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BioC 3.1: CHECK report for viper on moscato2

This page was generated on 2015-10-09 09:31:04 -0700 (Fri, 09 Oct 2015).

Package 1009/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
viper 1.4.0
Mariano J Alvarez
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/viper
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: viper
Version: 1.4.0
Command: rm -rf viper.buildbin-libdir viper.Rcheck && mkdir viper.buildbin-libdir viper.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=viper.buildbin-libdir viper_1.4.0.tar.gz >viper.Rcheck\00install.out 2>&1 && cp viper.Rcheck\00install.out viper-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=viper.buildbin-libdir --install="check:viper-install.out" --force-multiarch --no-vignettes --timings viper_1.4.0.tar.gz
StartedAt: 2015-10-09 07:03:46 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 07:39:59 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 2172.9 seconds
RetCode: 0
Status:  OK  
CheckDir: viper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf viper.buildbin-libdir viper.Rcheck && mkdir viper.buildbin-libdir viper.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=viper.buildbin-libdir viper_1.4.0.tar.gz >viper.Rcheck\00install.out 2>&1 && cp viper.Rcheck\00install.out viper-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=viper.buildbin-libdir --install="check:viper-install.out" --force-multiarch --no-vignettes --timings viper_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/viper.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 'viper/DESCRIPTION' ... OK
* this is package 'viper' version '1.4.0'
* 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 'viper' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [18m] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
shadow                 429.92  19.35  449.36
viperSignature-methods 198.13  14.82  212.98
bootstrapViper          99.41   9.14  108.56
msviperSynergy          81.84   0.55   82.38
msviperCombinatorial    71.43   0.57   72.03
msviper                 49.63   0.23   49.87
plot.msviper            45.53   0.17   45.85
ledge                    8.08   0.00    8.09
bootstrapTtest-methods   7.30   0.06    7.36
viperRPT                 7.07   0.06    7.13
ttestNull-methods        6.68   0.11    6.78
bootstrapmsviper         6.70   0.06    6.75
viper                    6.13   0.03    6.17
** running examples for arch 'x64' ... [17m] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
shadow                 443.22   7.64  450.90
viperSignature-methods 185.52  16.07  201.60
bootstrapViper          69.70   4.32   74.04
msviperSynergy          70.23   0.36   70.59
msviperCombinatorial    63.20   0.76   63.96
msviper                 43.85   0.73   44.58
plot.msviper            42.38   0.11   42.51
viperRPT                 6.94   0.05    6.99
ledge                    6.48   0.05    6.52
ttestNull-methods        6.34   0.12    6.47
viper                    6.12   0.11    6.22
bootstrapmsviper         5.96   0.05    6.00
bootstrapTtest-methods   5.75   0.11    5.85
* 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-3.1-bioc/meat/viper.Rcheck/00check.log'
for details.


viper.Rcheck/00install.out:


install for i386

* installing *source* package 'viper' ...
** R
** 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 'viper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'viper' as viper_1.4.0.zip
* DONE (viper)

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

nameusersystemelapsed
approxk2d0.170.000.18
aracne2regulon4.100.034.79
bootstrapTtest-methods7.300.067.36
bootstrapViper 99.41 9.14108.56
bootstrapmsviper6.700.066.75
distMode1.460.041.50
fcvarna1.640.011.66
filterCV-methods2.040.022.05
frcv1.910.011.92
frvarna1.870.061.94
integrateSignatures3.630.043.66
ledge8.080.008.09
msviper49.63 0.2349.87
msviperAnnot4.210.004.21
msviperClass2.840.022.86
msviperCombinatorial71.43 0.5772.03
msviperSynergy81.84 0.5582.38
plot.msviper45.53 0.1745.85
pruneRegulon1.520.031.54
rowTtest-methods2.960.033.00
scaleGroups1.640.001.64
shadow429.92 19.35449.36
signatureDistance4.540.034.57
ttestNull-methods6.680.116.78
viper6.130.036.17
viperRPT7.070.067.13
viperSignature-methods198.13 14.82212.98

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

nameusersystemelapsed
approxk2d0.190.010.20
aracne2regulon3.460.083.54
bootstrapTtest-methods5.750.115.85
bootstrapViper69.70 4.3274.04
bootstrapmsviper5.960.056.00
distMode1.240.001.25
fcvarna1.210.011.22
filterCV-methods1.290.031.32
frcv1.200.021.22
frvarna1.200.021.22
integrateSignatures2.790.012.81
ledge6.480.056.52
msviper43.85 0.7344.58
msviperAnnot4.120.004.12
msviperClass2.730.022.75
msviperCombinatorial63.20 0.7663.96
msviperSynergy70.23 0.3670.59
plot.msviper42.38 0.1142.51
pruneRegulon1.250.031.28
rowTtest-methods2.400.052.45
scaleGroups1.280.001.28
shadow443.22 7.64450.90
signatureDistance4.260.054.31
ttestNull-methods6.340.126.47
viper6.120.116.22
viperRPT6.940.056.99
viperSignature-methods185.52 16.07201.60