Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:29:01 -0400 (Wed, 17 Oct 2018).
Package 956/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
msPurity 1.6.2 Thomas N. Lawson
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | ![]() | ||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: msPurity |
Version: 1.6.2 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings msPurity_1.6.2.tar.gz |
StartedAt: 2018-10-16 02:13:22 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 02:20:49 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 446.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: msPurity.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings msPurity_1.6.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/msPurity.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘msPurity/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘msPurity’ version ‘1.6.2’ * 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 ‘msPurity’ 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 ... NOTE Package in Depends field not imported from: ‘Rcpp’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE CV: no visible global function definition for ‘sd’ Getfiles: no visible global function definition for ‘fix’ assessPuritySingle: no visible binding for global variable ‘parallel’ averageCluster: no visible global function definition for ‘sd’ averageCluster: no visible global function definition for ‘median’ averageSpectraSingle: no visible binding for global variable ‘scanid’ covar: no visible global function definition for ‘sd’ dimsPredictPuritySingle: no visible global function definition for ‘read.csv’ dimsPredictPuritySingleMz: no visible global function definition for ‘png’ dimsPredictPuritySingleMz: no visible binding for global variable ‘mtchi’ dimsPredictPuritySingleMz: no visible binding for global variable ‘alli’ dimsPredictPuritySingleMz: no visible global function definition for ‘points’ dimsPredictPuritySingleMz: no visible binding for global variable ‘mtch’ dimsPredictPuritySingleMz: no visible global function definition for ‘text’ dimsPredictPuritySingleMz: no visible global function definition for ‘dev.off’ dimsPredictPuritySingleMz: no visible global function definition for ‘median’ dimsPredictPuritySingleMz: no visible global function definition for ‘sd’ export_2_sqlite: no visible global function definition for ‘read.table’ export_2_sqlite: no visible global function definition for ‘read.csv’ get_topn: no visible binding for global variable ‘topn’ groupPeaksEx: no visible binding for global variable ‘median’ iwNormGauss: no visible global function definition for ‘dnorm’ iwNormGauss: no visible global function definition for ‘approxfun’ iwNormQE.5: no visible global function definition for ‘approxfun’ iwNormRcosine: no visible global function definition for ‘approxfun’ linearPurity: no visible global function definition for ‘approxfun’ medGroup: no visible binding for global variable ‘median’ median_match_results: no visible global function definition for ‘median’ msfrProcess: no visible global function definition for ‘read.csv’ performHc: no visible global function definition for ‘dist’ performHc: no visible global function definition for ‘as.dist’ plotPurity: no visible global function definition for ‘png’ plotPurity: no visible binding for global variable ‘idx’ plotPurity: no visible binding for global variable ‘purity’ plotPurity: no visible binding for global variable ‘variable’ plotPurity: no visible global function definition for ‘dev.off’ plotPurity: no visible global function definition for ‘write.csv’ pp4file: no visible global function definition for ‘png’ pp4file: no visible global function definition for ‘plot’ pp4file: no visible global function definition for ‘lines’ pp4file: no visible global function definition for ‘legend’ pp4file: no visible global function definition for ‘abline’ pp4file: no visible global function definition for ‘dev.off’ pp4file: no visible global function definition for ‘median’ predictPurityLCMSloop: no visible global function definition for ‘median’ predictPurityLCMSloop : <anonymous>: no visible global function definition for ‘na.omit’ predictPurityLCMSloop : <anonymous>: no visible global function definition for ‘median’ predictPurityLCMSloop : <anonymous>: no visible global function definition for ‘sd’ purityA: no visible binding for global variable ‘i’ removeIsotopes: no visible global function definition for ‘write.csv’ rsde: no visible global function definition for ‘sd’ snrFilter: no visible global function definition for ‘median’ stde: no visible global function definition for ‘sd’ stderror: no visible global function definition for ‘sd’ xcmsGroupPurity: no visible binding for global variable ‘median’ xcmsGroupPurity: no visible global function definition for ‘median’ averageSpectra,purityD: no visible binding for global variable ‘i’ subtract,purityD: no visible binding for global variable ‘i’ validate,purityA: no visible global function definition for ‘head’ writeOut,purityD: no visible global function definition for ‘write.csv’ Undefined global functions or variables: abline alli approxfun as.dist dev.off dist dnorm fix head i idx legend lines median mtch mtchi na.omit parallel plot png points purity read.csv read.table scanid sd text topn variable write.csv Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "abline", "legend", "lines", "plot", "points", "text") importFrom("stats", "approxfun", "as.dist", "dist", "dnorm", "median", "na.omit", "sd") importFrom("utils", "fix", "head", "read.csv", "read.table", "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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed spectral_matching 65.800 0.740 68.295 frag4feature-purityA-method 42.028 0.452 43.174 dimsPredictPurity-purityD-method 28.968 0.944 29.947 purityX 11.388 0.224 11.693 assessPuritySingle 9.280 0.028 9.374 purityA 8.588 0.020 8.615 subtract-purityD-method 6.340 0.880 7.232 groupPeaks-purityD-method 6.032 0.916 6.960 groupPeaksEx 4.104 0.980 5.097 * 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 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/msPurity.Rcheck/00check.log’ for details.
msPurity.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL msPurity ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘msPurity’ ... ** 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 * DONE (msPurity)
msPurity.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 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(msPurity) Loading required package: Rcpp > Sys.setenv("R_TESTS" = "") > test_check("msPurity") [1] "########################################################" [1] "## Checking LCMS based class and functions ##" [1] "########################################################" [1] 6 [1] "########################################################" [1] "## Checking file list function ##" [1] "########################################################" [1] "=== check for using csv ===" [1] "=== check for using mzML ===" [1] "########################################################" [1] "## Check average spectra (function only) ##" [1] "########################################################" [1] "=== check single core ===" [1] "=== check simple clustering ===" [1] "=== check using MsFileReader output (median SNR thres) ===" snmeth: median[1] "=== check using MsFileReader output (precalc SNR thres) ===" snmeth: precalc[1] "########################################################" [1] "## Check mz subtraction (function only) ##" [1] "########################################################" [1] "########################################################" [1] "## Check predict purity (function only) ##" [1] "########################################################" [1] "=== Check predicted purity for mzML files ===" [1] "########################################################" [1] "## Check groupPeaks (function only) ##" [1] "########################################################" [1] "=== check single core ===" [1] "########################################################" [1] "## Check mzML Workflow ##" [1] "########################################################" [1] "averaging spectra" [1] "filtering spectra" [1] "subtracting" [1] "purity prediction" [1] "########################################################" [1] "## Checking LCMS based class and functions ##" [1] "########################################################" [1] 4 [1] "########################################################" [1] "## Checking pcalc functions ##" [1] "########################################################" [1] "########################################################" [1] "## Spectral matching functions ##" [1] "########################################################" ══ testthat results ═══════════════════════════════════════════════════════════ OK: 86 SKIPPED: 0 FAILED: 0 Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 195.072 4.448 200.151
msPurity.Rcheck/msPurity-Ex.timings
name | user | system | elapsed | |
Getfiles | 0.008 | 0.000 | 0.019 | |
assessPuritySingle | 9.280 | 0.028 | 9.374 | |
averageSpectra-purityD-method | 2.768 | 0.864 | 3.699 | |
averageSpectraSingle | 1.176 | 0.496 | 1.678 | |
dimsPredictPurity-purityD-method | 28.968 | 0.944 | 29.947 | |
dimsPredictPuritySingle | 0.052 | 0.000 | 0.050 | |
filterp-purityD-method | 2.680 | 0.912 | 3.601 | |
frag4feature-purityA-method | 42.028 | 0.452 | 43.174 | |
getP-purityD-method | 0.004 | 0.000 | 0.002 | |
get_additional_mzml_meta | 0.024 | 0.000 | 0.023 | |
groupPeaks-purityD-method | 6.032 | 0.916 | 6.960 | |
groupPeaksEx | 4.104 | 0.980 | 5.097 | |
initialize-purityD-method | 0.000 | 0.000 | 0.003 | |
iwNormGauss | 0.000 | 0.000 | 0.002 | |
iwNormQE.5 | 0.004 | 0.000 | 0.001 | |
iwNormRcosine | 0.000 | 0.000 | 0.001 | |
pcalc | 0.000 | 0.000 | 0.004 | |
purityA | 8.588 | 0.020 | 8.615 | |
purityD-class | 0.000 | 0.000 | 0.003 | |
purityX | 11.388 | 0.224 | 11.693 | |
spectral_matching | 65.800 | 0.740 | 68.295 | |
subtract-purityD-method | 6.340 | 0.880 | 7.232 | |
subtractMZ | 0.000 | 0.000 | 0.001 | |