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CHECK report for isobar on tokay2

This page was generated on 2018-10-17 08:35:51 -0400 (Wed, 17 Oct 2018).

Package 754/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isobar 1.26.0
Florian P Breitwieser
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/isobar
Branch: RELEASE_3_7
Last Commit: e470f8b
Last Changed Date: 2018-04-30 10:35:22 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: isobar
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:isobar.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings isobar_1.26.0.tar.gz
StartedAt: 2018-10-17 02:50:35 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:54:40 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 244.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: isobar.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:isobar.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings isobar_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/isobar.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.26.0'
* 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") 
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:175: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:176: missing file link 'MSnbase'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:178: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:232: file link 'ProteinGroup' in package 'isobar' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/ProteinGroup-class.Rd:177: file link 'IBSpectra' in package 'isobar' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/fit-distr.Rd:28: file link 'Cauchy' in package 'distr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/fit-distr.Rd:28: file link 'Norm' in package 'distr' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
NoiseModel-class 10.53   0.24   10.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
NoiseModel-class 13.96   0.06   14.02
* 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-3.7-bioc/meat/isobar.Rcheck/00check.log'
for details.



Installation output

isobar.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/isobar_1.26.0.tar.gz && rm -rf isobar.buildbin-libdir && mkdir isobar.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=isobar.buildbin-libdir isobar_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL isobar_1.26.0.zip && rm isobar_1.26.0.tar.gz isobar_1.26.0.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
100 2189k  100 2189k    0     0  21.6M      0 --:--:-- --:--:-- --:--:-- 23.2M

install for i386

* installing *source* package 'isobar' ...
** 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

Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:175: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:176: missing file link 'MSnbase'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:178: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:232: file link 'ProteinGroup' in package 'isobar' does not exist and so has been treated as a topic
    NoiseModel-class                        html  
    ProteinGroup-class                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/ProteinGroup-class.Rd:177: file link 'IBSpectra' in package 'isobar' does not exist and so has been treated as a topic
    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-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/fit-distr.Rd:28: file link 'Cauchy' in package 'distr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/fit-distr.Rd:28: file link 'Norm' in package 'distr' does not exist and so has been treated as a topic
    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_1.26.0.zip
* DONE (isobar)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'isobar' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

isobar.Rcheck/examples_i386/isobar-Ex.timings

nameusersystemelapsed
IBSpectra-class0.670.040.81
NoiseModel-class10.53 0.2410.77
ProteinGroup-class0.460.000.45
TlsParameter-class000
Tlsd-class000
calculate-pvalues0.050.000.05
calculate.dNSAF3.440.013.45
calculate.emPAI0.470.020.53
distr-methods0.040.020.16
fit-distr3.600.173.78
getPtmInfo000
groupMemberPeptides0.490.010.50
isobar-analysis0.980.051.04
isobar-data0.380.000.37
isobar-import1.280.031.31
isobar-log1.510.011.53
isobar-plots1.970.162.13
isobar-preprocessing1.960.112.06
number.ranges000
observedKnownSites0.420.000.53
peptide.count3.920.063.99
proteinInfo-methods0.380.020.39
proteinNameAndDescription0.440.010.45
ratio-summ0.510.030.55
sanitize000
spectra.count20.440.000.43
subsetIBSpectra2.360.002.36
utils000

isobar.Rcheck/examples_x64/isobar-Ex.timings

nameusersystemelapsed
IBSpectra-class0.580.000.58
NoiseModel-class13.96 0.0614.02
ProteinGroup-class0.270.000.27
TlsParameter-class000
Tlsd-class000
calculate-pvalues0.030.000.03
calculate.dNSAF2.830.002.83
calculate.emPAI0.260.020.28
distr-methods0.030.000.03
fit-distr3.420.013.43
getPtmInfo000
groupMemberPeptides0.450.040.49
isobar-analysis0.410.010.42
isobar-data0.360.020.38
isobar-import1.440.031.46
isobar-log1.140.041.19
isobar-plots1.450.081.53
isobar-preprocessing1.310.051.36
number.ranges000
observedKnownSites0.350.020.36
peptide.count3.390.013.41
proteinInfo-methods0.330.020.34
proteinNameAndDescription0.370.030.41
ratio-summ0.470.010.48
sanitize000
spectra.count20.440.000.44
subsetIBSpectra2.700.032.73
utils000