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This page was generated on 2022-01-26 13:05:40 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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

CHECK results for msPurity on nebbiolo2


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.

raw results

Package 1225/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msPurity 1.20.0  (landing page)
Thomas N. Lawson
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/msPurity
git_branch: RELEASE_3_14
git_last_commit: 82cfdcb
git_last_commit_date: 2021-10-26 12:28:01 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: msPurity
Version: 1.20.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings msPurity_1.20.0.tar.gz
StartedAt: 2022-01-25 08:38:17 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 08:48:41 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 624.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: msPurity.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings msPurity_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/msPurity.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.20.0’
* 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 ... 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’
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                   160.829  6.011 135.658
frag4feature-purityA-method      148.660  4.816 120.897
flag_remove                       35.122  6.052  20.760
dimsPredictPurity-purityD-method  29.502  1.029  30.530
purityX                           11.491  2.632   9.141
combineAnnotations                 8.566  0.075   8.645
groupPeaks-purityD-method          7.129  1.188   8.318
assessPuritySingle                 7.323  0.049   7.365
purityA                            6.849  0.023   6.870
spectralMatching                   5.356  1.053   6.845
subtract-purityD-method            5.116  1.272   6.388
filterp-purityD-method             4.377  1.047   5.425
groupPeaksEx                       4.161  1.140   5.301
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/msPurity.Rcheck/00check.log’
for details.



Installation output

msPurity.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL msPurity
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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)

Tests output

msPurity.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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] "\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-3.14-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xcmsnexp.rds"
[1] "/home/biocbuild/bbs-3.14-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 
177.663  15.380 187.807 

Example timings

msPurity.Rcheck/msPurity-Ex.timings

nameusersystemelapsed
Getfiles0.0050.0000.005
assessPuritySingle7.3230.0497.365
averageAllFragSpectra-purityA-method0.1680.0000.169
averageInterFragSpectra-purityA-method0.2970.0000.298
averageIntraFragSpectra-purityA-method0.4470.0030.452
averageSpectra-purityD-method2.6091.3893.999
averageSpectraSingle1.2660.6721.938
combineAnnotations8.5660.0758.645
createDatabase160.829 6.011135.658
createMSP-purityA-method0.0870.0030.091
create_database1.1300.0481.178
dimsPredictPurity-purityD-method29.502 1.02930.530
dimsPredictPuritySingle0.0310.0000.032
filterFragSpectra-purityA-method0.0580.0000.058
filterp-purityD-method4.3771.0475.425
flag_remove35.122 6.05220.760
frag4feature-purityA-method148.660 4.816120.897
getP-purityD-method0.0030.0000.002
get_additional_mzml_meta0.0190.0040.022
groupPeaks-purityD-method7.1291.1888.318
groupPeaksEx4.1611.1405.301
initialize-purityD-method0.0020.0000.002
iwNormGauss0.0010.0000.001
iwNormQE.50.0010.0000.001
iwNormRcosine0.0010.0000.001
pcalc0.0030.0000.003
purityA6.8490.0236.870
purityD-class0.0020.0000.002
purityX11.491 2.632 9.141
spectralMatching5.3561.0536.845
spectral_matching000
subtract-purityD-method5.1161.2726.388
subtractMZ000