Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:38:28 -0400 (Wed, 17 Oct 2018).
Package 875/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
metaMS 1.16.0 Ron Wehrens
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: metaMS |
Version: 1.16.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings metaMS_1.16.0.tar.gz |
StartedAt: 2018-10-17 03:12:01 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 03:16:53 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 292.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: metaMS.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings metaMS_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/metaMS.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'metaMS/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'metaMS' version '1.16.0' * 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 whether package 'metaMS' 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 AnnotateFeature: no visible global function definition for 'predict' AnnotateTable: no visible global function definition for 'predict' AnnotateTable : <anonymous>: no visible global function definition for 'hclust' AnnotateTable : <anonymous>: no visible global function definition for 'dist' AnnotateTable : <anonymous>: no visible global function definition for 'cutree' addRI : <anonymous>: no visible global function definition for 'approx' getAnnotationLC: no visible binding for global variable 'median' matchExpSpec: no visible global function definition for 'plot' matchExpSpec: no visible global function definition for 'lines' matchExpSpec: no visible global function definition for 'legend' plotPseudoSpectrum: no visible global function definition for 'plot' read.msp : read.compound: no visible global function definition for 'aggregate' readStdInfo: no visible global function definition for 'read.table' relInt: no visible global function definition for 'coef' relInt: no visible global function definition for 'lm' removeDoubleMasses : <anonymous>: no visible global function definition for 'aggregate' runCAMERA: no visible global function definition for 'capture.output' runGC: no visible global function definition for 'sessionInfo' runLC: no visible global function definition for 'sessionInfo' Undefined global functions or variables: aggregate approx capture.output coef cutree dist hclust legend lines lm median plot predict read.table sessionInfo Consider adding importFrom("graphics", "legend", "lines", "plot") importFrom("stats", "aggregate", "approx", "coef", "cutree", "dist", "hclust", "lm", "median", "predict") importFrom("utils", "capture.output", "read.table", "sessionInfo") 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 ... WARNING Documented arguments not in \usage in documentation object 'matchExpSpec': 'spec1' 'spec2' 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.7-bioc/meat/metaMS.Rcheck/00check.log' for details.
metaMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/metaMS_1.16.0.tar.gz && rm -rf metaMS.buildbin-libdir && mkdir metaMS.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaMS.buildbin-libdir metaMS_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL metaMS_1.16.0.zip && rm metaMS_1.16.0.tar.gz metaMS_1.16.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 3420k 100 3420k 0 0 37.5M 0 --:--:-- --:--:-- --:--:-- 40.7M install for i386 * installing *source* package 'metaMS' ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'metaMS' finding HTML links ... done AnnotateTable html FEMsettings html finding level-2 HTML links ... done GCresults html LCDBtest html LCresults html addRI html alignmentLC html annotations2tab html constructExpPseudoSpectra html createSTDdbGC html createSTDdbLC html errf html exptable html getAnnotationLC html getAnnotationMat html getFeatureInfo html getPeakTable html match2ExtDB html matchExpSpec html matchSamples2DB html matchSamples2Samples html metaMS-package html metaMSsettings-class html metaSetting-methods html msp html peakDetection html plotPseudoSpectrum html printString html processStandards html readStdInfo html removeDoubleMasses html runCAMERA html runGC html runLC html threeStdsDB html treat.DB html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'metaMS' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'metaMS' as metaMS_1.16.0.zip * DONE (metaMS) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'metaMS' successfully unpacked and MD5 sums checked In R CMD INSTALL
metaMS.Rcheck/tests_i386/runTests.Rout R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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("metaMS") 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, lengths, 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")'. This is MSnbase version 2.6.4 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 3.2.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma < -------- Experiment of 4 samples ------------------------------------- > < -------- Instrument: TSQXLS.QQQ.GC ----------------------------------- > < -------- Annotation using database of 3 spectra ---------------------- > < -------- Using xcmsSet object - only doing annotation ---------------- > < -------- Removing artefacts (Bleeding, Plasticizers) ----------------- > < -------- Matching with database of standards ------------------------- > < -------- Matching unknowns across samples ---------------------------- > < -------- Formatting results ------------------------------------------ > < -------- Done! ------------------------------------------------------- > < -------- Experiment of 4 samples ------------------------------------- > < -------- Instrument: Synapt.QTOF.RP - polarity: positive ------------ > < -------- Database of 4 compounds ------------------------------------- > < -------- Using xcmsSet object - only doing annotation ---------------- > < -------- Performing annotation --------------------------------------- > Fixed mass tolerance 0.005 Feature-wise Annotation ... < -------- Formatting the output --------------------------------------- > < -------- Done ! ------------------------------------------------------ > RUNIT TEST PROTOCOL -- Wed Oct 17 03:16:30 2018 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : metaMS RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 16.14 1.14 17.60 |
metaMS.Rcheck/tests_x64/runTests.Rout R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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("metaMS") 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, lengths, 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")'. This is MSnbase version 2.6.4 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 3.2.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma < -------- Experiment of 4 samples ------------------------------------- > < -------- Instrument: TSQXLS.QQQ.GC ----------------------------------- > < -------- Annotation using database of 3 spectra ---------------------- > < -------- Using xcmsSet object - only doing annotation ---------------- > < -------- Removing artefacts (Bleeding, Plasticizers) ----------------- > < -------- Matching with database of standards ------------------------- > < -------- Matching unknowns across samples ---------------------------- > < -------- Formatting results ------------------------------------------ > < -------- Done! ------------------------------------------------------- > < -------- Experiment of 4 samples ------------------------------------- > < -------- Instrument: Synapt.QTOF.RP - polarity: positive ------------ > < -------- Database of 4 compounds ------------------------------------- > < -------- Using xcmsSet object - only doing annotation ---------------- > < -------- Performing annotation --------------------------------------- > Fixed mass tolerance 0.005 Feature-wise Annotation ... < -------- Formatting the output --------------------------------------- > < -------- Done ! ------------------------------------------------------ > RUNIT TEST PROTOCOL -- Wed Oct 17 03:16:47 2018 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : metaMS RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 14.79 0.64 15.59 |
metaMS.Rcheck/examples_i386/metaMS-Ex.timings
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metaMS.Rcheck/examples_x64/metaMS-Ex.timings
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