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BioC 2.13: CHECK report for sSeq on moscato1

This page was generated on 2014-04-05 09:51:21 -0700 (Sat, 05 Apr 2014).

Package 691/750HostnameOS / ArchBUILDCHECKBUILD BIN
sSeq 1.0.0
Danni Yu
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/sSeq
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: sSeq
Version: 1.0.0
Command: rm -rf sSeq.buildbin-libdir && mkdir sSeq.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sSeq.buildbin-libdir sSeq_1.0.0.tar.gz >sSeq-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=sSeq.buildbin-libdir --install="check:sSeq-install.out" --force-multiarch --no-vignettes --timings sSeq_1.0.0.tar.gz && mv sSeq.buildbin-libdir/* sSeq.Rcheck/ && rmdir sSeq.buildbin-libdir
StartedAt: 2014-04-05 06:59:06 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 07:15:32 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 986.3 seconds
RetCode: 0
Status:  OK  
CheckDir: sSeq.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/sSeq.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-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 '1.0.0'
* 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
* 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
'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.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'sSeq.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [496s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
nbTestSH       164.41   0.53  164.96
getTgroup      158.65   0.90  159.56
sSeq-package   156.53   0.50  157.03
plotDispersion   5.19   0.02    5.22
** running examples for arch 'x64' ... [454s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
nbTestSH       147.34   0.50  148.16
sSeq-package   146.34   0.40  146.81
getTgroup      140.62   0.91  141.59
plotDispersion   6.63   0.00    6.63
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-2.13-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_1.0.0.zip
* DONE (sSeq)

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

nameusersystemelapsed
Hammer2months0.070.000.08
Sultan0.080.000.07
Tuch0.070.000.06
countsTable0.030.000.03
drawMA_vol0.360.000.36
ecdfAUC0.010.000.02
equalSpace0.380.000.37
exactNBtest1000
getAdjustDisp0.360.000.36
getNormFactor0.030.000.03
getQ2.650.002.66
getT3.540.003.54
getTgroup158.65 0.90159.56
nbTestSH164.41 0.53164.96
plotDispersion5.190.025.22
rnbinomMV000
rowVars0.020.000.02
sSeq-package156.53 0.50157.03
sim0.70.00.7

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

nameusersystemelapsed
Hammer2months0.090.010.11
Sultan0.160.000.16
Tuch0.090.000.09
countsTable0.030.000.03
drawMA_vol0.390.020.41
ecdfAUC0.030.000.93
equalSpace0.480.010.50
exactNBtest10.020.000.02
getAdjustDisp0.440.000.43
getNormFactor0.030.000.04
getQ3.090.023.10
getT2.950.012.96
getTgroup140.62 0.91141.59
nbTestSH147.34 0.50148.16
plotDispersion6.630.006.63
rnbinomMV0.020.000.01
rowVars000
sSeq-package146.34 0.40146.81
sim0.710.000.71