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BioC 3.1: CHECK report for graphite on moscato2

This page was generated on 2015-10-09 09:29:24 -0700 (Fri, 09 Oct 2015).

Package 437/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.14.1
Gabriele Sales
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/graphite
Last Changed Rev: 105077 / Revision: 109384
Last Changed Date: 2015-06-17 07:05:48 -0700 (Wed, 17 Jun 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: graphite
Version: 1.14.1
Command: rm -rf graphite.buildbin-libdir graphite.Rcheck && mkdir graphite.buildbin-libdir graphite.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=graphite.buildbin-libdir graphite_1.14.1.tar.gz >graphite.Rcheck\00install.out 2>&1 && cp graphite.Rcheck\00install.out graphite-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=graphite.buildbin-libdir --install="check:graphite-install.out" --force-multiarch --no-vignettes --timings graphite_1.14.1.tar.gz
StartedAt: 2015-10-09 02:36:28 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:46:34 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 605.7 seconds
RetCode: 0
Status:  OK  
CheckDir: graphite.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf graphite.buildbin-libdir graphite.Rcheck && mkdir graphite.buildbin-libdir graphite.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=graphite.buildbin-libdir graphite_1.14.1.tar.gz >graphite.Rcheck\00install.out 2>&1 && cp graphite.Rcheck\00install.out graphite-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=graphite.buildbin-libdir --install="check:graphite-install.out" --force-multiarch --no-vignettes --timings graphite_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/graphite.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 'graphite/DESCRIPTION' ... OK
* this is package 'graphite' version '1.14.1'
* 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 'graphite' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
runTopologyGSA,list : .local: no visible binding for global variable
  'expr'
runTopologyGSA,list : .local: no visible binding for global variable
  'classes'
* 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 ... NOTE
  Note: found 32 marked UTF-8 strings
* 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' ... [215s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
runClipperMulti 178.07   0.08  178.15
runClipper       18.00   0.20   18.78
runSPIA           4.99   0.02    5.17
** running examples for arch 'x64' ... [223s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
runClipperMulti 178.56   0.11  178.67
runClipper       22.04   0.11   22.26
runSPIA           6.66   0.07    6.74
* 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: 4 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/graphite.Rcheck/00check.log'
for details.


graphite.Rcheck/00install.out:


install for i386

* installing *source* package 'graphite' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Creating a generic function for 'plot' from package 'graphics' in package 'graphite'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'graphite' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'graphite' as graphite_1.14.1.zip
* DONE (graphite)

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

nameusersystemelapsed
as.list.DeprecatedPathwayList1.510.111.63
as.list.PathwayList0.140.000.14
convertIdentifiers0.670.010.68
cytoscapePlot000
pathwayDatabases0.010.000.01
pathwayGraph0.030.000.03
pathways000
runClipper18.00 0.2018.78
runClipperMulti178.07 0.08178.15
runDEGraph1.620.191.96
runDEGraphMulti0.670.010.84
runSPIA4.990.025.17
runTopologyGSA1.070.001.11
runTopologyGSAMulti0.990.021.00

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

nameusersystemelapsed
as.list.DeprecatedPathwayList1.820.161.98
as.list.PathwayList0.220.000.22
convertIdentifiers1.030.031.06
cytoscapePlot000
pathwayDatabases0.050.000.05
pathwayGraph0.050.000.05
pathways000
runClipper22.04 0.1122.26
runClipperMulti178.56 0.11178.67
runDEGraph2.080.232.30
runDEGraphMulti0.920.020.94
runSPIA6.660.076.74
runTopologyGSA1.730.001.89
runTopologyGSAMulti1.030.021.04