Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:45 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1271/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
msPurity 1.25.0 (landing page) Thomas N. Lawson
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: msPurity |
Version: 1.25.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings msPurity_1.25.0.tar.gz |
StartedAt: 2023-02-28 09:10:40 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 09:38:45 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1685.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: msPurity.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings msPurity_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/msPurity.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘msPurity/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘msPurity’ version ‘1.25.0’ * 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: .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 19.6Mb sub-directories of 1Mb or more: extdata 18.8Mb * 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 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’ createDatabase: no visible global function definition for ‘featureValues’ create_database : getxcmsSetObject: no visible global function definition for ‘sampclass<-’ 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’ flag_remove: no visible global function definition for ‘PeakDensityParam’ flag_remove: no visible global function definition for ‘chromPeaks<-’ flag_remove: no visible global function definition for ‘chromPeaks’ 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’ 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’ sum_calc_peaklist: no visible global function definition for ‘phenoData’ averageSpectra,purityD: no visible binding for global variable ‘i’ subtract,purityD: no visible binding for global variable ‘i’ Undefined global functions or variables: PeakDensityParam accession alli chromPeaks chromPeaks<- compoundDbname count.fields featureValues grpid i idx inPurity instrument instrument_type l_speakmetaFiltered library_spectra_meta_id lower match_factor mtch mtchi name.y parallel pass_flag phenoData 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 createDatabase 254.204 6.478 217.159 frag4feature-purityA-method 236.224 6.627 197.420 flag_remove 43.047 7.735 25.872 dimsPredictPurity-purityD-method 47.907 1.124 49.032 purityX 16.750 3.955 13.828 combineAnnotations 12.926 0.184 13.125 purityA 12.457 0.136 12.593 assessPuritySingle 11.596 0.175 11.776 groupPeaks-purityD-method 10.326 1.255 11.583 subtract-purityD-method 8.980 1.392 10.373 spectralMatching 7.195 1.880 10.352 groupPeaksEx 7.857 0.932 8.790 filterp-purityD-method 6.769 1.095 7.864 averageSpectra-purityD-method 6.192 1.179 7.380 * 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 ... ‘msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd’ using ‘UTF-8’... OK ‘msPurity-spectral-database-vignette.Rmd’ using ‘UTF-8’... OK ‘msPurity-vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/msPurity.Rcheck/00check.log’ for details.
msPurity.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL msPurity ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘msPurity’ ... ** using staged installation ** 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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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] "\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 (fillpeaks) ##" [1] "########################################################" [1] "/home/biocbuild/bbs-3.17-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xcmsnexp.rds" [1] "/home/biocbuild/bbs-3.17-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xset.rds" [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 frag4feature (xcms v2 functions) ##" [1] "########################################################" [1] "\n" [1] "####################################################################" [1] "## Checking frag4feature (fillpeaks) (xcms v2 functions) ##" [1] "####################################################################" [1] "\n" [1] "########################################################" [1] "## Checking filterFragSpectra (xcms v2 functions) ##" [1] "########################################################" [1] "\n" [1] "##############################################################" [1] "## Checking averageIntraFragSpectra (xcms v2 functions) ##" [1] "##############################################################" [1] "\n" [1] "#############################################################" [1] "## Checking averageInterFragSpectra (xcms v2 functions) #" [1] "#############################################################" [1] "\n" [1] "########################################################" [1] "## Checking averageAllFragSpectra (xcms v2 functions) #" [1] "########################################################" [1] "\n" [1] "###########################################################################" [1] "## Checking averageIntraFragSpectra (with filter) (xcms v2 functions) ##" [1] "###########################################################################" [1] "\n" [1] "############################################################################" [1] "## Checking averageInterFragSpectra (with filter) (xcms v2 functions) ##" [1] "############################################################################" [1] "\n" [1] "#########################################################################" [1] "## Checking averageAllFragSpectra (with filter) (xcms v2 functions) ##" [1] "#########################################################################" [1] "\n" [1] "########################################################" [1] "## Checking createMSP functions (xcms v2 functions) ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## checking flag and remove (lc-ms) ##" [1] "########################################################" [1] "\n" [1] "#######################################################" [1] "## Checking database (new schema) ##" [1] "#######################################################" [1] "\n" [1] "###############################################################" [1] "## Checking database (new schema) (xcms v2 functions) ##" [1] "###############################################################" [1] "\n" [1] "########################################################" [1] "## Checking database (old 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] "## Testing spectral matching (spectralMatching) qvl (xcms v2 functions) ##" [1] "############################################################################" [1] "\n" [1] "############################################################################" [1] "## Testing spectral matching (spectralMatching) qvq (xcms v2 functions) ##" [1] "############################################################################" [1] "\n" [1] "######################################################################################" [1] "## Testing spectral matching (spectralMatching) q(scan) v q (xcms v2 functions) ##" [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 306 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 283.017 22.117 299.281
msPurity.Rcheck/msPurity-Ex.timings
name | user | system | elapsed | |
Getfiles | 0.004 | 0.000 | 0.006 | |
assessPuritySingle | 11.596 | 0.175 | 11.776 | |
averageAllFragSpectra-purityA-method | 0.221 | 0.000 | 0.223 | |
averageInterFragSpectra-purityA-method | 0.455 | 0.004 | 0.460 | |
averageIntraFragSpectra-purityA-method | 0.659 | 0.004 | 0.665 | |
averageSpectra-purityD-method | 6.192 | 1.179 | 7.380 | |
averageSpectraSingle | 2.839 | 0.584 | 3.423 | |
combineAnnotations | 12.926 | 0.184 | 13.125 | |
createDatabase | 254.204 | 6.478 | 217.159 | |
createMSP-purityA-method | 0.124 | 0.004 | 0.130 | |
create_database | 1.633 | 0.032 | 1.668 | |
dimsPredictPurity-purityD-method | 47.907 | 1.124 | 49.032 | |
dimsPredictPuritySingle | 0.053 | 0.000 | 0.053 | |
filterFragSpectra-purityA-method | 0.089 | 0.004 | 0.093 | |
filterp-purityD-method | 6.769 | 1.095 | 7.864 | |
flag_remove | 43.047 | 7.735 | 25.872 | |
frag4feature-purityA-method | 236.224 | 6.627 | 197.420 | |
getP-purityD-method | 0.003 | 0.000 | 0.003 | |
get_additional_mzml_meta | 0.021 | 0.004 | 0.025 | |
groupPeaks-purityD-method | 10.326 | 1.255 | 11.583 | |
groupPeaksEx | 7.857 | 0.932 | 8.790 | |
initialize-purityD-method | 0.003 | 0.000 | 0.003 | |
iwNormGauss | 0.001 | 0.000 | 0.002 | |
iwNormQE.5 | 0.001 | 0.000 | 0.001 | |
iwNormRcosine | 0.000 | 0.000 | 0.001 | |
pcalc | 0.005 | 0.000 | 0.005 | |
purityA | 12.457 | 0.136 | 12.593 | |
purityD-class | 0.002 | 0.000 | 0.002 | |
purityX | 16.750 | 3.955 | 13.828 | |
spectralMatching | 7.195 | 1.880 | 10.352 | |
spectral_matching | 0 | 0 | 0 | |
subtract-purityD-method | 8.980 | 1.392 | 10.373 | |
subtractMZ | 0 | 0 | 0 | |