Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:05:47 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the proFIA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/proFIA.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1463/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
proFIA 1.20.0 (landing page) Alexis Delabriere
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: proFIA |
Version: 1.20.0 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:proFIA.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings proFIA_1.20.0.tar.gz |
StartedAt: 2022-04-12 08:49:21 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 08:54:56 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 335.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: proFIA.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:proFIA.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings proFIA_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/proFIA.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘proFIA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘proFIA’ version ‘1.20.0’ * 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 ‘proFIA’ 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 ... WARNING Undocumented arguments in documentation object 'proFIAset' ‘f’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 proFIAset 72.011 0.631 72.653 impute.FIA-proFIAset-method 11.701 0.140 11.841 findFIASignal 11.129 0.204 11.333 impute.randomForest-proFIAset-method 10.881 0.092 10.973 estimateNoiseMS 5.370 0.255 5.625 plotFlowgrams-proFIAset-method 5.332 0.108 5.439 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.14-bioc/meat/proFIA.Rcheck/00check.log’ for details.
proFIA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL proFIA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘proFIA’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c UtilFunc.c -o UtilFunc.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastMatchPpm.c -o fastMatchPpm.o gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-proFIA/00new/proFIA/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** 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 (proFIA)
proFIA.Rcheck/tests/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > BiocGenerics:::testPackage("proFIA") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.20.4 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Loading required package: plasFIA A mass interval of 0.0153m/z will be used for the density estimation. 0 :0 10 :29 20 :54 30 :78 30 :105 40 :141 50 :174 60 :196 70 :208 80 :215 90 :219 219 groups have been done . RUNIT TEST PROTOCOL -- Tue Apr 12 08:54:53 2022 *********************************************** Number of test functions: 5 Number of errors: 0 Number of failures: 0 1 Test Suite : proFIA RUnit Tests - 5 test functions, 0 errors, 0 failures Number of test functions: 5 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 12.410 0.580 12.977
proFIA.Rcheck/proFIA-Ex.timings
name | user | system | elapsed | |
acquisitionDirectory | 0.053 | 0.008 | 0.061 | |
analyzeAcquisitionFIA | 0.013 | 0.000 | 0.013 | |
determiningInjectionZone | 0.997 | 0.024 | 1.021 | |
determiningSizePeak.Geom | 0.998 | 0.064 | 1.062 | |
estimateNoiseMS | 5.370 | 0.255 | 5.625 | |
exportDataMatrix-proFIAset-method | 0.024 | 0.000 | 0.024 | |
exportExpressionSet-proFIAset-method | 0.075 | 0.000 | 0.074 | |
exportPeakTable-proFIAset-method | 0.027 | 0.000 | 0.027 | |
exportSampleMetadata-proFIAset-method | 0.02 | 0.00 | 0.02 | |
exportVariableMetadata-proFIAset-method | 0.022 | 0.000 | 0.021 | |
findBandsFIA | 2.193 | 0.036 | 2.229 | |
findFIASignal | 11.129 | 0.204 | 11.333 | |
findMzGroup-proFIAset-method | 0.028 | 0.000 | 0.028 | |
getInjectionPeak | 2.714 | 0.104 | 2.818 | |
group.FIA-proFIAset-method | 1.726 | 0.020 | 1.746 | |
impute.FIA-proFIAset-method | 11.701 | 0.140 | 11.841 | |
impute.KNN_TN-proFIAset-method | 0.321 | 0.004 | 0.324 | |
impute.randomForest-proFIAset-method | 10.881 | 0.092 | 10.973 | |
makeDataMatrix-proFIAset-method | 0.027 | 0.000 | 0.027 | |
peaksGroup-proFIAset-method | 0.036 | 0.012 | 0.048 | |
plot | 0.752 | 0.092 | 0.844 | |
plotFlowgrams-proFIAset-method | 5.332 | 0.108 | 5.439 | |
plotNoise | 0.195 | 0.000 | 0.195 | |
plotRaw-proFIAset-method | 1.827 | 0.007 | 1.835 | |
plotSamplePeaks-proFIAset-method | 0.023 | 0.001 | 0.022 | |
proFIAset | 72.011 | 0.631 | 72.653 | |