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BioC 3.4: CHECK report for sSeq on moscato1

This page was generated on 2016-09-21 03:44:49 -0700 (Wed, 21 Sep 2016).

Package 1162/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sSeq 1.11.0
Danni Yu
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sSeq
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: sSeq
Version: 1.11.0
Command: rm -rf sSeq.buildbin-libdir sSeq.Rcheck && mkdir sSeq.buildbin-libdir sSeq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sSeq.buildbin-libdir sSeq_1.11.0.tar.gz >sSeq.Rcheck\00install.out 2>&1 && cp sSeq.Rcheck\00install.out sSeq-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=sSeq.buildbin-libdir --install="check:sSeq-install.out" --force-multiarch --no-vignettes --timings sSeq_1.11.0.tar.gz
StartedAt: 2016-09-20 17:08:58 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 17:24:05 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 907.2 seconds
RetCode: 0
Status:  OK  
CheckDir: sSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf sSeq.buildbin-libdir sSeq.Rcheck && mkdir sSeq.buildbin-libdir sSeq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sSeq.buildbin-libdir sSeq_1.11.0.tar.gz >sSeq.Rcheck\00install.out 2>&1 && cp sSeq.Rcheck\00install.out sSeq-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=sSeq.buildbin-libdir --install="check:sSeq-install.out" --force-multiarch --no-vignettes --timings sSeq_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/sSeq.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sSeq' version '1.11.0'
* 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 'sSeq' 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 ... NOTE
'library' or 'require' call to 'caTools' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RColorBrewer' 'caTools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
drawMA_vol: no visible global function definition for 'par'
drawMA_vol: no visible global function definition for 'plot'
drawMA_vol: no visible global function definition for 'points'
drawMA_vol: no visible global function definition for 'abline'
ecdfAUC: no visible global function definition for 'ecdf'
ecdfAUC: no visible global function definition for 'trapz'
ecdfAUC: no visible global function definition for 'plot'
ecdfAUC: no visible global function definition for 'mtext'
ecdfAUC: no visible global function definition for 'axis'
ecdfAUC: no visible global function definition for 'box'
ecdfAUC: no visible global function definition for 'lines'
ecdfAUC: no visible global function definition for 'abline'
ecdfAUC: no visible global function definition for 'legend'
exactNBtest1: no visible global function definition for 'dnbinom'
getAdjustDisp: no visible global function definition for 'quantile'
getAdjustDisp: no visible global function definition for 'var'
getNormFactor : <anonymous>: no visible global function definition for
  'median'
getQ: no visible global function definition for 'quantile'
getQ: no visible global function definition for 'cov'
getQ: no visible global function definition for 'var'
getQ: no visible global function definition for 'plot'
getQ: no visible global function definition for 'abline'
getQ: no visible global function definition for 'mtext'
getT: no visible global function definition for 'quantile'
getT: no visible global function definition for 'sd'
getT: no visible global function definition for 'cov'
getT: no visible global function definition for 'var'
getT: no visible global function definition for 'plot'
getT: no visible global function definition for 'mtext'
getT: no visible global function definition for 'axis'
getT: no visible global function definition for 'abline'
getTgroup: no visible global function definition for 'quantile'
getTgroup: no visible global function definition for 'cov'
getTgroup: no visible global function definition for 'var'
getTgroup: no visible global function definition for 'plot'
getTgroup: no visible global function definition for 'mtext'
getTgroup: no visible global function definition for 'box'
getTgroup: no visible global function definition for 'axis'
getTgroup: no visible global function definition for 'abline'
nbinomTestForMatricesSH : int.func: no visible global function
  definition for 'median'
nbinomTestForMatricesSH: no visible global function definition for
  'dnbinom'
nbinomTestForMatricesSH: no visible global function definition for
  'pchisq'
plotDispersion: no visible global function definition for 'brewer.pal'
plotDispersion: no visible global function definition for
  'smoothScatter'
plotDispersion: no visible binding for global variable 'blues9'
plotDispersion: no visible global function definition for 'points'
plotDispersion: no visible global function definition for 'legend'
plotDispersion: no visible global function definition for 'plot'
rnbinomMV: no visible global function definition for 'rnbinom'
rowVars: no visible binding for global variable 'var'
sim: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis blues9 box brewer.pal cov dnbinom ecdf legend lines
  median mtext par pchisq plot points quantile rnbinom rnorm sd
  smoothScatter trapz var
Consider adding
  importFrom("grDevices", "blues9")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "mtext", "par", "plot", "points", "smoothScatter")
  importFrom("stats", "cov", "dnbinom", "ecdf", "median", "pchisq",
             "quantile", "rnbinom", "rnorm", "sd", "var")
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
nbTestSH     148.70   0.33  149.06
getTgroup    145.43   0.59  146.01
sSeq-package 143.05   0.54  143.60
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
nbTestSH     138.12   0.50  138.64
getTgroup    135.37   0.52  135.88
sSeq-package 133.43   0.22  133.64
* 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 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/sSeq.Rcheck/00check.log'
for details.


sSeq.Rcheck/00install.out:


install for i386

* installing *source* package 'sSeq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'sSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sSeq' as sSeq_1.11.0.zip
* DONE (sSeq)

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

nameusersystemelapsed
Hammer2months0.040.020.06
Sultan0.070.010.08
Tuch0.040.000.04
countsTable0.020.000.02
drawMA_vol0.330.001.15
ecdfAUC0.010.000.02
equalSpace0.340.000.34
exactNBtest1000
getAdjustDisp0.370.000.37
getNormFactor0.040.000.03
getQ1.630.021.66
getT2.340.002.34
getTgroup145.43 0.59146.01
nbTestSH148.70 0.33149.06
plotDispersion4.810.004.80
rnbinomMV000
rowVars000
sSeq-package143.05 0.54143.60
sim0.470.000.47

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

nameusersystemelapsed
Hammer2months0.050.000.05
Sultan0.070.000.06
Tuch0.060.000.06
countsTable0.010.000.02
drawMA_vol0.350.000.34
ecdfAUC0.020.000.01
equalSpace0.370.000.38
exactNBtest1000
getAdjustDisp0.330.000.34
getNormFactor0.020.020.03
getQ1.480.011.50
getT2.240.002.24
getTgroup135.37 0.52135.88
nbTestSH138.12 0.50138.64
plotDispersion4.740.034.77
rnbinomMV000
rowVars000
sSeq-package133.43 0.22133.64
sim0.510.000.52