Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-04-02 19:32 -0400 (Wed, 02 Apr 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
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 1616/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ptairMS 1.14.0 (landing page) camille Roquencourt
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | 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 | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ptairMS_1.14.0.tar.gz |
StartedAt: 2025-04-01 07:28:49 -0400 (Tue, 01 Apr 2025) |
EndedAt: 2025-04-01 07:46:03 -0400 (Tue, 01 Apr 2025) |
EllapsedTime: 1033.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ptairMS.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ptairMS_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck’ * using R version 4.4.3 (2025-02-28) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ptairMS/DESCRIPTION’ ... OK * this is package ‘ptairMS’ version ‘1.14.0’ * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 182.542 3.843 189.114 alignSamples 30.337 1.136 31.737 imputeMat 29.723 0.948 31.941 impute 28.621 0.846 29.720 writeEset 28.484 0.762 29.696 getPeakList 26.802 0.819 28.463 annotation 26.538 0.773 27.938 convert_to_mzML 22.232 0.902 23.388 plot 22.517 0.529 23.767 plotTIC 21.378 0.587 22.156 plotRaw 21.079 0.680 22.534 plotFeatures 20.904 0.532 21.715 defineKnots 19.467 0.481 20.212 plotCalib 19.061 0.539 19.764 rmPeakList 18.816 0.436 19.478 resetSampleMetadata 18.726 0.421 19.401 exportSampleMetada 17.997 0.461 18.550 getFileNames 17.932 0.463 18.886 getSampleMetadata 17.670 0.388 18.949 changeTimeLimits 17.556 0.443 18.095 createPtrSet 17.116 0.772 18.253 importSampleMetadata 17.026 0.454 17.842 setSampleMetadata 16.977 0.475 17.894 getDirectory 16.920 0.480 17.577 updatePtrSet 16.859 0.429 17.539 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck/00check.log’ for details.
ptairMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ptairMS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ptairMS’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c align.cpp -o align.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findEqualGreaterM.cpp -o findEqualGreaterM.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ptairMS.so RcppExports.o align.o findEqualGreaterM.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 : 4 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 : 6 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 151.623 4.583 164.344
ptairMS.Rcheck/ptairMS-Ex.timings
name | user | system | elapsed | |
LocalMaximaSG | 0.050 | 0.007 | 0.114 | |
PeakList | 1.599 | 0.191 | 1.852 | |
RunShinnyApp | 0 | 0 | 0 | |
alignSamples | 30.337 | 1.136 | 31.737 | |
annotation | 26.538 | 0.773 | 27.938 | |
calibration | 1.353 | 0.050 | 1.418 | |
changeTimeLimits | 17.556 | 0.443 | 18.095 | |
convert_to_mzML | 22.232 | 0.902 | 23.388 | |
createPtrSet | 17.116 | 0.772 | 18.253 | |
defineKnots | 19.467 | 0.481 | 20.212 | |
detectPeak | 182.542 | 3.843 | 189.114 | |
exportSampleMetada | 17.997 | 0.461 | 18.550 | |
formula2mass | 0.005 | 0.001 | 0.007 | |
getDirectory | 16.920 | 0.480 | 17.577 | |
getFileNames | 17.932 | 0.463 | 18.886 | |
getPeakList | 26.802 | 0.819 | 28.463 | |
getSampleMetadata | 17.670 | 0.388 | 18.949 | |
importSampleMetadata | 17.026 | 0.454 | 17.842 | |
impute | 28.621 | 0.846 | 29.720 | |
imputeMat | 29.723 | 0.948 | 31.941 | |
plot | 22.517 | 0.529 | 23.767 | |
plotCalib | 19.061 | 0.539 | 19.764 | |
plotFeatures | 20.904 | 0.532 | 21.715 | |
plotRaw | 21.079 | 0.680 | 22.534 | |
plotTIC | 21.378 | 0.587 | 22.156 | |
readRaw | 0.223 | 0.027 | 0.249 | |
resetSampleMetadata | 18.726 | 0.421 | 19.401 | |
rmPeakList | 18.816 | 0.436 | 19.478 | |
setSampleMetadata | 16.977 | 0.475 | 17.894 | |
timeLimits | 2.335 | 0.047 | 2.391 | |
updatePtrSet | 16.859 | 0.429 | 17.539 | |
writeEset | 28.484 | 0.762 | 29.696 | |