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BioC 3.3: CHECK report for SigCheck on moscato2

This page was generated on 2016-10-13 12:53:15 -0700 (Thu, 13 Oct 2016).

Package 1068/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SigCheck 2.4.0
Rory Stark
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/SigCheck
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: SigCheck
Version: 2.4.0
Command: rm -rf SigCheck.buildbin-libdir SigCheck.Rcheck && mkdir SigCheck.buildbin-libdir SigCheck.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SigCheck.buildbin-libdir SigCheck_2.4.0.tar.gz >SigCheck.Rcheck\00install.out 2>&1 && cp SigCheck.Rcheck\00install.out SigCheck-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=SigCheck.buildbin-libdir --install="check:SigCheck-install.out" --force-multiarch --no-vignettes --timings SigCheck_2.4.0.tar.gz
StartedAt: 2016-10-13 08:55:21 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 09:10:22 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 901.2 seconds
RetCode: 0
Status:  OK  
CheckDir: SigCheck.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SigCheck.buildbin-libdir SigCheck.Rcheck && mkdir SigCheck.buildbin-libdir SigCheck.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SigCheck.buildbin-libdir SigCheck_2.4.0.tar.gz >SigCheck.Rcheck\00install.out 2>&1 && cp SigCheck.Rcheck\00install.out SigCheck-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=SigCheck.buildbin-libdir --install="check:SigCheck-install.out" --force-multiarch --no-vignettes --timings SigCheck_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/SigCheck.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 'SigCheck/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SigCheck' version '2.4.0'
* 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 'SigCheck' 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
sigCheckKnown: no visible binding for global variable 'knownSignatures'
Undefined global functions or variables:
  knownSignatures
* 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
sigCheckAll      151.25   5.39  156.64
sigCheckKnown     73.13   2.80   75.92
sigCheckPlot      19.63   0.76   20.38
sigCheckPermuted  19.20   0.35   19.55
sigCheck          15.30   0.57   18.40
sigCheckRandom    13.55   0.42   13.98
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
sigCheckAll      142.25   6.11  148.39
sigCheckKnown     80.38   2.97   83.35
sigCheckPlot      22.22   0.91   23.12
sigCheckPermuted  19.81   0.85   20.68
sigCheckRandom    16.82   0.65   17.48
sigCheck          16.46   0.42   16.88
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/SigCheck.Rcheck/00check.log'
for details.


SigCheck.Rcheck/00install.out:


install for i386

* installing *source* package 'SigCheck' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'signature' in package 'SigCheck'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'SigCheck' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SigCheck' as SigCheck_2.4.0.zip
* DONE (SigCheck)

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

nameusersystemelapsed
SigCheckObject-class000
classifyResults0.030.020.05
knownSignatures0.080.000.08
nkiResults0.030.010.04
sigCheck15.30 0.5718.40
sigCheckAll151.25 5.39156.64
sigCheckKnown73.13 2.8075.92
sigCheckPermuted19.20 0.3519.55
sigCheckPlot19.63 0.7620.38
sigCheckRandom13.55 0.4213.98

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

nameusersystemelapsed
SigCheckObject-class000
classifyResults0.050.000.04
knownSignatures0.020.050.07
nkiResults0.060.020.07
sigCheck16.46 0.4216.88
sigCheckAll142.25 6.11148.39
sigCheckKnown80.38 2.9783.35
sigCheckPermuted19.81 0.8520.68
sigCheckPlot22.22 0.9123.12
sigCheckRandom16.82 0.6517.48