##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:msPurity.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings msPurity_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/msPurity.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'msPurity/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'msPurity' version '1.33.0'
* package encoding: UTF-8
* checking package namespace information ... NOTE
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
* 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 ... INFO
  installed size is 19.5Mb
  sub-directories of 1Mb or more:
    extdata  18.8Mb
* 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 code 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
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
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'
createDatabase: no visible global function definition for
  'featureValues'
create_database : getxcmsSetObject: no visible global function
  definition for 'sampclass<-'
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'
flag_remove: no visible global function definition for
  'PeakDensityParam'
flag_remove: no visible global function definition for 'chromPeaks<-'
flag_remove: no visible global function definition for 'chromPeaks'
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'
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'
sum_calc_peaklist: no visible global function definition for
  'phenoData'
averageSpectra,purityD: no visible binding for global variable 'i'
subtract,purityD: no visible binding for global variable 'i'
Undefined global functions or variables:
  PeakDensityParam accession alli chromPeaks chromPeaks<-
  compoundDbname count.fields featureValues grpid i idx inPurity
  instrument instrument_type l_speakmetaFiltered
  library_spectra_meta_id lower match_factor mtch mtchi name.y parallel
  pass_flag phenoData 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 ... NOTE
checkRd: (-1) createMSP-purityA-method.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{msp_file_pth}{character; Name of the output msp file, if NULL the file "frag_spectra_{time stamp}.msp" will be created in the current directory}
       |                                                                                            ^
* 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
createDatabase                   144.17   1.95  267.93
frag4feature-purityA-method      117.27   0.80  239.45
purityX                           41.56   4.33   45.82
dimsPredictPurity-purityD-method  39.17   1.58   40.75
flag_remove                       12.00   0.31   44.09
combineAnnotations                11.70   0.41   12.20
purityA                            9.53   0.18    9.72
assessPuritySingle                 9.33   0.09    9.55
groupPeaks-purityD-method          7.65   1.08    8.72
spectralMatching                   5.69   3.04   17.65
subtract-purityD-method            5.47   1.10    6.56
averageSpectra-purityD-method      4.47   0.93    5.45
groupPeaksEx                       4.23   1.11    5.35
filterp-purityD-method             4.14   0.89    5.04
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/msPurity.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL msPurity
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 (fillpeaks)                  ##"
[1] "########################################################"
[1] "E:/biocbuild/bbs-3.21-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xcmsnexp.rds"
[1] "E:/biocbuild/bbs-3.21-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xset.rds"
[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 frag4feature    (xcms v2 functions)       ##"
[1] "########################################################"
[1] "\n"
[1] "####################################################################"
[1] "## Checking frag4feature (fillpeaks)  (xcms v2 functions)         ##"
[1] "####################################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking filterFragSpectra  (xcms v2 functions)    ##"
[1] "########################################################"
[1] "\n"
[1] "##############################################################"
[1] "## Checking averageIntraFragSpectra (xcms v2 functions)     ##"
[1] "##############################################################"
[1] "\n"
[1] "#############################################################"
[1] "## Checking averageInterFragSpectra    (xcms v2 functions)  #"
[1] "#############################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking averageAllFragSpectra  (xcms v2 functions) #"
[1] "########################################################"
[1] "\n"
[1] "###########################################################################"
[1] "## Checking averageIntraFragSpectra (with filter)  (xcms v2 functions)   ##"
[1] "###########################################################################"
[1] "\n"
[1] "############################################################################"
[1] "## Checking averageInterFragSpectra (with filter)   (xcms v2 functions)   ##"
[1] "############################################################################"
[1] "\n"
[1] "#########################################################################"
[1] "## Checking averageAllFragSpectra  (with filter)  (xcms v2 functions)  ##"
[1] "#########################################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking createMSP functions   (xcms v2 functions) ##"
[1] "########################################################"
[1] "\n"
[1] "########################################################"
[1] "## checking flag and remove (lc-ms)                   ##"
[1] "########################################################"
[1] "\n"
[1] "#######################################################"
[1] "## Checking database (new schema)                    ##"
[1] "#######################################################"
[1] "\n"
[1] "###############################################################"
[1] "## Checking database (new schema)  (xcms v2 functions)       ##"
[1] "###############################################################"
[1] "\n"
[1] "########################################################"
[1] "## Checking database (old 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] "## Testing spectral matching (spectralMatching)  qvl (xcms v2 functions)  ##"
[1] "############################################################################"
[1] "\n"
[1] "############################################################################"
[1] "## Testing spectral matching (spectralMatching)   qvq (xcms v2 functions) ##"
[1] "############################################################################"
[1] "\n"
[1] "######################################################################################"
[1] "## Testing spectral matching (spectralMatching)   q(scan) v q  (xcms v2 functions)  ##"
[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 306 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 236.21   21.09  321.31