Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:13:06 -0400 (Tue, 09 Apr 2019).
Package 940/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Metab 1.17.1 Raphael Aggio
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![]() | ||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: Metab |
Version: 1.17.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Metab.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Metab_1.17.1.tar.gz |
StartedAt: 2019-04-09 03:22:30 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 03:26:24 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 233.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Metab.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Metab.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Metab_1.17.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Metab.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Metab/DESCRIPTION’ ... OK * this is package ‘Metab’ version ‘1.17.1’ * 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 ‘Metab’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 ... NOTE MetReport: no visible global function definition for ‘read.csv’ MetReport: no visible global function definition for ‘write.csv’ MetReportNames: no visible global function definition for ‘read.csv’ MetReportNames: no visible global function definition for ‘write.csv’ buildLib: no visible global function definition for ‘read.csv’ buildLib: no visible global function definition for ‘txtProgressBar’ buildLib: no visible global function definition for ‘setTxtProgressBar’ buildLib: no visible global function definition for ‘write.csv’ htest : test.t : <anonymous>: no visible global function definition for ‘t.test’ htest : anova.t : <anonymous>: no visible global function definition for ‘lm’ htest : anova.t: no visible binding for global variable ‘anova’ htest: no visible global function definition for ‘read.csv’ htest: no visible global function definition for ‘p.adjust’ htest: no visible global function definition for ‘write.csv’ normalizeByBiomass: no visible global function definition for ‘read.csv’ normalizeByBiomass: no visible global function definition for ‘write.csv’ normalizeByInternalStandard: no visible global function definition for ‘read.csv’ normalizeByInternalStandard: no visible global function definition for ‘select.list’ normalizeByInternalStandard: no visible global function definition for ‘write.csv’ removeFalsePositives: no visible global function definition for ‘read.csv’ removeFalsePositives: no visible global function definition for ‘write.csv’ Undefined global functions or variables: anova lm p.adjust read.csv select.list setTxtProgressBar t.test txtProgressBar write.csv Consider adding importFrom("stats", "anova", "lm", "p.adjust", "t.test") importFrom("utils", "read.csv", "select.list", "setTxtProgressBar", "txtProgressBar", "write.csv") to your NAMESPACE file. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.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 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/Metab.Rcheck/00check.log’ for details.
Metab.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Metab ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘Metab’ ... ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Metab)
Metab.Rcheck/tests/test-all.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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("Metab") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, 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 object is masked from 'package:base': expand.grid This is MSnbase version 2.9.3 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:stats': smooth The following object is masked from 'package:base': trimws This is xcms version 3.5.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma AMDIS Report - Data frame loaded... File 1 (130513_REF_SOL2_2_50_50_1.CDF) done! AmdisReport - Data frame loaded... File 130513_REF_SOL2_2_100_1 done! Data frame loaded... Biomass loaded... Data frame loaded... Data frame loaded... RUNIT TEST PROTOCOL -- Tue Apr 9 03:26:16 2019 *********************************************** Number of test functions: 5 Number of errors: 0 Number of failures: 0 1 Test Suite : Metab 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 9.980 0.973 10.909
Metab.Rcheck/Metab-Ex.timings
name | user | system | elapsed | |
MetReport | 0.119 | 0.098 | 0.231 | |
MetReportNames | 0.150 | 0.005 | 0.155 | |
Metab-package | 0.011 | 0.006 | 0.017 | |
buildLib | 1.767 | 0.032 | 1.800 | |
exampleAMDISReport | 0.076 | 0.038 | 0.114 | |
exampleBiomass | 0.002 | 0.002 | 0.004 | |
exampleHtest | 0.002 | 0.002 | 0.004 | |
exampleIonLib | 0.007 | 0.005 | 0.012 | |
exampleMSLfile | 0.013 | 0.006 | 0.018 | |
exampleMetReport | 0.002 | 0.003 | 0.004 | |
htest | 0.127 | 0.029 | 0.156 | |
normalizeByBiomass | 0.028 | 0.012 | 0.040 | |
normalizeByInternalStandard | 0.021 | 0.008 | 0.029 | |
removeFalsePositives | 0.042 | 0.014 | 0.055 | |