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This page was generated on 2021-09-17 15:05:46 -0400 (Fri, 17 Sep 2021).

CHECK results for msPurity on nebbiolo1

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 1206/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msPurity 1.18.0  (landing page)
Thomas N. Lawson
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/msPurity
git_branch: RELEASE_3_13
git_last_commit: d9cf561
git_last_commit_date: 2021-05-19 12:20:39 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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    OK    ERROR    OK  

Summary

Package: msPurity
Version: 1.18.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings msPurity_1.18.0.tar.gz
StartedAt: 2021-09-16 10:42:51 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 10:48:55 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 364.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: msPurity.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings msPurity_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/msPurity.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .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  8.3Mb
  sub-directories of 1Mb or more:
    extdata   7.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
 NOTE
Authors@R field gives persons with no role:
  Mark ths Viant
  Warwick ths Dunn
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
Namespaces in Imports field not imported from:
  ‘dbplyr’ ‘jsonlite’ ‘uuid’
  All declared Imports should be used.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘stats::mean’
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addGenericMS1LookupResults: no visible global function definition for
  ‘count.fields’
addMetFragResults: no visible global function definition for
  ‘count.fields’
addSiriusResults: no visible global function definition for
  ‘count.fields’
assessPuritySingle: no visible binding for global variable ‘parallel’
combineAnnotations: no visible binding for global variable
  ‘compoundDbname’
dimsPredictPuritySingleMz: no visible binding for global variable
  ‘mtchi’
dimsPredictPuritySingleMz: no visible binding for global variable
  ‘alli’
dimsPredictPuritySingleMz: no visible binding for global variable
  ‘mtch’
filterPrecursors: no visible binding for global variable
  ‘l_speakmetaFiltered’
filterSMeta: no visible binding for global variable ‘accession’
filterSMeta: no visible binding for global variable ‘inPurity’
filterSMeta: no visible global function definition for ‘lower’
filterSMeta: no visible binding for global variable ‘polarity’
filterSMeta: no visible binding for global variable ‘instrument_type’
filterSMeta: no visible binding for global variable ‘instrument’
filterSMeta: no visible binding for global variable ‘name.y’
filterSMeta: no visible binding for global variable ‘retention_time’
filterSMeta: no visible binding for global variable ‘grpid’
filterSMeta: no visible binding for global variable ‘pid’
filterSMeta: no visible binding for global variable ‘spectrum_type’
getScanPeaksSqlite: no visible binding for global variable ‘pid’
getScanPeaksSqlite: no visible binding for global variable
  ‘library_spectra_meta_id’
getScanPeaksSqlite: no visible binding for global variable ‘pass_flag’
getScanPeaksSqlite: no visible binding for global variable ‘type’
getScanPeaksSqlite: no visible binding for global variable
  ‘spectraType’
getScanPeaksSqlite: no visible binding for global variable ‘ra’
getSmeta: no visible binding for global variable ‘pid’
get_topn: no visible binding for global variable ‘topn’
getxcmsSetObject: no visible global function definition for
  ‘sampclass<-’
matchi: no visible global function definition for ‘match_factor’
plotPurity: no visible binding for global variable ‘idx’
plotPurity: no visible binding for global variable ‘purity’
plotPurity: no visible binding for global variable ‘variable’
purityA: no visible binding for global variable ‘i’
queryVlibrary: no visible binding for global variable ‘precursor_mz’
queryVlibrary: no visible binding for global variable ‘retention_time’
queryVlibrarySingle: no visible binding for global variable ‘pid’
queryVlibrarySingle: no visible binding for global variable
  ‘library_spectra_meta_id’
averageSpectra,purityD: no visible binding for global variable ‘i’
subtract,purityD: no visible binding for global variable ‘i’
Undefined global functions or variables:
  accession alli compoundDbname count.fields grpid i idx inPurity
  instrument instrument_type l_speakmetaFiltered
  library_spectra_meta_id lower match_factor mtch mtchi name.y parallel
  pass_flag pid polarity precursor_mz purity ra retention_time
  sampclass<- spectraType spectrum_type topn type variable
Consider adding
  importFrom("utils", "count.fields")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
frag4feature-purityA-method      31.878  1.940  30.656
dimsPredictPurity-purityD-method 26.895  1.260  28.156
flag_remove                      19.716  4.121  11.692
purityX                          10.616  2.418   8.507
combineAnnotations                8.597  0.096   8.699
createDatabase                    8.125  0.416   8.550
assessPuritySingle                7.346  0.044   7.387
spectralMatching                  4.845  2.402   7.491
purityA                           6.660  0.107   6.764
groupPeaks-purityD-method         5.357  1.188   6.546
groupPeaksEx                      3.946  1.624   5.574
subtract-purityD-method           3.858  1.156   5.016
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/msPurity.Rcheck/00check.log’
for details.



Installation output

msPurity.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL msPurity
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘msPurity’ ...
** using staged installation
It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (msPurity)

Tests output

msPurity.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-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                              ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking filterFragSpectra                         ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageIntraFragSpectra                   ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageInterFragSpectra                   ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageAllFragSpectra                   ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageIntraFragSpectra (with filter)     ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageInterFragSpectra (with filter)     ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageAllFragSpectra  (with filter)    ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking createMSP functions                       ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## checking flag and remove (lc-ms)                   ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking database (old schema)                     ##"
[1] "########################################################"
[1] "\n"
[1] "#######################################################"
[1] "## Checking database (new schema)                    ##"
[1] "#######################################################"
[1] "\n"
[1] "########################################################"
[1] "## Testing spectral matching (spectralMatching)  qvl  ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Testing spectral matching (spectralMatching)  lvl  ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Testing spectral matching (spectralMatching)   qvq ##"
[1] "########################################################"
[1] "\n"
[1] "#################################################################"
[1] "## Testing spectral matching (spectralMatching)   q(scan) v q ##"
[1] "#################################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking combine annotations based functions       ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking purityX (grouped)                         ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking purityX (single file)                     ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking file list function                        ##"
[1] "########################################################"
[1] "=== check for using csv ==="
[1] "=== check for using mzML ==="
[1] "########################################################"
[1] "## Check average spectra (function only)              ##"
[1] "########################################################"
[1] "=== check single core ==="
[1] "=== check simple clustering ==="
[1] "=== check using MsFileReader output (median SNR thres) ==="
snmeth: median[1] "=== check using MsFileReader output (precalc SNR thres) ==="
snmeth: precalc[1] "########################################################"
[1] "## Check mz subtraction (function only)               ##"
[1] "########################################################"
[1] "########################################################"
[1] "## Check predict purity (function only)               ##"
[1] "########################################################"
[1] "=== Check predicted purity for mzML files ==="
[1] "########################################################"
[1] "## Check groupPeaks (function only)               ##"
[1] "########################################################"
[1] "=== check single core ==="
[1] "########################################################"
[1] "## Check mzML Workflow                                ##"
[1] "########################################################"
[1] "averaging spectra"
[1] "filtering spectra"
[1] "subtracting"
[1] "purity prediction"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 184 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
157.261  18.031 159.561 

Example timings

msPurity.Rcheck/msPurity-Ex.timings

nameusersystemelapsed
Getfiles0.0050.0000.005
assessPuritySingle7.3460.0447.387
averageAllFragSpectra-purityA-method0.5770.0080.588
averageInterFragSpectra-purityA-method1.0880.0001.090
averageIntraFragSpectra-purityA-method1.9030.0041.909
averageSpectra-purityD-method2.5491.0563.606
averageSpectraSingle1.1020.6041.706
combineAnnotations8.5970.0968.699
createDatabase8.1250.4168.550
createMSP-purityA-method0.3600.0640.425
create_database1.0650.0761.141
dimsPredictPurity-purityD-method26.895 1.26028.156
dimsPredictPuritySingle0.0330.0000.033
filterFragSpectra-purityA-method0.1090.0000.109
filterp-purityD-method3.4771.0964.573
flag_remove19.716 4.12111.692
frag4feature-purityA-method31.878 1.94030.656
getP-purityD-method0.0020.0000.002
get_additional_mzml_meta0.0180.0040.022
groupPeaks-purityD-method5.3571.1886.546
groupPeaksEx3.9461.6245.574
initialize-purityD-method0.0020.0000.002
iwNormGauss0.0010.0000.002
iwNormQE.50.0010.0000.001
iwNormRcosine0.0010.0000.001
pcalc0.0030.0000.003
purityA6.6600.1076.764
purityD-class0.0010.0000.002
purityX10.616 2.418 8.507
spectralMatching4.8452.4027.491
spectral_matching0.0000.0000.001
subtract-purityD-method3.8581.1565.016
subtractMZ0.0010.0000.001