Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 20:24 -0400 (Fri, 07 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1630/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ptairMS 1.12.0 (landing page) camille Roquencourt
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the ptairMS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ptairMS.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: ptairMS |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ptairMS_1.12.0.tar.gz |
StartedAt: 2024-06-06 02:21:59 -0400 (Thu, 06 Jun 2024) |
EndedAt: 2024-06-06 02:31:56 -0400 (Thu, 06 Jun 2024) |
EllapsedTime: 596.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ptairMS.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ptairMS_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘ptairMS/DESCRIPTION’ ... OK * this is package ‘ptairMS’ version ‘1.12.0’ * 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 ‘ptairMS’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’ See ‘/home/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (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 dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘htmlwidgets’ ‘plyr’ There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘getCalibrationInfo’ ‘getPeakList’ ‘getPeaksInfo’ ‘getTimeInfo’ ‘processFileTemporalNominalMass’ ‘tofToMz’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * 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 detectPeak 77.510 0.584 78.096 imputeMat 14.713 0.208 14.922 writeEset 14.619 0.153 14.771 alignSamples 14.307 0.368 14.685 annotation 13.000 0.252 13.253 getPeakList 12.818 0.187 13.004 impute 12.651 0.172 12.822 convert_to_mzML 11.503 0.376 11.879 plotRaw 10.664 0.076 10.741 plot 10.524 0.079 10.603 plotTIC 9.712 0.116 9.829 resetSampleMetadata 9.735 0.088 9.823 updatePtrSet 9.411 0.132 9.542 defineKnots 9.320 0.128 9.448 plotCalib 9.278 0.116 9.394 plotFeatures 8.901 0.092 8.993 exportSampleMetada 8.677 0.100 8.777 setSampleMetadata 8.678 0.060 8.738 rmPeakList 8.588 0.080 8.668 importSampleMetadata 8.540 0.047 8.587 getDirectory 8.460 0.108 8.567 changeTimeLimits 8.338 0.120 8.458 getSampleMetadata 7.886 0.017 7.903 getFileNames 7.748 0.108 7.857 createPtrSet 7.276 0.088 7.372 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck/00check.log’ for details.
ptairMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ptairMS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘ptairMS’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c align.cpp -o align.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c findEqualGreaterM.cpp -o findEqualGreaterM.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o ptairMS.so RcppExports.o align.o findEqualGreaterM.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-ptairMS/00new/ptairMS/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’ ** testing if installed package keeps a record of temporary installation path * DONE (ptairMS)
ptairMS.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(ptairMS) Warning message: replacing previous import 'Biobase::cache' by 'bit64::cache' when loading 'ptairMS' > > test_check("ptairMS") Control1.h5 : 3 peaks detected Control2.h5 : 3 peaks detected Specie-a1.h5 : 2 peaks detected Specie-a2.h5 : 3 peaks detected specie-b1.h5 : 4 peaks detected specie-b2.h5 : 3 peaks detected Control1.h5 : 2 peaks detected Control2.h5 : 2 peaks detected Specie-a1.h5 : 3 peaks detected Specie-a2.h5 : 3 peaks detected specie-b1.h5 : 2 peaks detected specie-b2.h5 : 3 peaks detected Control1.h5 : 4 peaks detected Control2.h5 : 5 peaks detected Specie-a1.h5 : 3 peaks detected Specie-a2.h5 : 4 peaks detected specie-b1.h5 : 5 peaks detected specie-b2.h5 : 4 peaks detected Control1.h5 : 3 peaks detected Control2.h5 : 2 peaks detected Specie-a1.h5 : 3 peaks detected Specie-a2.h5 : 3 peaks detected specie-b1.h5 : 4 peaks detected specie-b2.h5 : 4 peaks detected [ FAIL 0 | WARN 0 | SKIP 0 | PASS 59 ] > > proc.time() user system elapsed 67.970 0.925 68.886
ptairMS.Rcheck/ptairMS-Ex.timings
name | user | system | elapsed | |
LocalMaximaSG | 0.024 | 0.000 | 0.024 | |
PeakList | 0.817 | 0.088 | 0.907 | |
RunShinnyApp | 0 | 0 | 0 | |
alignSamples | 14.307 | 0.368 | 14.685 | |
annotation | 13.000 | 0.252 | 13.253 | |
calibration | 0.635 | 0.004 | 0.639 | |
changeTimeLimits | 8.338 | 0.120 | 8.458 | |
convert_to_mzML | 11.503 | 0.376 | 11.879 | |
createPtrSet | 7.276 | 0.088 | 7.372 | |
defineKnots | 9.320 | 0.128 | 9.448 | |
detectPeak | 77.510 | 0.584 | 78.096 | |
exportSampleMetada | 8.677 | 0.100 | 8.777 | |
formula2mass | 0.003 | 0.000 | 0.003 | |
getDirectory | 8.460 | 0.108 | 8.567 | |
getFileNames | 7.748 | 0.108 | 7.857 | |
getPeakList | 12.818 | 0.187 | 13.004 | |
getSampleMetadata | 7.886 | 0.017 | 7.903 | |
importSampleMetadata | 8.540 | 0.047 | 8.587 | |
impute | 12.651 | 0.172 | 12.822 | |
imputeMat | 14.713 | 0.208 | 14.922 | |
plot | 10.524 | 0.079 | 10.603 | |
plotCalib | 9.278 | 0.116 | 9.394 | |
plotFeatures | 8.901 | 0.092 | 8.993 | |
plotRaw | 10.664 | 0.076 | 10.741 | |
plotTIC | 9.712 | 0.116 | 9.829 | |
readRaw | 0.128 | 0.016 | 0.144 | |
resetSampleMetadata | 9.735 | 0.088 | 9.823 | |
rmPeakList | 8.588 | 0.080 | 8.668 | |
setSampleMetadata | 8.678 | 0.060 | 8.738 | |
timeLimits | 0.972 | 0.008 | 0.981 | |
updatePtrSet | 9.411 | 0.132 | 9.542 | |
writeEset | 14.619 | 0.153 | 14.771 | |