Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:38:06 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 1611/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ptairMS 1.10.0 (landing page) camille Roquencourt
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.10.0 |
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_1.10.0.tar.gz |
StartedAt: 2024-03-28 07:14:22 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 07:30:51 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 988.6 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_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/ptairMS.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ptairMS/DESCRIPTION’ ... OK * this is package ‘ptairMS’ version ‘1.10.0’ * 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-3.18-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 R 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 173.071 3.416 180.373 imputeMat 30.517 0.833 33.115 alignSamples 28.843 0.929 31.849 impute 25.925 0.765 27.315 writeEset 25.325 0.772 26.792 annotation 24.992 0.807 30.177 getPeakList 24.437 0.682 25.232 plot 23.347 0.465 24.558 plotFeatures 21.652 0.572 22.586 plotTIC 21.351 0.567 22.526 plotRaw 19.065 0.685 20.151 plotCalib 17.923 0.591 18.925 defineKnots 17.506 0.420 18.480 exportSampleMetada 16.936 0.519 17.627 resetSampleMetadata 16.838 0.434 17.550 importSampleMetadata 16.682 0.459 17.548 setSampleMetadata 16.686 0.408 18.406 updatePtrSet 16.496 0.470 17.971 getFileNames 16.502 0.384 17.066 getDirectory 16.440 0.410 17.032 rmPeakList 16.322 0.466 17.015 changeTimeLimits 16.412 0.356 18.394 getSampleMetadata 16.292 0.460 16.902 createPtrSet 15.576 0.492 17.061 convert_to_mzML 11.000 0.306 11.964 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.18-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (64-bit) 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 143.626 4.371 159.447
ptairMS.Rcheck/ptairMS-Ex.timings
name | user | system | elapsed | |
LocalMaximaSG | 0.060 | 0.008 | 0.071 | |
PeakList | 1.544 | 0.156 | 1.812 | |
RunShinnyApp | 0.000 | 0.000 | 0.001 | |
alignSamples | 28.843 | 0.929 | 31.849 | |
annotation | 24.992 | 0.807 | 30.177 | |
calibration | 1.242 | 0.042 | 1.517 | |
changeTimeLimits | 16.412 | 0.356 | 18.394 | |
convert_to_mzML | 11.000 | 0.306 | 11.964 | |
createPtrSet | 15.576 | 0.492 | 17.061 | |
defineKnots | 17.506 | 0.420 | 18.480 | |
detectPeak | 173.071 | 3.416 | 180.373 | |
exportSampleMetada | 16.936 | 0.519 | 17.627 | |
formula2mass | 0.006 | 0.002 | 0.007 | |
getDirectory | 16.440 | 0.410 | 17.032 | |
getFileNames | 16.502 | 0.384 | 17.066 | |
getPeakList | 24.437 | 0.682 | 25.232 | |
getSampleMetadata | 16.292 | 0.460 | 16.902 | |
importSampleMetadata | 16.682 | 0.459 | 17.548 | |
impute | 25.925 | 0.765 | 27.315 | |
imputeMat | 30.517 | 0.833 | 33.115 | |
plot | 23.347 | 0.465 | 24.558 | |
plotCalib | 17.923 | 0.591 | 18.925 | |
plotFeatures | 21.652 | 0.572 | 22.586 | |
plotRaw | 19.065 | 0.685 | 20.151 | |
plotTIC | 21.351 | 0.567 | 22.526 | |
readRaw | 0.222 | 0.024 | 0.252 | |
resetSampleMetadata | 16.838 | 0.434 | 17.550 | |
rmPeakList | 16.322 | 0.466 | 17.015 | |
setSampleMetadata | 16.686 | 0.408 | 18.406 | |
timeLimits | 2.179 | 0.061 | 2.246 | |
updatePtrSet | 16.496 | 0.470 | 17.971 | |
writeEset | 25.325 | 0.772 | 26.792 | |