Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-29 12:05 -0400 (Mon, 29 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4833 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4621 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4566 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
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 1379/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
msPurity 1.35.0 (landing page) Thomas N. Lawson
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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: 1.35.0 |
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_1.35.0.tar.gz |
StartedAt: 2025-09-28 22:46:21 -0400 (Sun, 28 Sep 2025) |
EndedAt: 2025-09-28 22:59:05 -0400 (Sun, 28 Sep 2025) |
EllapsedTime: 764.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: msPurity.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/msPurity.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * 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 ‘1.35.0’ * 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 ... INFO 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 ... ERROR Running examples in ‘msPurity-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: purityX > ### Title: Assessing anticipated purity of XCMS features from an LC-MS run > ### Aliases: purityX > > ### ** Examples > > > msPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "LCMS_") > xset <- readRDS(system.file("extdata", "tests", "xcms", "ms_only_xset_OLD.rds", package="msPurity")) > xset@filepaths[1] <- msPths[basename(msPths)=="LCMS_1.mzML"] > xset@filepaths[2] <- msPths[basename(msPths)=="LCMS_2.mzML"] > px <- purityX(xset, singleFile = 1) Sizes of mz and intensity arrays don't match. Error in object@backend$getPeakList(scans) : dims [product 4516] do not match the length of object [2258] Calls: purityX ... <Anonymous> -> .local -> .peaks -> <Anonymous> -> .External Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed createDatabase 214.470 8.401 180.189 frag4feature-purityA-method 186.441 7.886 153.268 flag_remove 43.295 9.475 25.768 dimsPredictPurity-purityD-method 35.870 1.350 37.512 combineAnnotations 11.287 0.404 11.771 assessPuritySingle 9.318 0.120 9.493 purityA 8.562 0.103 8.701 groupPeaks-purityD-method 6.922 0.887 7.866 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ▆ 1. └─msPurity::purityX(xset, singleFile = 1) at test.7_purityX.R:54:3 2. └─msPurity:::xcmsSinglePurity(...) 3. └─msPurity:::getscans(filepth, mzRback) 4. ├─mzR::peaks(mr) 5. └─mzR::peaks(mr) 6. └─mzR (local) .local(object, ...) 7. └─mzR:::.peaks(object, scans) 8. └─object@backend$getPeakList(scans) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 301 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection Execution halted * 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: 2 ERRORs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/library’ * installing *source* package ‘msPurity’ ... ** this is package ‘msPurity’ version ‘1.35.0’ ** 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.fail
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 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/4.5-x86_64/Resources/library/msPurity/extdata/tests/xcms/msms_only_xcmsnexp.rds" [1] "/Library/Frameworks/R.framework/Versions/4.5-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] "########################################################" 2025-09-28 22:57:29.240 R[69522:404167540] XType: com.apple.fonts is not accessible. 2025-09-28 22:57:29.240 R[69522:404167540] XType: XTFontStaticRegistry is enabled. [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] "########################################################" Sizes of mz and intensity arrays don't match. [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 1 | WARN 0 | SKIP 0 | PASS 301 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test.7_purityX.R:54:3'): checking purityX (single file) ───────────── Error in `object@backend$getPeakList(scans)`: dims [product 4516] do not match the length of object [2258] Backtrace: ▆ 1. └─msPurity::purityX(xset, singleFile = 1) at test.7_purityX.R:54:3 2. └─msPurity:::xcmsSinglePurity(...) 3. └─msPurity:::getscans(filepth, mzRback) 4. ├─mzR::peaks(mr) 5. └─mzR::peaks(mr) 6. └─mzR (local) .local(object, ...) 7. └─mzR:::.peaks(object, scans) 8. └─object@backend$getPeakList(scans) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 301 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection Execution halted
msPurity.Rcheck/msPurity-Ex.timings
name | user | system | elapsed | |
Getfiles | 0.004 | 0.001 | 0.005 | |
assessPuritySingle | 9.318 | 0.120 | 9.493 | |
averageAllFragSpectra-purityA-method | 0.202 | 0.003 | 0.207 | |
averageInterFragSpectra-purityA-method | 0.557 | 0.014 | 0.577 | |
averageIntraFragSpectra-purityA-method | 0.544 | 0.009 | 0.556 | |
averageSpectra-purityD-method | 3.351 | 0.878 | 4.265 | |
averageSpectraSingle | 1.222 | 0.221 | 1.460 | |
combineAnnotations | 11.287 | 0.404 | 11.771 | |
createDatabase | 214.470 | 8.401 | 180.189 | |
createMSP-purityA-method | 0.103 | 0.019 | 0.124 | |
create_database | 1.204 | 0.062 | 1.280 | |
dimsPredictPurity-purityD-method | 35.870 | 1.350 | 37.512 | |
dimsPredictPuritySingle | 0.039 | 0.001 | 0.041 | |
filterFragSpectra-purityA-method | 0.068 | 0.002 | 0.072 | |
filterp-purityD-method | 3.199 | 0.572 | 3.823 | |
flag_remove | 43.295 | 9.475 | 25.768 | |
frag4feature-purityA-method | 186.441 | 7.886 | 153.268 | |
getP-purityD-method | 0.002 | 0.000 | 0.004 | |
get_additional_mzml_meta | 0.024 | 0.001 | 0.025 | |
groupPeaks-purityD-method | 6.922 | 0.887 | 7.866 | |
groupPeaksEx | 3.461 | 0.473 | 3.994 | |
initialize-purityD-method | 0.002 | 0.001 | 0.003 | |
iwNormGauss | 0.001 | 0.001 | 0.001 | |
iwNormQE.5 | 0.001 | 0.001 | 0.002 | |
iwNormRcosine | 0.000 | 0.000 | 0.001 | |
pcalc | 0.003 | 0.000 | 0.003 | |
purityA | 8.562 | 0.103 | 8.701 | |
purityD-class | 0.003 | 0.001 | 0.004 | |