Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-11 20:38 -0400 (Fri, 11 Oct 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" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings flagme_1.60.0.tar.gz |
StartedAt: 2024-10-09 23:23:07 -0400 (Wed, 09 Oct 2024) |
EndedAt: 2024-10-09 23:39:09 -0400 (Wed, 09 Oct 2024) |
EllapsedTime: 962.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flagme.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings flagme_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/flagme.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.5 LTS * using session charset: UTF-8 * 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: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotAlignedFrags 88.231 16.805 54.461 peaksAlignment-class 46.103 10.759 39.864 addXCMSPeaks 45.998 7.809 39.370 dynRT 44.670 9.099 38.044 progressiveAlignment-class 43.656 10.103 38.537 corPrt 43.203 8.895 36.355 plotFrags 43.691 8.275 36.522 ndpRT 41.362 10.132 35.957 plotAlignment-peaksAlignment-method 44.310 6.806 34.484 retFatMatrix 43.838 7.231 35.521 imputePeaks 10.273 0.552 10.827 plotChrom-peaksDataset-method 9.056 0.204 9.260 gatherInfo 7.382 0.624 8.006 multipleAlignment-class 6.823 0.279 7.102 calcTimeDiffs 6.493 0.536 7.031 rmaFitUnit 6.600 0.112 6.711 dp 6.155 0.524 6.679 normDotProduct 6.001 0.288 6.289 clusterAlignment 5.691 0.384 6.075 plotClustAlignment-clusterAlignment-method 5.270 0.104 5.374 * 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-3.19-bioc/meat/flagme.Rcheck/00check.log’ for details.
flagme.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL flagme ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘flagme’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dp.c -o dp.o dp.c: In function ‘dp’: dp.c:263:33: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized] 263 | D[(i+1)+(j+1)*(nr+1)] = cur_min; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ dp.c:264:35: warning: ‘tb’ may be used uninitialized in this function [-Wmaybe-uninitialized] 264 | phi[(i+1)+(j+1)*(nr+1)] = tb; | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pearson.c -o pearson.o gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-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 | 4.715 | 0.164 | 4.887 | |
addChromaTOFPeaks | 3.822 | 0.180 | 4.001 | |
addXCMSPeaks | 45.998 | 7.809 | 39.370 | |
betweenAlignment | 0.001 | 0.000 | 0.001 | |
calcTimeDiffs | 6.493 | 0.536 | 7.031 | |
clusterAlignment | 5.691 | 0.384 | 6.075 | |
corPrt | 43.203 | 8.895 | 36.355 | |
dp | 6.155 | 0.524 | 6.679 | |
dynRT | 44.670 | 9.099 | 38.044 | |
gatherInfo | 7.382 | 0.624 | 8.006 | |
imputePeaks | 10.273 | 0.552 | 10.827 | |
multipleAlignment-class | 6.823 | 0.279 | 7.102 | |
ndpRT | 41.362 | 10.132 | 35.957 | |
normDotProduct | 6.001 | 0.288 | 6.289 | |
parseChromaTOF | 1.896 | 0.019 | 1.917 | |
parseELU | 1.676 | 0.012 | 1.688 | |
peaksAlignment-class | 46.103 | 10.759 | 39.864 | |
peaksDataset | 4.678 | 0.243 | 4.922 | |
plotAlignedFrags | 88.231 | 16.805 | 54.461 | |
plotAlignment-peaksAlignment-method | 44.310 | 6.806 | 34.484 | |
plotChrom-peaksDataset-method | 9.056 | 0.204 | 9.260 | |
plotClustAlignment-clusterAlignment-method | 5.270 | 0.104 | 5.374 | |
plotFrags | 43.691 | 8.275 | 36.522 | |
plotImage | 3.107 | 0.224 | 3.331 | |
progressiveAlignment-class | 43.656 | 10.103 | 38.537 | |
retFatMatrix | 43.838 | 7.231 | 35.521 | |
rmaFitUnit | 6.600 | 0.112 | 6.711 | |