| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 734/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flagme 1.64.0 (landing page) Mark Robinson
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
| kunpeng2 | 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: 1.64.0 |
| 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_1.64.0.tar.gz |
| StartedAt: 2025-10-14 21:41:20 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 21:57:22 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 962.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flagme.Rcheck |
| Warnings: 2 |
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### Running command:
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### /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_1.64.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/flagme.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.64.0’
* 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 15.0.0 (clang-1500.0.40.1)’
* 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(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 103.200 21.196 67.700
addXCMSPeaks 61.355 10.132 52.865
plotAlignment-peaksAlignment-method 54.031 12.088 46.188
retFatMatrix 54.060 10.582 44.925
progressiveAlignment-class 51.317 11.377 44.245
peaksAlignment-class 51.483 10.748 44.466
ndpRT 50.595 10.861 43.313
plotFrags 50.599 10.264 42.378
corPrt 50.024 9.884 42.246
dynRT 49.276 9.788 42.530
imputePeaks 12.199 0.288 12.789
plotChrom-peaksDataset-method 10.269 0.391 10.731
gatherInfo 9.331 0.228 10.533
rmaFitUnit 8.953 0.487 9.532
multipleAlignment-class 9.209 0.209 9.576
dp 8.063 0.190 8.514
plotClustAlignment-clusterAlignment-method 7.830 0.245 8.205
calcTimeDiffs 7.720 0.280 8.079
clusterAlignment 6.750 0.240 7.204
normDotProduct 6.539 0.322 6.889
peaksDataset 6.145 0.177 6.517
addAMDISPeaks 5.518 0.156 5.721
plotImage 5.281 0.142 5.503
* 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-3.21-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-arm64/Resources/library’ * installing *source* package ‘flagme’ ... ** this is package ‘flagme’ version ‘1.64.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dp.c -o dp.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pearson.c -o pearson.o clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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 | 5.518 | 0.156 | 5.721 | |
| addChromaTOFPeaks | 4.061 | 0.135 | 4.219 | |
| addXCMSPeaks | 61.355 | 10.132 | 52.865 | |
| betweenAlignment | 0.000 | 0.000 | 0.001 | |
| calcTimeDiffs | 7.720 | 0.280 | 8.079 | |
| clusterAlignment | 6.750 | 0.240 | 7.204 | |
| corPrt | 50.024 | 9.884 | 42.246 | |
| dp | 8.063 | 0.190 | 8.514 | |
| dynRT | 49.276 | 9.788 | 42.530 | |
| gatherInfo | 9.331 | 0.228 | 10.533 | |
| imputePeaks | 12.199 | 0.288 | 12.789 | |
| multipleAlignment-class | 9.209 | 0.209 | 9.576 | |
| ndpRT | 50.595 | 10.861 | 43.313 | |
| normDotProduct | 6.539 | 0.322 | 6.889 | |
| parseChromaTOF | 2.232 | 0.094 | 2.351 | |
| parseELU | 1.722 | 0.011 | 1.737 | |
| peaksAlignment-class | 51.483 | 10.748 | 44.466 | |
| peaksDataset | 6.145 | 0.177 | 6.517 | |
| plotAlignedFrags | 103.200 | 21.196 | 67.700 | |
| plotAlignment-peaksAlignment-method | 54.031 | 12.088 | 46.188 | |
| plotChrom-peaksDataset-method | 10.269 | 0.391 | 10.731 | |
| plotClustAlignment-clusterAlignment-method | 7.830 | 0.245 | 8.205 | |
| plotFrags | 50.599 | 10.264 | 42.378 | |
| plotImage | 5.281 | 0.142 | 5.503 | |
| progressiveAlignment-class | 51.317 | 11.377 | 44.245 | |
| retFatMatrix | 54.060 | 10.582 | 44.925 | |
| rmaFitUnit | 8.953 | 0.487 | 9.532 | |