Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-06 13:52 -0400 (Wed, 06 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4813 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 727/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flagme 1.65.0 (landing page) Mark Robinson
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 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: 1.65.0 |
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: 2025-08-05 22:27:54 -0400 (Tue, 05 Aug 2025) |
EndedAt: 2025-08-05 22:44:14 -0400 (Tue, 05 Aug 2025) |
EllapsedTime: 980.2 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 24.04.2 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 97.401 17.492 59.102 addXCMSPeaks 50.055 9.900 43.619 peaksAlignment-class 48.245 8.760 40.043 dynRT 47.387 8.560 38.501 corPrt 47.972 7.565 38.460 ndpRT 44.713 7.908 36.505 retFatMatrix 43.201 8.388 36.583 progressiveAlignment-class 42.672 7.732 35.375 plotAlignment-peaksAlignment-method 42.139 7.298 34.205 plotFrags 40.862 8.490 34.851 imputePeaks 10.957 0.112 11.076 calcTimeDiffs 7.580 0.279 7.860 plotChrom-peaksDataset-method 7.512 0.280 7.794 gatherInfo 7.450 0.233 7.683 multipleAlignment-class 7.292 0.058 7.349 dp 6.590 0.187 6.777 clusterAlignment 6.442 0.139 6.584 rmaFitUnit 6.491 0.071 6.564 normDotProduct 5.545 0.059 5.604 peaksDataset 5.357 0.217 5.574 addAMDISPeaks 5.306 0.164 5.477 plotImage 4.673 0.644 5.317 plotClustAlignment-clusterAlignment-method 5.102 0.069 5.171 * 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 | 5.306 | 0.164 | 5.477 | |
addChromaTOFPeaks | 3.258 | 0.118 | 3.376 | |
addXCMSPeaks | 50.055 | 9.900 | 43.619 | |
betweenAlignment | 0 | 0 | 0 | |
calcTimeDiffs | 7.580 | 0.279 | 7.860 | |
clusterAlignment | 6.442 | 0.139 | 6.584 | |
corPrt | 47.972 | 7.565 | 38.460 | |
dp | 6.590 | 0.187 | 6.777 | |
dynRT | 47.387 | 8.560 | 38.501 | |
gatherInfo | 7.450 | 0.233 | 7.683 | |
imputePeaks | 10.957 | 0.112 | 11.076 | |
multipleAlignment-class | 7.292 | 0.058 | 7.349 | |
ndpRT | 44.713 | 7.908 | 36.505 | |
normDotProduct | 5.545 | 0.059 | 5.604 | |
parseChromaTOF | 1.979 | 0.003 | 1.983 | |
parseELU | 1.78 | 0.00 | 1.78 | |
peaksAlignment-class | 48.245 | 8.760 | 40.043 | |
peaksDataset | 5.357 | 0.217 | 5.574 | |
plotAlignedFrags | 97.401 | 17.492 | 59.102 | |
plotAlignment-peaksAlignment-method | 42.139 | 7.298 | 34.205 | |
plotChrom-peaksDataset-method | 7.512 | 0.280 | 7.794 | |
plotClustAlignment-clusterAlignment-method | 5.102 | 0.069 | 5.171 | |
plotFrags | 40.862 | 8.490 | 34.851 | |
plotImage | 4.673 | 0.644 | 5.317 | |
progressiveAlignment-class | 42.672 | 7.732 | 35.375 | |
retFatMatrix | 43.201 | 8.388 | 36.583 | |
rmaFitUnit | 6.491 | 0.071 | 6.564 | |