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BioC 3.0: CHECK report for ProCoNA on perceval

This page was generated on 2015-04-10 09:58:42 -0700 (Fri, 10 Apr 2015).

Package 684/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProCoNA 1.4.1
David L Gibbs
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ProCoNA
Last Changed Rev: 97529 / Revision: 102249
Last Changed Date: 2014-12-10 10:13:08 -0800 (Wed, 10 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: ProCoNA
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ProCoNA_1.4.1.tar.gz
StartedAt: 2015-04-10 05:01:37 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:10:55 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 557.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ProCoNA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ProCoNA_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ProCoNA.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ProCoNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ProCoNA’ version ‘1.4.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ProCoNA’ can be installed ... [45s/48s] 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
* 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
bootstrapProconaNetwork: no visible global function definition for
  ‘cutreeDynamic’
buildProconaNetwork: no visible global function definition for
  ‘cutreeDynamic’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [54s/54s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
bootstrapProconaNetwork 10.522  0.100  10.623
peptideCorrelationTest   6.024  0.121   6.146
buildProconaNetwork      5.992  0.099   6.092
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [38s/39s]
 [39s/39s] OK
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ProCoNA.Rcheck/00check.log’
for details.

ProCoNA.Rcheck/00install.out:

* installing *source* package ‘ProCoNA’ ...
** R
** data
** inst
** preparing package for lazy loading
==========================================================================
*
*  Package WGCNA 1.46 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=8
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=8
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
==========================================================================
*
*  Package WGCNA 1.46 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=8
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=8
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


* DONE (ProCoNA)

ProCoNA.Rcheck/ProCoNA-Ex.timings:

nameusersystemelapsed
MMvsPS0.3240.0270.351
MMvsPSallModules0.0010.0000.001
accessors0.2130.0220.235
bootstrapProconaNetwork10.522 0.10010.623
buildProconaNetwork5.9920.0996.092
compareNetworksWithFishersExactTest0.0010.0000.001
compareNetworksWithFishersExactTestProcona0.0010.0010.001
corBootstrap1.8840.0231.908
correlationWithPhenotypesHeatMap2.4860.0382.532
getFisherMatrix0.2500.0150.266
goStatTest0.0010.0000.001
hclust0.0020.0000.002
moduleMemberCorrelations0.2310.0120.244
modulePhenotypeCorrelations0.2210.0130.234
peptideConnectivityTest1.3110.0431.355
peptideCorrelationTest6.0240.1216.146
plotNet0.2180.0240.250
ppiPermTest0.3360.0210.357
printNet0.0010.0000.001
subsetPeptideData0.3140.1390.453
toPermTest0.7790.0540.834
utri0.0000.0000.001