Package: msPurity

Version: 1.4.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings msPurity_1.4.0.tar.gz

StartedAt: 2018-04-12 01:19:53 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:26:50 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 417.0 seconds

RetCode: 0

Status:  OK

CheckDir: msPurity.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings msPurity_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/msPurity.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.0’
* 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 ... OK
* 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 loading without being on the library search path ... 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
export_2_sqlite: warning in custom_dbWriteTable(name_pk = "grpid", fk =
  NA, table_name = "c_peak_groups", df = grp_peaklist, con = con):
  partial argument match of 'fk' to 'fks'
export_2_sqlite: warning in custom_dbWriteTable(name_pk = "pid", fk =
  fks_fileid, table_name = "s_peak_meta", df = scan_info, con = con):
  partial argument match of 'fk' to 'fks'
export_2_sqlite: warning in custom_dbWriteTable(name_pk = "sid", fk =
  append(fks_fileid, fks_pid), table_name = "s_peaks", df =
  scanpeaks_frag, con = con): partial argument match of 'fk' to 'fks'
export_2_sqlite: warning in custom_dbWriteTable(name_pk = "cXg_id", fk
  = append(fks_grpid, fks_cid), table_name = "c_peak_X_c_peak_group",
  df = c_peak_X_c_peak_group, con = con): partial argument match of
  'fk' to 'fks'
export_2_sqlite: warning in custom_dbWriteTable(name_pk = "cXp_id", fk
  = append(fks_pid, fks_cid), table_name = "c_peak_X_s_peak_meta", df =
  c_peak_X_s_peak_meta, con = con): partial argument match of 'fk' to
  'fks'
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’
averageSpectraSingle: no visible binding for global variable ‘scanid’
covar: no visible global function definition for ‘sd’
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’
get_interp_purity: possible error in splinePurity(rowi, roi_scns,
  minoff, maxoff, ppm, mostIntense, scanids, plotP, plotdir, isotopes,
  im): unused arguments (isotopes, im)
get_topn: no visible binding for global variable ‘topn’
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’
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’
performHc: no visible global function definition for ‘dist’
performHc: no visible global function definition for ‘as.dist’
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 : <anonymous>: no visible global function
  definition for ‘na.omit’
predictPurityLCMSloop : <anonymous>: no visible global function
  definition for ‘median’
predictPurityLCMSloop : <anonymous>: no visible global function
  definition for ‘sd’
purityA: no visible binding for global variable ‘i’
removeIsotopes: no visible global function definition for ‘write.csv’
rsde: no visible global function definition for ‘sd’
snrFilter: no visible global function definition for ‘median’
stde: no visible global function definition for ‘sd’
stderror: no visible global function definition for ‘sd’
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 alli approxfun as.dist dev.off dist dnorm fix head i idx
  legend lines median mtch mtchi na.omit parallel plot png points
  purity read.csv scanid sd text topn variable write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "legend", "lines", "plot", "points",
             "text")
  importFrom("stats", "approxfun", "as.dist", "dist", "dnorm", "median",
             "na.omit", "sd")
  importFrom("utils", "fix", "head", "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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
spectral_matching                67.296  0.744  68.507
frag4feature-purityA-method      45.796  0.260  46.554
dimsPredictPurity-purityD-method 31.404  0.932  32.371
purityX                          11.984  0.240  12.299
assessPuritySingle                9.212  0.040   9.339
purityA                           8.756  0.016   8.778
subtract-purityD-method           6.452  0.800   7.263
groupPeaks-purityD-method         5.580  0.916   6.502
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/msPurity.Rcheck/00check.log’
for details.

* installing *source* package ‘msPurity’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (msPurity)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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] "########################################################"
[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"
[1] "########################################################"
[1] "## Checking LCMS based class and functions            ##"
[1] "########################################################"
[1] 4
[1] "########################################################"
[1] "## Checking pcalc functions                           ##"
[1] "########################################################"
[1] "########################################################"
[1] "## Spectral matching functions                        ##"
[1] "########################################################"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 81 SKIPPED: 0 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
148.284   1.380 160.859 

name	user	system	elapsed
Getfiles	0.004	0.000	0.005
assessPuritySingle	9.212	0.040	9.339
averageSpectra-purityD-method	3.536	1.040	4.610
averageSpectraSingle	1.396	0.476	1.878
dimsPredictPurity-purityD-method	31.404	0.932	32.371
dimsPredictPuritySingle	0.044	0.004	0.051
filterp-purityD-method	2.944	0.840	3.798
frag4feature-purityA-method	45.796	0.260	46.554
getP-purityD-method	0.000	0.000	0.003
get_additional_mzml_meta	0.048	0.000	0.046
groupPeaks-purityD-method	5.580	0.916	6.502
groupPeaksEx	3.828	0.952	4.790
initialize-purityD-method	0.000	0.000	0.002
iwNormGauss	0.004	0.000	0.001
iwNormQE.5	0.000	0.000	0.001
iwNormRcosine	0.004	0.000	0.001
pcalc	0.004	0.000	0.004
purityA	8.756	0.016	8.778
purityD-class	0.004	0.000	0.002
purityX	11.984	0.240	12.299
spectral_matching	67.296	0.744	68.507
subtract-purityD-method	6.452	0.800	7.263
subtractMZ	0	0	0