Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1347/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
msPurity 1.32.0 (landing page) Thomas N. Lawson
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the msPurity package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: msPurity |
Version: 1.32.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:msPurity.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings msPurity_1.32.0.tar.gz |
StartedAt: 2024-12-20 06:34:16 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 07:05:58 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1902.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: msPurity.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:msPurity.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings msPurity_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/msPurity.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘msPurity/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘msPurity’ version ‘1.32.0’ * package encoding: UTF-8 * checking package namespace information ... NOTE Found export directive that requires package ‘methods’: ‘exportMethods’ Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains ‘methods’. * 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 code 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 ... NOTE checkRd: (-1) createMSP-purityA-method.Rd:25: Lost braces; missing escapes or markup? 25 | \item{msp_file_pth}{character; Name of the output msp file, if NULL the file "frag_spectra_{time stamp}.msp" will be created in the current directory} | ^ * 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 502.914 12.634 441.533 frag4feature-purityA-method 455.724 12.140 385.630 flag_remove 83.428 15.035 53.508 purityX 83.957 3.810 89.465 dimsPredictPurity-purityD-method 83.413 1.821 90.395 assessPuritySingle 22.634 0.216 25.212 combineAnnotations 22.164 0.592 24.959 purityA 22.576 0.146 23.255 spectralMatching 12.777 2.786 16.435 groupPeaks-purityD-method 10.171 1.220 11.477 subtract-purityD-method 8.700 0.518 9.275 groupPeaksEx 6.634 0.443 7.160 averageSpectra-purityD-method 5.625 1.268 7.756 filterp-purityD-method 5.557 0.660 8.130 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/msPurity.Rcheck/00check.log’ for details.
msPurity.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL msPurity ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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] "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/msPurity/extdata/tests/xcms/msms_only_xcmsnexp.rds" [1] "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 484.853 36.132 524.890
msPurity.Rcheck/msPurity-Ex.timings
name | user | system | elapsed | |
Getfiles | 0.006 | 0.002 | 0.007 | |
assessPuritySingle | 22.634 | 0.216 | 25.212 | |
averageAllFragSpectra-purityA-method | 0.457 | 0.005 | 0.501 | |
averageInterFragSpectra-purityA-method | 1.006 | 0.007 | 1.112 | |
averageIntraFragSpectra-purityA-method | 1.223 | 0.014 | 1.389 | |
averageSpectra-purityD-method | 5.625 | 1.268 | 7.756 | |
averageSpectraSingle | 2.321 | 0.167 | 2.770 | |
combineAnnotations | 22.164 | 0.592 | 24.959 | |
createDatabase | 502.914 | 12.634 | 441.533 | |
createMSP-purityA-method | 0.240 | 0.031 | 0.287 | |
create_database | 2.741 | 0.072 | 2.934 | |
dimsPredictPurity-purityD-method | 83.413 | 1.821 | 90.395 | |
dimsPredictPuritySingle | 0.083 | 0.002 | 0.106 | |
filterFragSpectra-purityA-method | 0.167 | 0.003 | 0.204 | |
filterp-purityD-method | 5.557 | 0.660 | 8.130 | |
flag_remove | 83.428 | 15.035 | 53.508 | |
frag4feature-purityA-method | 455.724 | 12.140 | 385.630 | |
getP-purityD-method | 0.005 | 0.002 | 0.006 | |
get_additional_mzml_meta | 0.036 | 0.002 | 0.039 | |
groupPeaks-purityD-method | 10.171 | 1.220 | 11.477 | |
groupPeaksEx | 6.634 | 0.443 | 7.160 | |
initialize-purityD-method | 0.005 | 0.002 | 0.006 | |
iwNormGauss | 0.002 | 0.001 | 0.003 | |
iwNormQE.5 | 0.002 | 0.001 | 0.003 | |
iwNormRcosine | 0.001 | 0.000 | 0.002 | |
pcalc | 0.009 | 0.001 | 0.010 | |
purityA | 22.576 | 0.146 | 23.255 | |
purityD-class | 0.004 | 0.001 | 0.005 | |
purityX | 83.957 | 3.810 | 89.465 | |
spectralMatching | 12.777 | 2.786 | 16.435 | |
spectral_matching | 0.000 | 0.000 | 0.001 | |
subtract-purityD-method | 8.700 | 0.518 | 9.275 | |
subtractMZ | 0.000 | 0.000 | 0.001 | |