Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:34:58 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the flagme package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 608/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flagme 1.46.0 (landing page) Mark Robinson
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: flagme |
Version: 1.46.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flagme_1.46.0.tar.gz |
StartedAt: 2021-05-06 01:46:04 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 01:57:22 -0400 (Thu, 06 May 2021) |
EllapsedTime: 678.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flagme.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flagme_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/flagme.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flagme/DESCRIPTION’ ... OK * this is package ‘flagme’ version ‘1.46.0’ * checking package namespace information ... NOTE Namespace with empty importFrom: ‘gcspikelite’ * 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 ‘flagme’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... WARNING man/plotMultipleSpectra.Rd: non-ASCII input and no declared encoding problem found in ‘plotMultipleSpectra.Rd’ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'show' and siglist 'betweenAlignment' 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMultipleSpectra 48.384 1.156 49.721 corPrt 35.704 0.804 36.588 dynRT 35.587 0.720 36.348 ndpRT 35.152 0.755 35.956 plotSpectra 34.673 0.811 35.532 peaksAlignment 33.888 0.815 34.758 retFatMatrix 20.219 0.348 20.592 addXCMSPeaks 12.395 0.256 12.671 imputePeaks 11.927 0.219 12.156 plot 9.532 0.206 9.753 rmaFitUnit 7.972 0.328 8.310 calcTimeDiffs 7.854 0.317 8.182 gatherInfo 7.852 0.180 8.043 multipleAlignment 7.543 0.136 7.691 progressiveAlignment 7.420 0.180 7.608 clusterAlignment 7.304 0.153 7.469 compress 7.128 0.117 7.253 normDotProduct 7.063 0.174 7.250 dp 6.958 0.118 7.083 peaksDataset 6.413 0.170 6.593 addAMDISPeaks 5.921 0.220 6.158 addChromaTOFPeaks 5.122 0.158 5.285 * 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: 2 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.12-bioc/meat/flagme.Rcheck/00check.log’ for details.
flagme.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flagme ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘flagme’ ... ** 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 dp.c -o dp.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pearson.c -o pearson.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 flagme.so dp.o init.o pearson.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-flagme/00new/flagme/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘flagme.Rnw’ using ‘UTF-8’ ** 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 (flagme)
flagme.Rcheck/flagme-Ex.timings
name | user | system | elapsed | |
addAMDISPeaks | 5.921 | 0.220 | 6.158 | |
addChromaTOFPeaks | 5.122 | 0.158 | 5.285 | |
addXCMSPeaks | 12.395 | 0.256 | 12.671 | |
betweenAlignment | 0 | 0 | 0 | |
calcTimeDiffs | 7.854 | 0.317 | 8.182 | |
clusterAlignment | 7.304 | 0.153 | 7.469 | |
compress | 7.128 | 0.117 | 7.253 | |
corPrt | 35.704 | 0.804 | 36.588 | |
dp | 6.958 | 0.118 | 7.083 | |
dynRT | 35.587 | 0.720 | 36.348 | |
gatherInfo | 7.852 | 0.180 | 8.043 | |
imputePeaks | 11.927 | 0.219 | 12.156 | |
multipleAlignment | 7.543 | 0.136 | 7.691 | |
ndpRT | 35.152 | 0.755 | 35.956 | |
normDotProduct | 7.063 | 0.174 | 7.250 | |
parseChromaTOF | 4.577 | 0.024 | 4.608 | |
parseELU | 3.619 | 0.012 | 3.635 | |
peaksAlignment | 33.888 | 0.815 | 34.758 | |
peaksDataset | 6.413 | 0.170 | 6.593 | |
plot | 9.532 | 0.206 | 9.753 | |
plotImage | 4.080 | 0.112 | 4.198 | |
plotMultipleSpectra | 48.384 | 1.156 | 49.721 | |
plotSpectra | 34.673 | 0.811 | 35.532 | |
progressiveAlignment | 7.420 | 0.180 | 7.608 | |
retFatMatrix | 20.219 | 0.348 | 20.592 | |
rmaFitUnit | 7.972 | 0.328 | 8.310 | |