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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:isobar.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings isobar_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/isobar.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'isobar/DESCRIPTION' ... OK
* this is package 'isobar' version '1.40.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'isobar' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'png(sprintf("pairwise_correlation_%s.png", ': unused argument (title = "Pairwise Correlation plot") 
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/isobar.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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
* 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.as.matrix' '.as.vect' '.convertPeptideModif'
  '.proteinGroupAsConciseDataFrame' '.read.idfile' '.sum.bool'
* checking S3 generic/method consistency ... WARNING
sequence:
  function(nvec, ...)
sequence.coverage:
  function(protein.group, protein.g, specificity, simplify, ...)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
  as.data.frame.IBSpectra as.data.frame.ProteinGroup plot.NoiseModel
  sequence.coverage summary.ProteinGroup
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calcProbXGreaterThanY.orig: no visible global function definition for
  'd'
.plot.pairs: possible error in
  png(sprintf("pairwise_correlation_%s.png", name), title = "Pairwise
  Correlation plot", width = 1000, height = 1000, pointsize = 14):
  unused argument (title = "Pairwise Correlation plot")
.read.peaklist: no visible binding for global variable 'type'
.round.distr: no visible global function definition for 'param'
.write.summarized.table: no visible binding for global variable 'name'
distrprint: no visible global function definition for 'param'
distrprint : <anonymous>: no visible global function definition for
  'param'
shared.ratios.sign: no visible binding for global variable 'ratio'
shared.ratios.sign: no visible binding for global variable 'g'
spectra.count2: no visible binding for global variable 'peptide'
twodistr.plot: no visible global function definition for 'd'
ProteinGroup,data.frame-missing: no visible binding for global variable
  'peptide'
coerce,IBSpectra-MSnSet: no visible global function definition for 'mz'
coerce,IBSpectra-MSnSet: no visible binding for global variable 'o'
coerce,MSnSet-IBSpectra: no visible global function definition for
  'qual'
df,Tlsd: no visible global function definition for 'param'
estimateRatio,IBSpectra-ANY-missing-missing-character-missing: no
  visible binding for global variable 'i'
estimateRatio,IBSpectra-ANY-missing-missing-missing-character: no
  visible binding for global variable 'i'
estimateRatioNumeric,numeric-numeric-NoiseModel: no visible binding for
  global variable 'center.var'
location,Tlsd: no visible global function definition for 'param'
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable 'pch'
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable 'noise.model.col'
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable 'pch.p'
scale,Tlsd: no visible global function definition for 'param'
Undefined global functions or variables:
  center.var d g i mz name noise.model.col o param pch pch.p peptide
  qual ratio type
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'IBSpectra-class.Rd':
  '[MSnbase]{MSnbase}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'peptide.count':
  'sequence.coverage'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
NoiseModel-class 8.65   0.23    8.89
fit-distr        3.69   0.13    7.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
NoiseModel-class 11.85   0.05   11.89
* 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 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/isobar.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/isobar_1.40.0.tar.gz && rm -rf isobar.buildbin-libdir && mkdir isobar.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=isobar.buildbin-libdir isobar_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL isobar_1.40.0.zip && rm isobar_1.40.0.tar.gz isobar_1.40.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  2 2191k    2 45687    0     0   290k      0  0:00:07 --:--:--  0:00:07  291k
 85 2191k   85 1865k    0     0  1619k      0  0:00:01  0:00:01 --:--:-- 1619k
100 2191k  100 2191k    0     0  1725k      0  0:00:01  0:00:01 --:--:-- 1725k

install for i386

* installing *source* package 'isobar' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'coerce' with signature '"MSnSet","IBSpectra"': no definition for class "MSnSet"
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "MSnSet"
Note: possible error in 'png(sprintf("pairwise_correlation_%s.png", ': unused argument (title = "Pairwise Correlation plot") 
** help
*** installing help indices
  converting help for package 'isobar'
    finding HTML links ... done
    IBSpectra-class                         html  
    finding level-2 HTML links ... done

    NoiseModel-class                        html  
    ProteinGroup-class                      html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/isobar.buildbin-libdir/00LOCK-isobar/00new/isobar/help/ProteinGroup.html
    TlsParameter-class                      html  
    Tlsd-class                              html  
    calc.delta.score                        html  
    calc.startpos                           html  
    calculate-pvalues                       html  
    calculate.dNSAF                         html  
    calculate.emPAI                         html  
    correct.peptide.ratios                  html  
    distr-methods                           html  
    fit-distr                               html  
    getPeptideModifContext                  html  
    getPhosphoRSProbabilities               html  
    getPtmInfo                              html  
    groupMemberPeptides                     html  
    human.protein.names                     html  
    isobar-analysis                         html  
    isobar-data                             html  
    isobar-import                           html  
    isobar-log                              html  
    isobar-package                          html  
    isobar-plots                            html  
    isobar-preprocessing                    html  
    isobar-reports                          html  
    maplot.protein                          html  
    number.ranges                           html  
    observedKnownSites                      html  
    peptide.count                           html  
    proteinInfo-methods                     html  
    proteinNameAndDescription               html  
    ratio-summ                              html  
    ratiosReshapeWide                       html  
    reporter.protein-methods                html  
    sanitize                                html  
    shared.ratios                           html  
    shared.ratios.sign                      html  
    specificities                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/isobar.buildbin-libdir/00LOCK-isobar/00new/isobar/help/UNSPECIFIC.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/isobar.buildbin-libdir/00LOCK-isobar/00new/isobar/help/SPECIFICITIES.html
    spectra.count2                          html  
    subsetIBSpectra                         html  
    utils                                   html  
    writeHscoreData                         html  
    writeIBSpectra                          html  
** 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

install for x64

* installing *source* package 'isobar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'isobar' as isobar_1.40.0.zip
* DONE (isobar)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'isobar' successfully unpacked and MD5 sums checked