Package: msPurity

Version: 1.10.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings msPurity_1.10.0.tar.gz

StartedAt: 2019-10-16 03:24:02 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:33:38 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 576.9 seconds

RetCode: 0

Status:  OK

CheckDir: msPurity.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings msPurity_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/msPurity.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.0’
* 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 11.8Mb
  sub-directories of 1Mb or more:
    extdata  11.1Mb
* 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
Namespace in Imports field not imported from: ‘dbplyr’
  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
CV: no visible global function definition for ‘sd’
Getfiles: no visible global function definition for ‘fix’
assessPuritySingle: no visible binding for global variable ‘parallel’
averageCluster: no visible global function definition for ‘sd’
averageCluster: no visible global function definition for ‘median’
covar: no visible global function definition for ‘sd’
custom_dbWriteTable: no visible global function definition for ‘head’
dimsPredictPuritySingle: no visible global function definition for
  ‘read.csv’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘png’
dimsPredictPuritySingleMz: no visible binding for global variable
  ‘mtchi’
dimsPredictPuritySingleMz: no visible binding for global variable
  ‘alli’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘points’
dimsPredictPuritySingleMz: no visible binding for global variable
  ‘mtch’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘text’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘dev.off’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘median’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘sd’
export2sqlite: no visible global function definition for
  ‘packageVersion’
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 ‘write.csv’
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’
getXcmsSmSummary: no visible binding for global variable ‘q_con’
get_topn: no visible binding for global variable ‘topn’
getxcmsSetObject: no visible global function definition for
  ‘sampclass<-’
groupPeaksEx: no visible binding for global variable ‘median’
iwNormGauss: no visible global function definition for ‘dnorm’
iwNormGauss: no visible global function definition for ‘approxfun’
iwNormQE.5: no visible global function definition for ‘approxfun’
iwNormRcosine: no visible global function definition for ‘approxfun’
linearPurity: no visible global function definition for ‘approxfun’
matchi: no visible global function definition for ‘match_factor’
medGroup: no visible binding for global variable ‘median’
median_match_results: no visible global function definition for
  ‘median’
msfrProcess: no visible global function definition for ‘read.csv’
plotPurity: no visible global function definition for ‘png’
plotPurity: no visible binding for global variable ‘idx’
plotPurity: no visible binding for global variable ‘purity’
plotPurity: no visible binding for global variable ‘variable’
plotPurity: no visible global function definition for ‘dev.off’
plotPurity: no visible global function definition for ‘write.csv’
pp4file: no visible global function definition for ‘png’
pp4file: no visible global function definition for ‘plot’
pp4file: no visible global function definition for ‘lines’
pp4file: no visible global function definition for ‘legend’
pp4file: no visible global function definition for ‘abline’
pp4file: no visible global function definition for ‘dev.off’
pp4file: no visible global function definition for ‘median’
predictPurityLCMSloop: no visible global function definition for
  ‘median’
predictPurityLCMSloop : : no visible global function
  definition for ‘na.omit’
predictPurityLCMSloop : : no visible global function
  definition for ‘median’
predictPurityLCMSloop : : no visible global function
  definition for ‘sd’
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’
removeIsotopes: no visible global function definition for ‘write.csv’
rsd: no visible global function definition for ‘sd’
rsde: no visible global function definition for ‘sd’
setFlagMatrix: no visible global function definition for ‘median’
set_snr_ra: no visible global function definition for ‘median’
snrFilter: no visible global function definition for ‘median’
stde: no visible global function definition for ‘sd’
stderror: no visible global function definition for ‘sd’
sum_calc_peaklist: no visible binding for global variable ‘median’
write_msp_single: no visible global function definition for
  ‘packageVersion’
xcmsGroupPurity: no visible binding for global variable ‘median’
xcmsGroupPurity: no visible global function definition for ‘median’
averageSpectra,purityD: no visible binding for global variable ‘i’
subtract,purityD: no visible binding for global variable ‘i’
validate,purityA: no visible global function definition for ‘head’
writeOut,purityD: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  abline accession alli approxfun dev.off dnorm fix grpid head i idx
  inPurity instrument instrument_type l_speakmetaFiltered legend
  library_spectra_meta_id lines lower match_factor median mtch mtchi
  na.omit name.y packageVersion parallel pass_flag pid plot png points
  polarity precursor_mz purity q_con ra read.csv retention_time
  sampclass<- sd spectraType spectrum_type text topn type variable
  write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "legend", "lines", "plot", "points",
             "text")
  importFrom("stats", "approxfun", "dnorm", "median", "na.omit", "sd")
  importFrom("utils", "fix", "head", "packageVersion", "read.csv",
             "write.csv")
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 or elapsed time > 5s
                                   user system elapsed
frag4feature-purityA-method      51.163  1.257  50.426
dimsPredictPurity-purityD-method 44.064  1.207  45.505
flag_remove                      22.523  3.160  15.426
purityX                          16.314  1.633  13.570
purityA                          10.944  0.036  11.002
assessPuritySingle               10.820  0.025  10.874
combineAnnotations               10.195  0.148  12.820
createDatabase                    9.727  0.371  10.652
groupPeaks-purityD-method         7.435  1.062   8.523
subtract-purityD-method           6.965  1.099   8.065
groupPeaksEx                      5.396  1.153   6.577
spectralMatching                  4.922  0.741  11.780
filterp-purityD-method            3.960  1.088   5.049
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/msPurity.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL msPurity
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 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: 175 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
206.977   6.660 281.959 

name	user	system	elapsed
Getfiles	0.008	0.000	0.020
assessPuritySingle	10.820	0.025	10.874
averageAllFragSpectra-purityA-method	1.138	0.015	1.506
averageInterFragSpectra-purityA-method	2.254	0.000	2.310
averageIntraFragSpectra-purityA-method	2.514	0.000	2.527
averageSpectra-purityD-method	3.442	1.012	4.469
averageSpectraSingle	1.879	0.527	2.441
combineAnnotations	10.195	0.148	12.820
createDatabase	9.727	0.371	10.652
createMSP-purityA-method	0.819	0.036	0.855
create_database	1.982	0.076	2.055
dimsPredictPurity-purityD-method	44.064	1.207	45.505
dimsPredictPuritySingle	0.075	0.000	0.074
filterFragSpectra-purityA-method	0.192	0.000	0.192
filterp-purityD-method	3.960	1.088	5.049
flag_remove	22.523	3.160	15.426
frag4feature-purityA-method	51.163	1.257	50.426
getP-purityD-method	0.002	0.000	0.003
get_additional_mzml_meta	0.036	0.000	0.035
groupPeaks-purityD-method	7.435	1.062	8.523
groupPeaksEx	5.396	1.153	6.577
initialize-purityD-method	0.003	0.000	0.003
iwNormGauss	0.001	0.000	0.001
iwNormQE.5	0.002	0.000	0.001
iwNormRcosine	0.001	0.000	0.001
pcalc	0.005	0.000	0.004
purityA	10.944	0.036	11.002
purityD-class	0.003	0.000	0.003
purityX	16.314	1.633	13.570
spectralMatching	4.922	0.741	11.780
spectral_matching	0.000	0.000	0.001
subtract-purityD-method	6.965	1.099	8.065
subtractMZ	0	0	0