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BioC 3.2: CHECK report for sSeq on moscato1

This page was generated on 2015-08-20 13:21:37 -0700 (Thu, 20 Aug 2015).

Package 984/1069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sSeq 1.7.0
Danni Yu
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sSeq
Last Changed Rev: 102594 / Revision: 107602
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sSeq
Version: 1.7.0
Command: rm -rf sSeq.buildbin-libdir sSeq.Rcheck && mkdir sSeq.buildbin-libdir sSeq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sSeq.buildbin-libdir sSeq_1.7.0.tar.gz >sSeq.Rcheck\00install.out 2>&1 && cp sSeq.Rcheck\00install.out sSeq-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=sSeq.buildbin-libdir --install="check:sSeq-install.out" --force-multiarch --no-vignettes --timings sSeq_1.7.0.tar.gz
StartedAt: 2015-08-20 10:46:59 -0700 (Thu, 20 Aug 2015)
EndedAt: 2015-08-20 11:04:24 -0700 (Thu, 20 Aug 2015)
EllapsedTime: 1045.5 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-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sSeq.buildbin-libdir sSeq_1.7.0.tar.gz >sSeq.Rcheck\00install.out 2>&1 && cp sSeq.Rcheck\00install.out sSeq-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=sSeq.buildbin-libdir --install="check:sSeq-install.out" --force-multiarch --no-vignettes --timings sSeq_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/sSeq.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.7.0'
* 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
ecdfAUC: no visible global function definition for 'trapz'
plotDispersion: no visible global function definition for 'brewer.pal'
* 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' ... [509s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
nbTestSH       168.11   0.34  168.45
getTgroup      164.89   0.70  165.63
sSeq-package   162.09   0.17  162.26
plotDispersion   5.49   0.02    5.55
** running examples for arch 'x64' ... [498s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getTgroup      163.21   0.66  163.90
nbTestSH       161.94   0.41  162.38
sSeq-package   156.56   0.53  157.15
plotDispersion   6.54   0.00    6.54
* 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-3.2-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_1.7.0.zip
* DONE (sSeq)

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

nameusersystemelapsed
Hammer2months0.080.000.08
Sultan0.110.000.11
Tuch0.050.000.05
countsTable0.010.000.01
drawMA_vol0.360.000.36
ecdfAUC0.010.000.01
equalSpace0.360.000.36
exactNBtest1000
getAdjustDisp0.290.000.29
getNormFactor0.030.000.03
getQ2.020.002.02
getT2.460.002.46
getTgroup164.89 0.70165.63
nbTestSH168.11 0.34168.45
plotDispersion5.490.025.55
rnbinomMV000
rowVars000
sSeq-package162.09 0.17162.26
sim0.610.000.61

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

nameusersystemelapsed
Hammer2months0.060.010.08
Sultan0.080.000.08
Tuch0.070.000.08
countsTable0.020.000.01
drawMA_vol0.610.000.61
ecdfAUC0.010.000.02
equalSpace0.560.000.57
exactNBtest1000
getAdjustDisp0.360.000.35
getNormFactor0.030.000.04
getQ2.140.002.13
getT3.120.003.12
getTgroup163.21 0.66163.90
nbTestSH161.94 0.41162.38
plotDispersion6.540.006.54
rnbinomMV000
rowVars000
sSeq-package156.56 0.53157.15
sim0.610.000.61