BioC 2.14: CHECK report for ProCoNA on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ProCoNA_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/ProCoNA.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ProCoNA’ can be installed ... [49s/50s] 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 ... NOTE
Packages in Depends field not imported from:
  ‘MSnbase’ ‘WGCNA’
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [60s/61s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
bootstrapProconaNetwork 9.709  0.105   9.860
peptideCorrelationTest  6.103  0.108   6.297
buildProconaNetwork     5.841  0.095   5.970
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [43s/44s]
 [44s/44s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/ProCoNA.Rcheck/00check.log’
for details.

* installing *source* package ‘ProCoNA’ ...
** R
** data
** inst
** preparing package for lazy loading
==========================================================================
*
*  Package WGCNA 1.41.1 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=16
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=16
*
*     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 1.41.1 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=16
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=16
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


* DONE (ProCoNA)

name	user	system	elapsed
MMvsPS	0.481	0.027	0.514
MMvsPSallModules	0.002	0.000	0.001
accessors	0.344	0.017	0.369
bootstrapProconaNetwork	9.709	0.105	9.860
buildProconaNetwork	5.841	0.095	5.970
compareNetworksWithFishersExactTest	0.001	0.000	0.001
compareNetworksWithFishersExactTestProcona	0.002	0.001	0.002
corBootstrap	1.735	0.028	1.772
correlationWithPhenotypesHeatMap	2.589	0.044	2.644
getFisherMatrix	0.458	0.020	0.479
goStatTest	0.001	0.000	0.001
hclust	0.576	0.007	0.584
moduleMemberCorrelations	0.363	0.022	0.388
modulePhenotypeCorrelations	0.341	0.016	0.360
peptideConnectivityTest	3.183	0.140	3.350
peptideCorrelationTest	6.103	0.108	6.297
plotNet	0.353	0.026	0.418
ppiPermTest	0.562	0.024	0.592
printNet	0.001	0.000	0.001
subsetPeptideData	0.487	0.166	0.654
toPermTest	1.145	0.057	1.204
utri	0.001	0.000	0.001

BioC 2.14: CHECK report for ProCoNA on petty

Summary

Command output