##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings msPurity_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/msPurity.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘msPurity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msPurity’ version ‘1.25.0’
* 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 19.6Mb
  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 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
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 ... 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
createDatabase                   253.805  6.332 215.854
frag4feature-purityA-method      229.763  5.270 191.975
dimsPredictPurity-purityD-method  48.398  1.020  49.423
flag_remove                       42.792  5.684  24.653
purityX                           16.120  3.341  13.047
combineAnnotations                12.794  0.160  12.968
purityA                           12.195  0.100  12.293
assessPuritySingle                11.859  0.277  12.140
groupPeaks-purityD-method         10.096  1.020  11.117
subtract-purityD-method            8.704  1.192   9.895
spectralMatching                   7.415  1.735  10.321
groupPeaksEx                       7.439  1.088   8.527
filterp-purityD-method             6.681  1.020   7.701
averageSpectra-purityD-method      6.008  0.995   7.008
* 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 ...
  ‘msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd’ using ‘UTF-8’... OK
  ‘msPurity-spectral-database-vignette.Rmd’ using ‘UTF-8’... OK
  ‘msPurity-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd’ using rmarkdown
--- finished re-building ‘msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd’

--- re-building ‘msPurity-spectral-database-vignette.Rmd’ using rmarkdown
Could not fetch https://www.dbschema.com/images/favicon.ico
HttpExceptionRequest Request {
  host                 = "www.dbschema.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/images/favicon.ico"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ResponseTimeout
Error: processing vignette 'msPurity-spectral-database-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘msPurity-spectral-database-vignette.Rmd’

--- re-building ‘msPurity-vignette.Rmd’ using rmarkdown
--- finished re-building ‘msPurity-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘msPurity-spectral-database-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/msPurity.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL msPurity
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 frag4feature (fillpeaks)                  ##"
[1] "########################################################"
[1] "/home/biocbuild/bbs-3.17-bioc/R/library/msPurity/extdata/tests/xcms/msms_only_xcmsnexp.rds"
[1] "/home/biocbuild/bbs-3.17-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 
279.439  22.907 296.833