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CHECK report for isobar on tokay1

This page was generated on 2018-04-12 13:21:21 -0400 (Thu, 12 Apr 2018).

Package 715/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isobar 1.24.0
Florian P Breitwieser
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/isobar
Branch: RELEASE_3_6
Last Commit: 36f1baf
Last Changed Date: 2017-10-30 12:39:37 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: isobar
Version: 1.24.0
Command: rm -rf isobar.buildbin-libdir isobar.Rcheck && mkdir isobar.buildbin-libdir isobar.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=isobar.buildbin-libdir isobar_1.24.0.tar.gz >isobar.Rcheck\00install.out 2>&1 && cp isobar.Rcheck\00install.out isobar-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=isobar.buildbin-libdir --install="check:isobar-install.out" --force-multiarch --no-vignettes --timings isobar_1.24.0.tar.gz
StartedAt: 2018-04-12 00:53:39 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:57:47 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 247.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: isobar.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf isobar.buildbin-libdir isobar.Rcheck && mkdir isobar.buildbin-libdir isobar.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=isobar.buildbin-libdir isobar_1.24.0.tar.gz >isobar.Rcheck\00install.out 2>&1 && cp isobar.Rcheck\00install.out isobar-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=isobar.buildbin-libdir --install="check:isobar-install.out" --force-multiarch --no-vignettes --timings isobar_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/isobar.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 'isobar/DESCRIPTION' ... OK
* this is package 'isobar' version '1.24.0'
* 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:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/IBSpectra-class.Rd:175: missing file link 'MSnSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/IBSpectra-class.Rd:176: file link 'MSnbase' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/IBSpectra-class.Rd:178: missing file link 'MSnSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/IBSpectra-class.Rd:232: missing file link 'ProteinGroup'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/ProteinGroup-class.Rd:177: missing file link 'IBSpectra'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/fit-distr.Rd:28: missing file link 'Cauchy'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/fit-distr.Rd:28: missing file link 'Norm'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/isobar.Rcheck/00install.out' for details.
* 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
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 ... OK
* 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 ... OK
* 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 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
NoiseModel-class 9.91   0.13   10.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
NoiseModel-class 12.93   0.03   12.95
* 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: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/isobar.Rcheck/00check.log'
for details.

Installation output

isobar.Rcheck/00install.out


install for i386

* installing *source* package 'isobar' ...
** R
** data
** inst
** preparing 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"
** help
*** installing help indices
  converting help for package 'isobar'
    finding HTML links ... done
    IBSpectra-class                         html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/IBSpectra-class.Rd:175: missing file link 'MSnSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/IBSpectra-class.Rd:176: file link 'MSnbase' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/IBSpectra-class.Rd:178: missing file link 'MSnSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/IBSpectra-class.Rd:232: missing file link 'ProteinGroup'
    NoiseModel-class                        html  
    ProteinGroup-class                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/ProteinGroup-class.Rd:177: missing file link 'IBSpectra'
    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  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/fit-distr.Rd:28: missing file link 'Cauchy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpayWOpt/R.INSTALL10a010d420f4/isobar/man/fit-distr.Rd:28: missing file link 'Norm'
    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  
    spectra.count2                          html  
    subsetIBSpectra                         html  
    utils                                   html  
    writeHscoreData                         html  
    writeIBSpectra                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'isobar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'isobar' as isobar_1.24.0.zip
* DONE (isobar)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

isobar.Rcheck/examples_i386/isobar-Ex.timings

nameusersystemelapsed
IBSpectra-class0.660.020.67
NoiseModel-class 9.91 0.1310.03
ProteinGroup-class0.300.010.31
TlsParameter-class000
Tlsd-class000
calculate-pvalues0.020.000.02
calculate.dNSAF2.650.022.67
calculate.emPAI0.490.010.56
distr-methods0.030.000.22
fit-distr3.280.143.43
getPtmInfo000
groupMemberPeptides0.370.020.39
isobar-analysis0.300.010.32
isobar-data0.270.020.28
isobar-import1.220.031.25
isobar-log1.310.021.32
isobar-plots1.420.061.49
isobar-preprocessing1.440.051.48
number.ranges000
observedKnownSites0.250.030.28
peptide.count2.510.032.55
proteinInfo-methods0.240.000.24
proteinNameAndDescription0.280.000.28
ratio-summ0.530.000.53
sanitize000
spectra.count20.320.000.33
subsetIBSpectra1.580.051.63
utils000

isobar.Rcheck/examples_x64/isobar-Ex.timings

nameusersystemelapsed
IBSpectra-class0.710.010.74
NoiseModel-class12.93 0.0312.95
ProteinGroup-class0.280.000.28
TlsParameter-class000
Tlsd-class000
calculate-pvalues0.040.000.05
calculate.dNSAF2.430.002.42
calculate.emPAI0.570.030.61
distr-methods0.070.020.08
fit-distr3.970.084.04
getPtmInfo0.010.000.02
groupMemberPeptides0.340.010.36
isobar-analysis0.270.000.26
isobar-data0.230.000.24
isobar-import1.240.021.25
isobar-log1.310.011.33
isobar-plots1.740.021.75
isobar-preprocessing1.360.031.39
number.ranges000
observedKnownSites0.280.000.28
peptide.count2.570.002.58
proteinInfo-methods0.190.020.20
proteinNameAndDescription0.280.000.28
ratio-summ0.660.000.66
sanitize000
spectra.count20.270.030.29
subsetIBSpectra1.810.031.85
utils000