Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-06 12:04 -0400 (Sat, 06 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4618 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4565 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
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 729/2322 | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings flagme_1.65.0.tar.gz |
StartedAt: 2025-09-05 23:41:21 -0400 (Fri, 05 Sep 2025) |
EndedAt: 2025-09-05 23:57:50 -0400 (Fri, 05 Sep 2025) |
EllapsedTime: 989.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flagme.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings flagme_1.65.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/flagme.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotAlignedFrags 94.357 18.364 58.959 plotFrags 49.792 9.538 41.292 peaksAlignment-class 48.002 8.863 40.056 addXCMSPeaks 47.726 7.748 40.294 dynRT 45.558 8.526 37.404 plotAlignment-peaksAlignment-method 45.949 8.000 38.151 corPrt 44.561 8.514 36.802 retFatMatrix 44.185 8.806 37.232 progressiveAlignment-class 44.964 7.791 37.087 ndpRT 42.348 9.555 36.404 imputePeaks 10.318 0.452 10.778 plotChrom-peaksDataset-method 7.805 0.245 8.050 gatherInfo 7.378 0.542 7.920 dp 6.476 0.540 7.017 multipleAlignment-class 6.777 0.209 6.986 rmaFitUnit 6.653 0.154 6.808 calcTimeDiffs 6.239 0.500 6.740 addAMDISPeaks 6.073 0.175 6.267 plotClustAlignment-clusterAlignment-method 5.989 0.071 6.062 clusterAlignment 5.629 0.197 5.827 peaksDataset 5.318 0.266 5.585 normDotProduct 5.265 0.136 5.402 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/flagme.Rcheck/00check.log’ for details.
flagme.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL flagme ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘flagme’ ... ** this is package ‘flagme’ version ‘1.65.0’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c dp.c -o dp.o dp.c: In function ‘dp’: dp.c:264:35: warning: ‘tb’ may be used uninitialized [-Wmaybe-uninitialized] 264 | phi[(i+1)+(j+1)*(nr+1)] = tb; | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ dp.c:217:30: note: ‘tb’ was declared here 217 | int i,j, nr=*nr_, nc=*nc_, tb, count=0, done=0; | ^~ dp.c:263:33: warning: ‘cur_min’ may be used uninitialized [-Wmaybe-uninitialized] 263 | D[(i+1)+(j+1)*(nr+1)] = cur_min; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ dp.c:218:21: note: ‘cur_min’ was declared here 218 | double gap=*gap_, cur_min, a, b, c; | ^~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init.c -o init.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c pearson.c -o pearson.o gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 | 6.073 | 0.175 | 6.267 | |
addChromaTOFPeaks | 3.948 | 0.152 | 4.100 | |
addXCMSPeaks | 47.726 | 7.748 | 40.294 | |
betweenAlignment | 0 | 0 | 0 | |
calcTimeDiffs | 6.239 | 0.500 | 6.740 | |
clusterAlignment | 5.629 | 0.197 | 5.827 | |
corPrt | 44.561 | 8.514 | 36.802 | |
dp | 6.476 | 0.540 | 7.017 | |
dynRT | 45.558 | 8.526 | 37.404 | |
gatherInfo | 7.378 | 0.542 | 7.920 | |
imputePeaks | 10.318 | 0.452 | 10.778 | |
multipleAlignment-class | 6.777 | 0.209 | 6.986 | |
ndpRT | 42.348 | 9.555 | 36.404 | |
normDotProduct | 5.265 | 0.136 | 5.402 | |
parseChromaTOF | 1.997 | 0.013 | 2.011 | |
parseELU | 1.828 | 0.000 | 1.828 | |
peaksAlignment-class | 48.002 | 8.863 | 40.056 | |
peaksDataset | 5.318 | 0.266 | 5.585 | |
plotAlignedFrags | 94.357 | 18.364 | 58.959 | |
plotAlignment-peaksAlignment-method | 45.949 | 8.000 | 38.151 | |
plotChrom-peaksDataset-method | 7.805 | 0.245 | 8.050 | |
plotClustAlignment-clusterAlignment-method | 5.989 | 0.071 | 6.062 | |
plotFrags | 49.792 | 9.538 | 41.292 | |
plotImage | 4.108 | 0.204 | 4.312 | |
progressiveAlignment-class | 44.964 | 7.791 | 37.087 | |
retFatMatrix | 44.185 | 8.806 | 37.232 | |
rmaFitUnit | 6.653 | 0.154 | 6.808 | |