Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:49 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ptairMS package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1457/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ptairMS 1.0.1 (landing page) camille Roquencourt
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ptairMS |
Version: 1.0.1 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ptairMS_1.0.1.tar.gz |
StartedAt: 2021-10-14 11:08:41 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:15:49 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 428.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ptairMS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ptairMS_1.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ptairMS.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ptairMS/DESCRIPTION’ ... OK * this is package ‘ptairMS’ version ‘1.0.1’ * 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 ... OK * 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 ... OK * 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 77.668 0.276 77.947 alignSamples 15.833 0.327 16.179 annotation 13.157 0.260 13.421 imputeMat 12.867 0.084 12.952 impute 12.655 0.112 12.767 writeEset 12.212 0.124 12.338 getPeakList 10.965 0.076 11.040 defineKnots 9.167 0.732 9.898 plot 9.812 0.064 9.877 plotTIC 9.776 0.096 9.872 plotRaw 9.443 0.096 9.539 plotFeatures 9.256 0.076 9.333 rmPeakList 8.503 0.072 8.575 plotCalib 8.399 0.068 8.468 resetSampleMetadata 8.295 0.016 8.311 setSampleMetadata 8.228 0.076 8.305 createPtrSet 8.064 0.172 8.254 changeTimeLimits 8.062 0.072 8.140 updatePtrSet 7.904 0.096 8.001 importSampleMetadata 7.850 0.096 7.946 getSampleMetadata 7.824 0.072 7.896 getDirectory 7.652 0.028 7.680 exportSampleMetada 7.597 0.076 7.674 getFileNames 7.620 0.036 7.656 convert_to_mzML 5.933 0.129 6.032 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.13-bioc/meat/ptairMS.Rcheck/00check.log’ for details.
ptairMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ptairMS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘ptairMS’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c align.cpp -o align.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c findEqualGreaterM.cpp -o findEqualGreaterM.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o ptairMS.so RcppExports.o align.o findEqualGreaterM.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-ptairMS/00new/ptairMS/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘annotateVOC’ with signature ‘"ExpressionSet"’: no definition for class “ExpressionSet” in method for ‘writeEset’ with signature ‘"ExpressionSet"’: no definition for class “ExpressionSet” ** 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 (ptairMS)
ptairMS.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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) > > 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 : 5 peaks detected specie-b2.h5 : 4 peaks detected [ FAIL 0 | WARN 0 | SKIP 0 | PASS 59 ] > > proc.time() user system elapsed 69.520 1.162 70.675
ptairMS.Rcheck/ptairMS-Ex.timings
name | user | system | elapsed | |
LocalMaximaSG | 0.025 | 0.000 | 0.025 | |
PeakList | 0.607 | 0.080 | 0.691 | |
alignSamples | 15.833 | 0.327 | 16.179 | |
annotation | 13.157 | 0.260 | 13.421 | |
calibration | 0.661 | 0.004 | 0.666 | |
changeTimeLimits | 8.062 | 0.072 | 8.140 | |
convert_to_mzML | 5.933 | 0.129 | 6.032 | |
createPtrSet | 8.064 | 0.172 | 8.254 | |
defineKnots | 9.167 | 0.732 | 9.898 | |
detectPeak | 77.668 | 0.276 | 77.947 | |
exportSampleMetada | 7.597 | 0.076 | 7.674 | |
formula2mass | 0.003 | 0.000 | 0.003 | |
getDirectory | 7.652 | 0.028 | 7.680 | |
getFileNames | 7.620 | 0.036 | 7.656 | |
getPeakList | 10.965 | 0.076 | 11.040 | |
getSampleMetadata | 7.824 | 0.072 | 7.896 | |
importSampleMetadata | 7.850 | 0.096 | 7.946 | |
impute | 12.655 | 0.112 | 12.767 | |
imputeMat | 12.867 | 0.084 | 12.952 | |
plot | 9.812 | 0.064 | 9.877 | |
plotCalib | 8.399 | 0.068 | 8.468 | |
plotFeatures | 9.256 | 0.076 | 9.333 | |
plotRaw | 9.443 | 0.096 | 9.539 | |
plotTIC | 9.776 | 0.096 | 9.872 | |
readRaw | 0.116 | 0.000 | 0.115 | |
resetSampleMetadata | 8.295 | 0.016 | 8.311 | |
rmPeakList | 8.503 | 0.072 | 8.575 | |
setSampleMetadata | 8.228 | 0.076 | 8.305 | |
timeLimits | 1.556 | 0.012 | 1.568 | |
updatePtrSet | 7.904 | 0.096 | 8.001 | |
writeEset | 12.212 | 0.124 | 12.338 | |