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BioC 3.4: CHECK report for TIN on tokay1

This page was generated on 2017-04-15 16:19:45 -0400 (Sat, 15 Apr 2017).

Package 1237/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TIN 1.6.0
Bjarne Johannessen
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/TIN
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TIN
Version: 1.6.0
Command: rm -rf TIN.buildbin-libdir TIN.Rcheck && mkdir TIN.buildbin-libdir TIN.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TIN.buildbin-libdir TIN_1.6.0.tar.gz >TIN.Rcheck\00install.out 2>&1 && cp TIN.Rcheck\00install.out TIN-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=TIN.buildbin-libdir --install="check:TIN-install.out" --force-multiarch --no-vignettes --timings TIN_1.6.0.tar.gz
StartedAt: 2017-04-15 01:10:06 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:15:32 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 325.5 seconds
RetCode: 0
Status:  OK  
CheckDir: TIN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf TIN.buildbin-libdir TIN.Rcheck && mkdir TIN.buildbin-libdir TIN.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TIN.buildbin-libdir TIN_1.6.0.tar.gz >TIN.Rcheck\00install.out 2>&1 && cp TIN.Rcheck\00install.out TIN-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=TIN.buildbin-libdir --install="check:TIN-install.out" --force-multiarch --no-vignettes --timings TIN_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/TIN.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TIN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TIN' version '1.6.0'
* 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 'TIN' can be installed ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aberrantExonUsage: no visible global function definition for 'quantile'
aberrantExonUsage: no visible global function definition for 'ave'
clusterPlot: no visible global function definition for 'dist'
clusterPlot: no visible global function definition for 'hclust'
clusterPlot: no visible global function definition for
  'colorRampPalette'
clusterPlot: no visible global function definition for 'par'
clusterPlot: no visible global function definition for 'png'
clusterPlot: no visible global function definition for 'jpeg'
clusterPlot: no visible global function definition for 'postscript'
clusterPlot: no visible global function definition for 'pdf'
clusterPlot: no visible global function definition for 'bmp'
clusterPlot: no visible global function definition for 'dev.off'
correlationPlot: no visible global function definition for 'png'
correlationPlot: no visible global function definition for 'jpeg'
correlationPlot: no visible global function definition for 'postscript'
correlationPlot: no visible global function definition for 'pdf'
correlationPlot: no visible global function definition for 'bmp'
correlationPlot: no visible global function definition for 'hist'
correlationPlot: no visible global function definition for 'plot'
correlationPlot: no visible global function definition for 'axis'
correlationPlot: no visible global function definition for 'points'
correlationPlot: no visible global function definition for 'dev.off'
firmaAnalysis: no visible global function definition for 'data'
geneSetCorrelation: no visible global function definition for 'median'
posNegCorrPlot: no visible global function definition for 'png'
posNegCorrPlot: no visible global function definition for 'jpeg'
posNegCorrPlot: no visible global function definition for 'postscript'
posNegCorrPlot: no visible global function definition for 'pdf'
posNegCorrPlot: no visible global function definition for 'bmp'
posNegCorrPlot: no visible global function definition for 'plot'
posNegCorrPlot: no visible global function definition for 'axis'
posNegCorrPlot: no visible global function definition for 'points'
posNegCorrPlot: no visible global function definition for 'dev.off'
readGeneSummaries: no visible global function definition for 'data'
readGeneSummaries: no visible global function definition for
  'read.table'
scatterPlot: no visible global function definition for 'png'
scatterPlot: no visible global function definition for 'jpeg'
scatterPlot: no visible global function definition for 'postscript'
scatterPlot: no visible global function definition for 'pdf'
scatterPlot: no visible global function definition for 'bmp'
scatterPlot: no visible global function definition for 'plot'
scatterPlot: no visible global function definition for 'ave'
scatterPlot: no visible global function definition for 'axis'
scatterPlot: no visible global function definition for 'text'
scatterPlot: no visible global function definition for 'mtext'
scatterPlot: no visible global function definition for 'points'
scatterPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  ave axis bmp colorRampPalette data dev.off dist hclust hist jpeg
  median mtext par pdf plot png points postscript quantile read.table
  text
Consider adding
  importFrom("grDevices", "bmp", "colorRampPalette", "dev.off", "jpeg",
             "pdf", "png", "postscript")
  importFrom("graphics", "axis", "hist", "mtext", "par", "plot",
             "points", "text")
  importFrom("stats", "ave", "dist", "hclust", "median", "quantile")
  importFrom("utils", "data", "read.table")
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 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
geneSetCorrelation 11.72   0.09   11.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
geneSetCorrelation 17.11   0.07   17.18
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/TIN.Rcheck/00check.log'
for details.


TIN.Rcheck/00install.out:


install for i386

* installing *source* package 'TIN' ...
** R
** data
** inst
** preparing package for lazy loading
The following object is masked _by_ package:aroma.affymetrix:

    writeCdf

The following object is masked from package:R.utils:

    findFiles

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
The following object is masked _by_ package:aroma.affymetrix:

    writeCdf

The following object is masked from package:R.utils:

    findFiles


install for x64

* installing *source* package 'TIN' ...
** testing if installed package can be loaded
The following object is masked _by_ package:aroma.affymetrix:

    writeCdf

The following object is masked from package:R.utils:

    findFiles

* MD5 sums
packaged installation of 'TIN' as TIN_1.6.0.zip
* DONE (TIN)

TIN.Rcheck/examples_i386/TIN-Ex.timings:

nameusersystemelapsed
aberrantExonUsage0.310.030.35
clusterPlot0.390.010.40
correlation0.350.020.36
correlationPlot3.430.003.44
firmaAnalysis0.020.000.02
geneSetCorrelation11.72 0.0911.81
posNegCorrPlot3.730.083.81
probesetPermutations0.350.000.35
readGeneSummaries0.030.020.04
scatterPlot0.510.030.55

TIN.Rcheck/examples_x64/TIN-Ex.timings:

nameusersystemelapsed
aberrantExonUsage0.370.040.41
clusterPlot0.190.000.19
correlation0.440.030.46
correlationPlot3.450.033.49
firmaAnalysis0.000.010.01
geneSetCorrelation17.11 0.0717.18
posNegCorrPlot4.000.044.04
probesetPermutations0.740.000.74
readGeneSummaries0.030.000.03
scatterPlot0.260.020.28