Multiple platform build/check report for BioC 3.6 - CHECK report for msPurity on tokay1

Package: msPurity

Version: 1.4.0

Command: rm -rf msPurity.buildbin-libdir msPurity.Rcheck && mkdir msPurity.buildbin-libdir msPurity.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msPurity.buildbin-libdir msPurity_1.4.0.tar.gz >msPurity.Rcheck\00install.out 2>&1 && cp msPurity.Rcheck\00install.out msPurity-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=msPurity.buildbin-libdir --install="check:msPurity-install.out" --force-multiarch --no-vignettes --timings msPurity_1.4.0.tar.gz

StartedAt: 2018-04-12 01:40:15 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:00:19 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 1204.0 seconds

RetCode: 0

Status: OK

CheckDir: msPurity.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf msPurity.buildbin-libdir msPurity.Rcheck && mkdir msPurity.buildbin-libdir msPurity.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msPurity.buildbin-libdir msPurity_1.4.0.tar.gz >msPurity.Rcheck\00install.out 2>&1 && cp msPurity.Rcheck\00install.out msPurity-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=msPurity.buildbin-libdir --install="check:msPurity-install.out" --force-multiarch --no-vignettes --timings msPurity_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/msPurity.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
spectral_matching                67.29   1.87  287.58
frag4feature-purityA-method      46.00   0.53   47.28
dimsPredictPurity-purityD-method 33.68   1.27   34.95
purityX                          13.89   1.05   17.72
assessPuritySingle               11.00   0.03   12.17
purityA                           9.33   0.06    9.37
subtract-purityD-method           6.56   1.21    7.76
groupPeaks-purityD-method         6.09   1.34    7.44
groupPeaksEx                      5.42   1.47    6.89
averageSpectra-purityD-method     4.32   1.25    5.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
spectral_matching                82.15   1.97   84.19
frag4feature-purityA-method      52.62   0.38   53.07
dimsPredictPurity-purityD-method 39.78   0.97   40.76
purityX                          12.10   0.50   12.56
subtract-purityD-method          10.00   1.41   11.40
assessPuritySingle               10.99   0.06   11.40
purityA                           9.58   0.03    9.61
groupPeaks-purityD-method         6.45   1.32    7.78
groupPeaksEx                      4.98   1.19    6.17
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/msPurity.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'msPurity' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'msPurity'
    finding HTML links ... done
    Getfiles                                html  
    assessPuritySingle                      html  
    averageSpectra-purityD-method           html  
    averageSpectraSingle                    html  
    dimsPredictPurity-purityD-method        html  
    dimsPredictPuritySingle                 html  
    filterp-purityD-method                  html  
    frag4feature-purityA-method             html  
    getP-purityD-method                     html  
    get_additional_mzml_meta                html  
    groupPeaks-purityD-method               html  
    groupPeaksEx                            html  
    initialize-purityD-method               html  
    iwNormGauss                             html  
    iwNormQE.5                              html  
    iwNormRcosine                           html  
    pcalc                                   html  
    purityA                                 html  
    purityD-class                           html  
    purityX                                 html  
    show-purityA-method                     html  
    show-purityD-method                     html  
    show-purityX-method                     html  
    spectral_matching                       html  
    subtract-purityD-method                 html  
    subtractMZ                              html  
    validate-purityA-method                 html  
    writeOut-purityD-method                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'msPurity' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'msPurity' as msPurity_1.4.0.zip
* DONE (msPurity)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
 148.53    2.53  186.40


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
 205.01    2.45  245.82

name	user	system	elapsed
Getfiles	0.00	0.00	0.02
assessPuritySingle	11.00	0.03	12.17
averageSpectra-purityD-method	4.32	1.25	5.97
averageSpectraSingle	1.86	0.72	2.58
dimsPredictPurity-purityD-method	33.68	1.27	34.95
dimsPredictPuritySingle	0.07	0.00	0.06
filterp-purityD-method	3.45	1.44	4.89
frag4feature-purityA-method	46.00	0.53	47.28
getP-purityD-method	0	0	0
get_additional_mzml_meta	0.05	0.00	0.05
groupPeaks-purityD-method	6.09	1.34	7.44
groupPeaksEx	5.42	1.47	6.89
initialize-purityD-method	0	0	0
iwNormGauss	0	0	0
iwNormQE.5	0	0	0
iwNormRcosine	0	0	0
pcalc	0	0	0
purityA	9.33	0.06	9.37
purityD-class	0	0	0
purityX	13.89	1.05	17.72
spectral_matching	67.29	1.87	287.58
subtract-purityD-method	6.56	1.21	7.76
subtractMZ	0	0	0

name	user	system	elapsed
Getfiles	0	0	0
assessPuritySingle	10.99	0.06	11.40
averageSpectra-purityD-method	3.87	1.05	4.96
averageSpectraSingle	1.82	0.53	2.34
dimsPredictPurity-purityD-method	39.78	0.97	40.76
dimsPredictPuritySingle	0.06	0.00	0.07
filterp-purityD-method	3.63	0.98	4.61
frag4feature-purityA-method	52.62	0.38	53.07
getP-purityD-method	0	0	0
get_additional_mzml_meta	0.05	0.00	0.05
groupPeaks-purityD-method	6.45	1.32	7.78
groupPeaksEx	4.98	1.19	6.17
initialize-purityD-method	0	0	0
iwNormGauss	0	0	0
iwNormQE.5	0	0	0
iwNormRcosine	0	0	0
pcalc	0	0	0
purityA	9.58	0.03	9.61
purityD-class	0.01	0.00	0.02
purityX	12.10	0.50	12.56
spectral_matching	82.15	1.97	84.19
subtract-purityD-method	10.00	1.41	11.40
subtractMZ	0	0	0

CHECK report for msPurity on tokay1

Summary

Command output

Installation output

Tests output

Example timings