Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 720/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flagme 1.62.0 (landing page) Mark Robinson
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.62.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings flagme_1.62.0.tar.gz |
StartedAt: 2024-11-20 02:58:21 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 03:15:54 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 1052.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flagme.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings flagme_1.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/flagme.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘flagme/DESCRIPTION’ ... OK * this is package ‘flagme’ version ‘1.62.0’ * 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 13.2.0-23ubuntu4) 13.2.0’ * 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 84.740 14.566 63.572 addXCMSPeaks 48.990 9.554 46.723 corPrt 40.956 9.016 42.480 dynRT 41.972 7.805 40.212 peaksAlignment-class 40.113 7.105 33.689 progressiveAlignment-class 38.078 8.787 34.519 plotAlignment-peaksAlignment-method 38.471 7.581 37.745 plotFrags 37.320 8.513 36.828 ndpRT 37.366 7.664 32.879 retFatMatrix 36.615 7.460 36.901 imputePeaks 10.710 0.120 11.293 plotChrom-peaksDataset-method 8.943 0.099 10.322 calcTimeDiffs 7.773 0.072 8.603 clusterAlignment 7.663 0.049 8.566 gatherInfo 7.330 0.081 7.968 multipleAlignment-class 7.053 0.058 7.158 rmaFitUnit 6.529 0.117 7.011 dp 6.196 0.139 7.567 normDotProduct 6.196 0.050 7.172 peaksDataset 5.880 0.078 6.170 addAMDISPeaks 5.818 0.131 6.296 plotClustAlignment-clusterAlignment-method 4.986 0.083 5.296 plotImage 4.764 0.032 6.398 * 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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/flagme.Rcheck/00check.log’ for details.
flagme.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL flagme ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘flagme’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/biocbuild/bbs-3.20-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: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 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pearson.c -o pearson.o gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-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 | 5.818 | 0.131 | 6.296 | |
addChromaTOFPeaks | 4.813 | 0.131 | 4.991 | |
addXCMSPeaks | 48.990 | 9.554 | 46.723 | |
betweenAlignment | 0 | 0 | 0 | |
calcTimeDiffs | 7.773 | 0.072 | 8.603 | |
clusterAlignment | 7.663 | 0.049 | 8.566 | |
corPrt | 40.956 | 9.016 | 42.480 | |
dp | 6.196 | 0.139 | 7.567 | |
dynRT | 41.972 | 7.805 | 40.212 | |
gatherInfo | 7.330 | 0.081 | 7.968 | |
imputePeaks | 10.710 | 0.120 | 11.293 | |
multipleAlignment-class | 7.053 | 0.058 | 7.158 | |
ndpRT | 37.366 | 7.664 | 32.879 | |
normDotProduct | 6.196 | 0.050 | 7.172 | |
parseChromaTOF | 1.506 | 0.000 | 1.797 | |
parseELU | 1.443 | 0.000 | 1.493 | |
peaksAlignment-class | 40.113 | 7.105 | 33.689 | |
peaksDataset | 5.880 | 0.078 | 6.170 | |
plotAlignedFrags | 84.740 | 14.566 | 63.572 | |
plotAlignment-peaksAlignment-method | 38.471 | 7.581 | 37.745 | |
plotChrom-peaksDataset-method | 8.943 | 0.099 | 10.322 | |
plotClustAlignment-clusterAlignment-method | 4.986 | 0.083 | 5.296 | |
plotFrags | 37.320 | 8.513 | 36.828 | |
plotImage | 4.764 | 0.032 | 6.398 | |
progressiveAlignment-class | 38.078 | 8.787 | 34.519 | |
retFatMatrix | 36.615 | 7.460 | 36.901 | |
rmaFitUnit | 6.529 | 0.117 | 7.011 | |