BioC 2.14: CHECK report for ProCoNA on moscato2

Package: ProCoNA

Version: 1.2.0

Command: rm -rf ProCoNA.buildbin-libdir && mkdir ProCoNA.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProCoNA.buildbin-libdir ProCoNA_1.2.0.tar.gz >ProCoNA-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=ProCoNA.buildbin-libdir --install="check:ProCoNA-install.out" --force-multiarch --no-vignettes --timings ProCoNA_1.2.0.tar.gz

StartedAt: 2014-10-08 04:01:53 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 04:09:33 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 459.9 seconds

RetCode: 0

Status:  OK

CheckDir: ProCoNA.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf ProCoNA.buildbin-libdir && mkdir ProCoNA.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProCoNA.buildbin-libdir ProCoNA_1.2.0.tar.gz >ProCoNA-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=ProCoNA.buildbin-libdir --install="check:ProCoNA-install.out" --force-multiarch --no-vignettes --timings ProCoNA_1.2.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/ProCoNA.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'ProCoNA' 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [33s] OK
** running examples for arch 'x64' ... [39s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapProconaNetwork 6.64   0.08    6.72
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [23s]
 [24s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [23s]
 [23s] 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
  'E:/biocbld/bbs-2.14-bioc/meat/ProCoNA.Rcheck/00check.log'
for details.

install for i386

* 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.
*
==========================================================================



install for x64

* installing *source* package 'ProCoNA' ...
** 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.
*
==========================================================================


* MD5 sums
packaged installation of 'ProCoNA' as ProCoNA_1.2.0.zip
* DONE (ProCoNA)

name	user	system	elapsed
MMvsPS	0.34	0.00	0.35
MMvsPSallModules	0	0	0
accessors	0.25	0.01	0.26
bootstrapProconaNetwork	4.91	0.05	4.96
buildProconaNetwork	3.12	0.03	3.15
compareNetworksWithFishersExactTest	0	0	0
compareNetworksWithFishersExactTestProcona	0	0	0
corBootstrap	1.06	0.00	1.06
correlationWithPhenotypesHeatMap	1.42	0.02	1.45
getFisherMatrix	0.37	0.00	0.38
goStatTest	0	0	0
hclust	0	0	0
moduleMemberCorrelations	0.72	0.00	0.72
modulePhenotypeCorrelations	0.36	0.01	0.37
peptideConnectivityTest	2.46	0.05	2.52
peptideCorrelationTest	3.65	0.03	3.68
plotNet	0.37	0.00	0.38
ppiPermTest	0.53	0.03	0.56
printNet	0	0	0
subsetPeptideData	0.53	0.08	0.61
toPermTest	0.86	0.00	0.85
utri	0	0	0

name	user	system	elapsed
MMvsPS	0.47	0.01	0.48
MMvsPSallModules	0	0	0
accessors	0.29	0.00	0.28
bootstrapProconaNetwork	6.64	0.08	6.72
buildProconaNetwork	4.23	0.06	4.29
compareNetworksWithFishersExactTest	0	0	0
compareNetworksWithFishersExactTestProcona	0	0	0
corBootstrap	1.28	0.02	1.30
correlationWithPhenotypesHeatMap	1.89	0.00	1.90
getFisherMatrix	0.29	0.00	0.30
goStatTest	0	0	0
hclust	0	0	0
moduleMemberCorrelations	0.25	0.00	0.25
modulePhenotypeCorrelations	0.22	0.02	0.24
peptideConnectivityTest	2.18	0.01	2.20
peptideCorrelationTest	3.56	0.02	3.57
plotNet	0.23	0.01	0.25
ppiPermTest	0.34	0.02	0.36
printNet	0	0	0
subsetPeptideData	0.32	0.03	0.36
toPermTest	0.65	0.00	0.65
utri	0	0	0