
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: multtest |
Version: 2.48.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:multtest.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings multtest_2.48.0.tar.gz |
StartedAt: 2021-10-14 21:34:10 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:35:50 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 100.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: multtest.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:multtest.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings multtest_2.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/multtest.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘multtest/DESCRIPTION’ ... OK * this is package ‘multtest’ version ‘2.48.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘multtest’ can be installed ... WARNING Found the following significant warnings: random.c:48:6: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] See ‘/Users/biocbuild/bbs-3.13-bioc/meat/multtest.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * 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 ... NOTE 'library' or 'require' call to ‘methods’ which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘multtest/R/zzz.R’: .onLoad calls: require(methods) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. EBMTP: no visible global function definition for ‘makeCluster’ EBMTP: no visible global function definition for ‘stopCluster’ MTP: no visible global function definition for ‘makeCluster’ MTP: no visible global function definition for ‘stopCluster’ EBupdate,EBMTP: no visible binding for global variable ‘y’ update,MTP: no visible binding for global variable ‘y’ Undefined global functions or variables: makeCluster stopCluster y * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'EBMTP,ANY,ANY,ANY' generic '[' and siglist 'MTP,ANY,ANY,ANY' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/multtest/libs/multtest.so’: Found ‘___stderrp’, possibly from ‘stderr’ (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. 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 files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘MTP.pdf’, ‘MTP.tex’, ‘MTPALL.pdf’, ‘golub.R’, ‘multtest.bib’, ‘multtest.pdf’ Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... OK * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/multtest.Rcheck/00check.log’ for details.
multtest.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL multtest ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘multtest’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c Rpack.c -o Rpack.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c VScount.c -o VScount.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c block_sampling_fixed.c -o block_sampling_fixed.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c bootloop.c -o bootloop.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c mt.c -o mt.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c pairt_sampling.c -o pairt_sampling.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c random.c -o random.o random.c:48:6: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] z1=abs(seed); /*setting the seed to z1 and initialize it*/ ^ random.c:48:6: note: use function 'labs' instead z1=abs(seed); /*setting the seed to z1 and initialize it*/ ^~~ labs 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c sampling.c -o sampling.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c sampling_fixed.c -o sampling_fixed.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c stat_func.c -o stat_func.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fPIC -Wall -g -O2 -c stat_order.c -o stat_order.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o multtest.so Rpack.o VScount.o block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o stat_order.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-multtest/00new/multtest/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 (multtest)
multtest.Rcheck/multtest-Ex.timings
name | user | system | elapsed | |
EBMTP-class | 0 | 0 | 0 | |
EBMTP | 0.254 | 0.015 | 0.269 | |
Hsets | 0.254 | 0.006 | 0.261 | |
MTP-class | 0 | 0 | 0 | |
MTP | 0.838 | 0.009 | 0.848 | |
boot.null | 0.061 | 0.003 | 0.063 | |
corr.null | 0.025 | 0.009 | 0.059 | |
fwer2gfwer | 3.901 | 0.029 | 3.933 | |
get.index | 0.503 | 0.008 | 0.512 | |
meanX | 0.009 | 0.001 | 0.010 | |
mt.maxT | 4.477 | 0.046 | 4.525 | |
mt.plot | 0.349 | 0.010 | 0.360 | |
mt.rawp2adjp | 0.342 | 0.007 | 0.349 | |
mt.reject | 0.342 | 0.007 | 0.349 | |
mt.sample.teststat | 0.142 | 0.013 | 0.156 | |
mt.teststat | 0.232 | 0.024 | 0.257 | |
ss.maxT | 0 | 0 | 0 | |
wapply | 0.001 | 0.000 | 0.001 | |