Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:41 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 727/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flagme 1.60.0 (landing page) Mark Robinson
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | 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 flagme package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flagme.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: flagme |
Version: 1.60.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.60.0.tar.gz |
StartedAt: 2024-08-12 04:35:13 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 05:03:21 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 1687.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flagme.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/flagme.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flagme/DESCRIPTION’ ... OK * this is package ‘flagme’ version ‘1.60.0’ * package encoding: UTF-8 * 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 ‘flagme’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘xcms:::rectUnique’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE addXCMSPeaks: no visible global function definition for ‘bpparam’ addXCMSPeaks: no visible global function definition for ‘sampnames’ addXCMSPeaks : <anonymous> : <anonymous>: no visible global function definition for ‘setNames’ importSpec : <anonymous>: no visible global function definition for ‘setNames’ Undefined global functions or variables: bpparam sampnames setNames Consider adding importFrom("stats", "setNames") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file 'addXCMSPeaks.Rd': ‘[xcms]{findPeaks-matchedFilter}’ ‘[xcms]{findPeaks-centWave}’ ‘[xcms]{peaksDataset}’ Missing link or links in Rd file 'plotAlignment-peaksAlignment-method.Rd': ‘plotAlignment’ Missing link or links in Rd file 'plotClustAlignment-clusterAlignment-method.Rd': ‘plotAlignment’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: ‘plotAlignment’ ‘plotChrom’ ‘plotClustAlignment’ 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotAlignedFrags 149.955 32.928 111.265 addXCMSPeaks 79.863 16.709 81.902 corPrt 78.841 17.012 79.956 plotAlignment-peaksAlignment-method 77.321 17.066 74.199 peaksAlignment-class 76.800 17.173 74.821 progressiveAlignment-class 76.548 17.246 75.019 dynRT 76.924 16.827 77.758 ndpRT 76.521 16.962 75.911 retFatMatrix 75.585 17.016 74.696 plotFrags 75.060 16.812 71.502 imputePeaks 18.178 0.339 21.034 plotChrom-peaksDataset-method 16.548 0.343 18.898 calcTimeDiffs 12.517 0.378 14.909 rmaFitUnit 12.264 0.324 14.343 gatherInfo 11.450 0.257 13.097 clusterAlignment 11.464 0.203 13.498 multipleAlignment-class 11.282 0.195 13.020 normDotProduct 10.564 0.277 12.307 dp 10.449 0.221 12.440 plotClustAlignment-clusterAlignment-method 10.284 0.201 12.033 peaksDataset 9.450 0.199 10.936 addAMDISPeaks 8.782 0.388 11.222 addChromaTOFPeaks 7.272 0.230 8.780 plotImage 6.326 0.188 7.384 parseChromaTOF 5.505 0.060 6.289 parseELU 5.116 0.037 5.855 * 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: 2 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/flagme.Rcheck/00check.log’ for details.
flagme.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flagme ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘flagme’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.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 dp.c -o dp.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 init.c -o init.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 pearson.c -o pearson.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 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/4.4-x86_64/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 ** 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 | 8.782 | 0.388 | 11.222 | |
addChromaTOFPeaks | 7.272 | 0.230 | 8.780 | |
addXCMSPeaks | 79.863 | 16.709 | 81.902 | |
betweenAlignment | 0.000 | 0.001 | 0.001 | |
calcTimeDiffs | 12.517 | 0.378 | 14.909 | |
clusterAlignment | 11.464 | 0.203 | 13.498 | |
corPrt | 78.841 | 17.012 | 79.956 | |
dp | 10.449 | 0.221 | 12.440 | |
dynRT | 76.924 | 16.827 | 77.758 | |
gatherInfo | 11.450 | 0.257 | 13.097 | |
imputePeaks | 18.178 | 0.339 | 21.034 | |
multipleAlignment-class | 11.282 | 0.195 | 13.020 | |
ndpRT | 76.521 | 16.962 | 75.911 | |
normDotProduct | 10.564 | 0.277 | 12.307 | |
parseChromaTOF | 5.505 | 0.060 | 6.289 | |
parseELU | 5.116 | 0.037 | 5.855 | |
peaksAlignment-class | 76.800 | 17.173 | 74.821 | |
peaksDataset | 9.450 | 0.199 | 10.936 | |
plotAlignedFrags | 149.955 | 32.928 | 111.265 | |
plotAlignment-peaksAlignment-method | 77.321 | 17.066 | 74.199 | |
plotChrom-peaksDataset-method | 16.548 | 0.343 | 18.898 | |
plotClustAlignment-clusterAlignment-method | 10.284 | 0.201 | 12.033 | |
plotFrags | 75.060 | 16.812 | 71.502 | |
plotImage | 6.326 | 0.188 | 7.384 | |
progressiveAlignment-class | 76.548 | 17.246 | 75.019 | |
retFatMatrix | 75.585 | 17.016 | 74.696 | |
rmaFitUnit | 12.264 | 0.324 | 14.343 | |