Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 734/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flagme 1.65.0 (landing page) Mark Robinson
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.65.0 |
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_1.65.0.tar.gz |
StartedAt: 2025-09-19 21:00:51 -0400 (Fri, 19 Sep 2025) |
EndedAt: 2025-09-19 21:16:16 -0400 (Fri, 19 Sep 2025) |
EllapsedTime: 924.9 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_1.65.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/flagme.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flagme/DESCRIPTION’ ... OK * this is package ‘flagme’ version ‘1.65.0’ * 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: ‘MacOSX11.3.1.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(s) in Rd file 'addXCMSPeaks.Rd': ‘[xcms]{findPeaks-matchedFilter}’ ‘[xcms]{findPeaks-centWave}’ ‘[xcms]{peaksDataset}’ Missing link(s) in Rd file 'plotAlignment-peaksAlignment-method.Rd': ‘plotAlignment’ Missing link(s) in Rd file 'plotClustAlignment-clusterAlignment-method.Rd': ‘plotAlignment’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: plotAlignment-peaksAlignment-method.Rd: plotAlignment plotClustAlignment-clusterAlignment-method.Rd: plotAlignment Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 97.169 23.678 61.168 corPrt 56.653 11.762 47.412 addXCMSPeaks 56.741 10.823 47.891 dynRT 55.366 11.491 46.998 ndpRT 52.785 11.636 43.700 peaksAlignment-class 50.715 11.670 43.276 retFatMatrix 49.362 11.365 41.824 progressiveAlignment-class 48.825 10.888 41.071 plotFrags 48.642 10.894 41.143 plotAlignment-peaksAlignment-method 48.632 10.774 40.963 imputePeaks 11.080 0.249 11.433 plotChrom-peaksDataset-method 9.162 0.271 9.525 gatherInfo 8.175 0.231 8.465 multipleAlignment-class 8.207 0.174 8.479 calcTimeDiffs 8.081 0.292 8.447 rmaFitUnit 8.072 0.284 8.423 dp 7.689 0.205 7.968 clusterAlignment 7.533 0.172 7.769 normDotProduct 6.092 0.179 6.335 plotClustAlignment-clusterAlignment-method 6.027 0.161 6.270 addAMDISPeaks 5.921 0.185 6.162 peaksDataset 5.681 0.188 5.935 * 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-3.22-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/4.5-x86_64/Resources/library’ * installing *source* package ‘flagme’ ... ** this is package ‘flagme’ version ‘1.65.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.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 installing to /Library/Frameworks/R.framework/Versions/4.5-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 | 5.921 | 0.185 | 6.162 | |
addChromaTOFPeaks | 4.644 | 0.156 | 4.815 | |
addXCMSPeaks | 56.741 | 10.823 | 47.891 | |
betweenAlignment | 0.000 | 0.000 | 0.001 | |
calcTimeDiffs | 8.081 | 0.292 | 8.447 | |
clusterAlignment | 7.533 | 0.172 | 7.769 | |
corPrt | 56.653 | 11.762 | 47.412 | |
dp | 7.689 | 0.205 | 7.968 | |
dynRT | 55.366 | 11.491 | 46.998 | |
gatherInfo | 8.175 | 0.231 | 8.465 | |
imputePeaks | 11.080 | 0.249 | 11.433 | |
multipleAlignment-class | 8.207 | 0.174 | 8.479 | |
ndpRT | 52.785 | 11.636 | 43.700 | |
normDotProduct | 6.092 | 0.179 | 6.335 | |
parseChromaTOF | 2.587 | 0.035 | 2.649 | |
parseELU | 2.085 | 0.017 | 2.121 | |
peaksAlignment-class | 50.715 | 11.670 | 43.276 | |
peaksDataset | 5.681 | 0.188 | 5.935 | |
plotAlignedFrags | 97.169 | 23.678 | 61.168 | |
plotAlignment-peaksAlignment-method | 48.632 | 10.774 | 40.963 | |
plotChrom-peaksDataset-method | 9.162 | 0.271 | 9.525 | |
plotClustAlignment-clusterAlignment-method | 6.027 | 0.161 | 6.270 | |
plotFrags | 48.642 | 10.894 | 41.143 | |
plotImage | 4.687 | 0.111 | 4.835 | |
progressiveAlignment-class | 48.825 | 10.888 | 41.071 | |
retFatMatrix | 49.362 | 11.365 | 41.824 | |
rmaFitUnit | 8.072 | 0.284 | 8.423 | |