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This page was generated on 2021-10-15 15:06:43 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the msPurity package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/msPurity.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 1206/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
msPurity 1.18.0 (landing page) Thomas N. Lawson
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: msPurity |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msPurity.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msPurity_1.18.0.tar.gz |
StartedAt: 2021-10-14 21:28:14 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:38:40 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 626.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: msPurity.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msPurity.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msPurity_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/msPurity.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (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 ‘1.18.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 ... NOTE installed size is 12.5Mb sub-directories of 1Mb or more: extdata 11.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’. It is recommended to use ‘given’ instead of ‘middle’. NOTE Authors@R field gives persons with no role: Mark ths Viant Warwick ths Dunn * 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 ... WARNING Namespaces in Imports field not imported from: ‘dbplyr’ ‘jsonlite’ ‘uuid’ All declared Imports should be used. 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. Missing or unexported object: ‘stats::mean’ 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 addGenericMS1LookupResults: no visible global function definition for ‘count.fields’ addMetFragResults: no visible global function definition for ‘count.fields’ addSiriusResults: no visible global function definition for ‘count.fields’ assessPuritySingle: no visible binding for global variable ‘parallel’ combineAnnotations: no visible binding for global variable ‘compoundDbname’ dimsPredictPuritySingleMz: no visible binding for global variable ‘mtchi’ dimsPredictPuritySingleMz: no visible binding for global variable ‘alli’ dimsPredictPuritySingleMz: no visible binding for global variable ‘mtch’ filterPrecursors: no visible binding for global variable ‘l_speakmetaFiltered’ filterSMeta: no visible binding for global variable ‘accession’ filterSMeta: no visible binding for global variable ‘inPurity’ filterSMeta: no visible global function definition for ‘lower’ filterSMeta: no visible binding for global variable ‘polarity’ filterSMeta: no visible binding for global variable ‘instrument_type’ filterSMeta: no visible binding for global variable ‘instrument’ filterSMeta: no visible binding for global variable ‘name.y’ filterSMeta: no visible binding for global variable ‘retention_time’ filterSMeta: no visible binding for global variable ‘grpid’ filterSMeta: no visible binding for global variable ‘pid’ filterSMeta: no visible binding for global variable ‘spectrum_type’ getScanPeaksSqlite: no visible binding for global variable ‘pid’ getScanPeaksSqlite: no visible binding for global variable ‘library_spectra_meta_id’ getScanPeaksSqlite: no visible binding for global variable ‘pass_flag’ getScanPeaksSqlite: no visible binding for global variable ‘type’ getScanPeaksSqlite: no visible binding for global variable ‘spectraType’ getScanPeaksSqlite: no visible binding for global variable ‘ra’ getSmeta: no visible binding for global variable ‘pid’ get_topn: no visible binding for global variable ‘topn’ getxcmsSetObject: no visible global function definition for ‘sampclass<-’ matchi: no visible global function definition for ‘match_factor’ plotPurity: no visible binding for global variable ‘idx’ plotPurity: no visible binding for global variable ‘purity’ plotPurity: no visible binding for global variable ‘variable’ purityA: no visible binding for global variable ‘i’ queryVlibrary: no visible binding for global variable ‘precursor_mz’ queryVlibrary: no visible binding for global variable ‘retention_time’ queryVlibrarySingle: no visible binding for global variable ‘pid’ queryVlibrarySingle: no visible binding for global variable ‘library_spectra_meta_id’ averageSpectra,purityD: no visible binding for global variable ‘i’ subtract,purityD: no visible binding for global variable ‘i’ Undefined global functions or variables: accession alli compoundDbname count.fields grpid i idx inPurity instrument instrument_type l_speakmetaFiltered library_spectra_meta_id lower match_factor mtch mtchi name.y parallel pass_flag pid polarity precursor_mz purity ra retention_time sampclass<- spectraType spectrum_type topn type variable Consider adding importFrom("utils", "count.fields") 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 (user + system) or elapsed time > 5s user system elapsed frag4feature-purityA-method 62.087 3.478 60.971 dimsPredictPurity-purityD-method 51.056 0.441 51.543 flag_remove 26.904 7.047 18.000 purityX 17.667 4.739 14.983 combineAnnotations 16.189 0.298 16.499 purityA 14.499 0.065 14.576 assessPuritySingle 13.781 0.093 13.889 createDatabase 12.750 0.529 13.295 spectralMatching 7.859 1.881 10.446 groupPeaks-purityD-method 7.807 0.866 8.683 subtract-purityD-method 5.974 0.640 6.625 groupPeaksEx 5.519 0.306 5.831 * 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 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/msPurity.Rcheck/00check.log’ for details.
msPurity.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL msPurity ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘msPurity’ ... ** using staged installation It is recommended to use ‘given’ instead of ‘middle’. It is recommended to use ‘given’ instead of ‘middle’. It is recommended to use ‘given’ instead of ‘middle’. It is recommended to use ‘given’ instead of ‘middle’. ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (msPurity)
msPurity.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-apple-darwin17.0 (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. > library(testthat) > library(msPurity) Loading required package: Rcpp > Sys.setenv("R_TESTS" = "") > test_check("msPurity") [1] "\n" [1] "########################################################" [1] "## Checking pcalc functions ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking purityA ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking frag4feature ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking frag4feature ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking filterFragSpectra ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking averageIntraFragSpectra ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking averageInterFragSpectra ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking averageAllFragSpectra ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking averageIntraFragSpectra (with filter) ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking averageInterFragSpectra (with filter) ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking averageAllFragSpectra (with filter) ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking createMSP functions ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## checking flag and remove (lc-ms) ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking database (old schema) ##" [1] "########################################################" [1] "\n" [1] "#######################################################" [1] "## Checking database (new schema) ##" [1] "#######################################################" [1] "\n" [1] "########################################################" [1] "## Testing spectral matching (spectralMatching) qvl ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Testing spectral matching (spectralMatching) lvl ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Testing spectral matching (spectralMatching) qvq ##" [1] "########################################################" [1] "\n" [1] "#################################################################" [1] "## Testing spectral matching (spectralMatching) q(scan) v q ##" [1] "#################################################################" [1] "\n" [1] "########################################################" [1] "## Checking combine annotations based functions ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking purityX (grouped) ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## Checking purityX (single file) ##" [1] "########################################################" [1] "\n" [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" [ FAIL 0 | WARN 0 | SKIP 0 | PASS 184 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 265.368 23.026 268.825
msPurity.Rcheck/msPurity-Ex.timings
name | user | system | elapsed | |
Getfiles | 0.006 | 0.001 | 0.007 | |
assessPuritySingle | 13.781 | 0.093 | 13.889 | |
averageAllFragSpectra-purityA-method | 1.062 | 0.022 | 1.085 | |
averageInterFragSpectra-purityA-method | 2.109 | 0.021 | 2.136 | |
averageIntraFragSpectra-purityA-method | 3.417 | 0.012 | 3.431 | |
averageSpectra-purityD-method | 4.107 | 0.807 | 4.918 | |
averageSpectraSingle | 1.915 | 0.168 | 2.084 | |
combineAnnotations | 16.189 | 0.298 | 16.499 | |
createDatabase | 12.750 | 0.529 | 13.295 | |
createMSP-purityA-method | 0.591 | 0.069 | 0.659 | |
create_database | 1.868 | 0.055 | 2.018 | |
dimsPredictPurity-purityD-method | 51.056 | 0.441 | 51.543 | |
dimsPredictPuritySingle | 0.061 | 0.000 | 0.062 | |
filterFragSpectra-purityA-method | 0.224 | 0.003 | 0.227 | |
filterp-purityD-method | 4.413 | 0.217 | 4.637 | |
flag_remove | 26.904 | 7.047 | 18.000 | |
frag4feature-purityA-method | 62.087 | 3.478 | 60.971 | |
getP-purityD-method | 0.004 | 0.000 | 0.005 | |
get_additional_mzml_meta | 0.038 | 0.002 | 0.039 | |
groupPeaks-purityD-method | 7.807 | 0.866 | 8.683 | |
groupPeaksEx | 5.519 | 0.306 | 5.831 | |
initialize-purityD-method | 0.003 | 0.001 | 0.003 | |
iwNormGauss | 0.002 | 0.001 | 0.002 | |
iwNormQE.5 | 0.001 | 0.000 | 0.002 | |
iwNormRcosine | 0.001 | 0.001 | 0.001 | |
pcalc | 0.006 | 0.000 | 0.007 | |
purityA | 14.499 | 0.065 | 14.576 | |
purityD-class | 0.002 | 0.000 | 0.003 | |
purityX | 17.667 | 4.739 | 14.983 | |
spectralMatching | 7.859 | 1.881 | 10.446 | |
spectral_matching | 0.000 | 0.000 | 0.001 | |
subtract-purityD-method | 5.974 | 0.640 | 6.625 | |
subtractMZ | 0.001 | 0.000 | 0.000 | |