Package: msPurity

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msPurity.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msPurity_1.13.0.tar.gz

StartedAt: 2020-01-16 06:46:09 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 06:59:50 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 820.6 seconds

RetCode: 0

Status:  OK

CheckDir: msPurity.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msPurity.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msPurity_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/msPurity.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.13.0’
* 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 12.4Mb
  sub-directories of 1Mb or more:
    extdata  11.8Mb
* 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
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
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 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
* 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            84.754  9.611  85.517
dimsPredictPurity-purityD-method       71.310  3.984  75.697
flag_remove                            39.306 17.125  30.359
purityX                                25.730 12.183  24.739
assessPuritySingle                     19.943  0.209  20.145
createDatabase                         17.300  1.611  18.927
purityA                                18.305  0.235  18.541
combineAnnotations                     18.104  0.297  18.418
groupPeaks-purityD-method              13.300  3.500  16.801
spectralMatching                        9.874  5.498  17.121
subtract-purityD-method                11.849  3.272  15.121
groupPeaksEx                           11.656  2.759  14.417
filterp-purityD-method                 11.130  2.698  14.318
averageSpectra-purityD-method           9.081  2.781  11.868
averageSpectraSingle                    4.456  1.235   5.692
averageIntraFragSpectra-purityA-method  5.121  0.019   5.140
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/msPurity.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL msPurity
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 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] "## 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"
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 169 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
290.992  37.006 302.608 

name	user	system	elapsed
Getfiles	0.011	0.001	0.014
assessPuritySingle	19.943	0.209	20.145
averageAllFragSpectra-purityA-method	1.699	0.071	1.771
averageInterFragSpectra-purityA-method	2.865	0.042	2.908
averageIntraFragSpectra-purityA-method	5.121	0.019	5.140
averageSpectra-purityD-method	9.081	2.781	11.868
averageSpectraSingle	4.456	1.235	5.692
combineAnnotations	18.104	0.297	18.418
createDatabase	17.300	1.611	18.927
createMSP-purityA-method	0.980	0.178	1.157
create_database	2.438	0.093	2.581
dimsPredictPurity-purityD-method	71.310	3.984	75.697
dimsPredictPuritySingle	0.078	0.002	0.081
filterFragSpectra-purityA-method	0.290	0.001	0.292
filterp-purityD-method	11.130	2.698	14.318
flag_remove	39.306	17.125	30.359
frag4feature-purityA-method	84.754	9.611	85.517
getP-purityD-method	0.004	0.000	0.005
get_additional_mzml_meta	0.034	0.002	0.036
groupPeaks-purityD-method	13.300	3.500	16.801
groupPeaksEx	11.656	2.759	14.417
initialize-purityD-method	0.006	0.000	0.007
iwNormGauss	0.001	0.000	0.002
iwNormQE.5	0.002	0.000	0.002
iwNormRcosine	0.002	0.000	0.003
pcalc	0.009	0.000	0.010
purityA	18.305	0.235	18.541
purityD-class	0.005	0.001	0.005
purityX	25.730	12.183	24.739
spectralMatching	9.874	5.498	17.121
spectral_matching	0.001	0.000	0.001
subtract-purityD-method	11.849	3.272	15.121
subtractMZ	0.000	0.001	0.001