Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-12 17:41 -0400 (Fri, 12 Jul 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" | 4741 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 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: /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_1.12.0.tar.gz |
StartedAt: 2024-07-11 09:47:16 -0400 (Thu, 11 Jul 2024) |
EndedAt: 2024-07-11 10:07:37 -0400 (Thu, 11 Jul 2024) |
EllapsedTime: 1220.9 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_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 ‘/Users/biocbuild/bbs-3.19-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 189.392 3.570 214.531 imputeMat 30.804 0.802 34.342 alignSamples 30.650 0.901 36.743 writeEset 30.636 0.724 36.634 impute 28.510 0.707 32.033 getPeakList 28.017 0.638 32.044 annotation 27.432 0.659 32.672 convert_to_mzML 23.690 1.015 28.286 plot 23.652 0.505 26.719 plotTIC 22.282 0.606 26.859 plotFeatures 21.146 0.529 24.346 plotRaw 20.098 0.592 23.524 resetSampleMetadata 20.032 0.489 26.073 plotCalib 19.999 0.481 22.927 updatePtrSet 19.626 0.457 25.229 defineKnots 19.516 0.401 22.614 setSampleMetadata 18.685 0.455 22.789 rmPeakList 18.590 0.422 21.741 getFileNames 18.484 0.416 20.443 importSampleMetadata 18.462 0.339 21.152 getDirectory 17.840 0.399 20.340 createPtrSet 17.582 0.566 20.461 exportSampleMetada 17.714 0.401 20.239 getSampleMetadata 17.630 0.369 20.122 changeTimeLimits 17.568 0.339 20.758 * 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-3.19-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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 155.803 4.649 192.136
ptairMS.Rcheck/ptairMS-Ex.timings
name | user | system | elapsed | |
LocalMaximaSG | 0.051 | 0.008 | 0.069 | |
PeakList | 1.740 | 0.159 | 2.209 | |
RunShinnyApp | 0.000 | 0.001 | 0.000 | |
alignSamples | 30.650 | 0.901 | 36.743 | |
annotation | 27.432 | 0.659 | 32.672 | |
calibration | 1.378 | 0.037 | 1.661 | |
changeTimeLimits | 17.568 | 0.339 | 20.758 | |
convert_to_mzML | 23.690 | 1.015 | 28.286 | |
createPtrSet | 17.582 | 0.566 | 20.461 | |
defineKnots | 19.516 | 0.401 | 22.614 | |
detectPeak | 189.392 | 3.570 | 214.531 | |
exportSampleMetada | 17.714 | 0.401 | 20.239 | |
formula2mass | 0.006 | 0.001 | 0.010 | |
getDirectory | 17.840 | 0.399 | 20.340 | |
getFileNames | 18.484 | 0.416 | 20.443 | |
getPeakList | 28.017 | 0.638 | 32.044 | |
getSampleMetadata | 17.630 | 0.369 | 20.122 | |
importSampleMetadata | 18.462 | 0.339 | 21.152 | |
impute | 28.510 | 0.707 | 32.033 | |
imputeMat | 30.804 | 0.802 | 34.342 | |
plot | 23.652 | 0.505 | 26.719 | |
plotCalib | 19.999 | 0.481 | 22.927 | |
plotFeatures | 21.146 | 0.529 | 24.346 | |
plotRaw | 20.098 | 0.592 | 23.524 | |
plotTIC | 22.282 | 0.606 | 26.859 | |
readRaw | 0.252 | 0.029 | 0.312 | |
resetSampleMetadata | 20.032 | 0.489 | 26.073 | |
rmPeakList | 18.590 | 0.422 | 21.741 | |
setSampleMetadata | 18.685 | 0.455 | 22.789 | |
timeLimits | 2.541 | 0.066 | 2.944 | |
updatePtrSet | 19.626 | 0.457 | 25.229 | |
writeEset | 30.636 | 0.724 | 36.634 | |