Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:13 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 maanova package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maanova.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1070/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maanova 1.68.2 (landing page) Keith Sheppard
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: maanova |
Version: 1.68.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maanova.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maanova_1.68.2.tar.gz |
StartedAt: 2023-04-10 20:57:30 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 20:58:12 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 42.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: maanova.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maanova.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maanova_1.68.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/maanova.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘maanova/DESCRIPTION’ ... OK * this is package ‘maanova’ version ‘1.68.2’ * 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 ‘maanova’ can be installed ... WARNING Found the following significant warnings: shift.c:48:17: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] See ‘/Users/biocbuild/bbs-3.16-bioc/meat/maanova.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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' calls in package code: ‘qvalue’ ‘snow’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: plot.consensus.hc plot.consensus.kmean print.madata print.summary.madata print.summary.mamodel subset.madata summary.madata summary.mamodel transform.madata transform.rawdata See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE fdr: no visible global function definition for ‘qvalue’ matest: no visible global function definition for ‘makeMPIcluster’ matest: no visible global function definition for ‘clusterApply’ matest: no visible global function definition for ‘clusterEvalQ’ matest: no visible global function definition for ‘stopCluster’ Undefined global functions or variables: clusterApply clusterEvalQ makeMPIcluster qvalue 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 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 * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/maanova.Rcheck/00check.log’ for details.
maanova.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maanova ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘maanova’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c makeratio.c -o makeratio.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c masvd.c -o masvd.o masvd.c:114:2: warning: '/*' within block comment [-Wcomment] /* work on a copy of x */ ^ masvd.c:154:1: warning: '/*' within block comment [-Wcomment] /*#ifndef IEEE_754 ^ masvd.c:161:5: warning: '/*' within block comment [-Wcomment] /* work on a copy of x */ ^ masvd.c:165:2: warning: '/*' within block comment [-Wcomment] /* ask for optimal size of work array */ ^ masvd.c:189:2: warning: '/*' within block comment [-Wcomment] /* ask for optimal size of work array */ ^ 5 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c shift.c -o shift.o shift.c:48:17: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] sad[i] += abs(x[j]-med); ^ shift.c:48:17: note: use function 'fabs' instead sad[i] += abs(x[j]-med); ^~~ fabs shift.c:27:13: warning: unused variable 'k' [-Wunused-variable] int i, j, k; ^ 2 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c util.c -o util.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 maanova.so makeratio.o masvd.o shift.o util.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13) ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13) installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-maanova/00new/maanova/libs ** R ** data ** demo ** 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 (maanova)
maanova.Rcheck/maanova-Ex.timings
name | user | system | elapsed | |
PairContrast | 0.066 | 0.004 | 0.070 | |
Rmaanova.version | 0.003 | 0.001 | 0.005 | |
abf1 | 0.007 | 0.001 | 0.008 | |
adjPval | 0.005 | 0.002 | 0.006 | |
arrayview | 0.001 | 0.000 | 0.000 | |
consensus | 0.005 | 0.001 | 0.005 | |
dyeswapfilter | 0.000 | 0.001 | 0.000 | |
fill.missing | 0.074 | 0.012 | 0.086 | |
fitmaanova | 0.005 | 0.001 | 0.005 | |
fom | 0.005 | 0.001 | 0.006 | |
geneprofile | 0.005 | 0.000 | 0.005 | |
gridcheck | 0 | 0 | 0 | |
kidney | 0.039 | 0.003 | 0.042 | |
maanova-internal | 0.001 | 0.001 | 0.002 | |
macluster | 0.005 | 0.001 | 0.006 | |
matest | 0.007 | 0.002 | 0.007 | |
read.madata | 0 | 0 | 0 | |
resiplot | 0.005 | 0.001 | 0.007 | |
riplot | 0 | 0 | 0 | |
subset.madata | 0.053 | 0.002 | 0.055 | |
summarytable | 0.006 | 0.001 | 0.007 | |
transform.madata | 0.045 | 0.003 | 0.048 | |
varplot | 0.005 | 0.001 | 0.006 | |
volcano | 0.000 | 0.001 | 0.000 | |
write.madata | 0.006 | 0.001 | 0.007 | |