Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-09-17 17:33 -0400 (Tue, 17 Sep 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" | 4760 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4497 |
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 | |||||||||
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: 2024-09-15 23:04:50 -0400 (Sun, 15 Sep 2024) |
EndedAt: 2024-09-15 23:21:58 -0400 (Sun, 15 Sep 2024) |
EllapsedTime: 1028.4 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 22.04.4 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 91.999 17.526 57.240 peaksAlignment-class 50.883 10.150 41.969 dynRT 49.564 10.565 41.810 corPrt 48.071 11.668 42.022 addXCMSPeaks 51.338 8.289 43.091 plotFrags 46.411 10.969 39.667 retFatMatrix 48.281 8.330 39.621 progressiveAlignment-class 47.517 8.751 38.535 ndpRT 44.072 10.557 37.878 plotAlignment-peaksAlignment-method 45.404 7.511 36.678 imputePeaks 11.223 0.388 11.613 plotChrom-peaksDataset-method 8.852 0.388 9.240 calcTimeDiffs 7.609 0.707 8.319 gatherInfo 7.868 0.384 8.253 multipleAlignment-class 7.709 0.228 7.937 rmaFitUnit 7.674 0.148 7.822 dp 7.078 0.703 7.781 clusterAlignment 6.868 0.472 7.340 normDotProduct 6.428 0.352 6.780 addAMDISPeaks 5.865 0.292 6.178 peaksDataset 5.497 0.100 5.597 plotClustAlignment-clusterAlignment-method 5.034 0.112 5.147 addChromaTOFPeaks 4.885 0.220 5.105 * 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 | 5.865 | 0.292 | 6.178 | |
addChromaTOFPeaks | 4.885 | 0.220 | 5.105 | |
addXCMSPeaks | 51.338 | 8.289 | 43.091 | |
betweenAlignment | 0.001 | 0.001 | 0.001 | |
calcTimeDiffs | 7.609 | 0.707 | 8.319 | |
clusterAlignment | 6.868 | 0.472 | 7.340 | |
corPrt | 48.071 | 11.668 | 42.022 | |
dp | 7.078 | 0.703 | 7.781 | |
dynRT | 49.564 | 10.565 | 41.810 | |
gatherInfo | 7.868 | 0.384 | 8.253 | |
imputePeaks | 11.223 | 0.388 | 11.613 | |
multipleAlignment-class | 7.709 | 0.228 | 7.937 | |
ndpRT | 44.072 | 10.557 | 37.878 | |
normDotProduct | 6.428 | 0.352 | 6.780 | |
parseChromaTOF | 1.973 | 0.048 | 2.021 | |
parseELU | 1.785 | 0.001 | 1.785 | |
peaksAlignment-class | 50.883 | 10.150 | 41.969 | |
peaksDataset | 5.497 | 0.100 | 5.597 | |
plotAlignedFrags | 91.999 | 17.526 | 57.240 | |
plotAlignment-peaksAlignment-method | 45.404 | 7.511 | 36.678 | |
plotChrom-peaksDataset-method | 8.852 | 0.388 | 9.240 | |
plotClustAlignment-clusterAlignment-method | 5.034 | 0.112 | 5.147 | |
plotFrags | 46.411 | 10.969 | 39.667 | |
plotImage | 3.659 | 0.128 | 3.787 | |
progressiveAlignment-class | 47.517 | 8.751 | 38.535 | |
retFatMatrix | 48.281 | 8.330 | 39.621 | |
rmaFitUnit | 7.674 | 0.148 | 7.822 | |