BioC 2.13: CHECK report for ProCoNA on moscato1

Package: ProCoNA

Version: 1.0.2

Command: rm -rf ProCoNA.buildbin-libdir && mkdir ProCoNA.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProCoNA.buildbin-libdir ProCoNA_1.0.2.tar.gz >ProCoNA-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=ProCoNA.buildbin-libdir --install="check:ProCoNA-install.out" --force-multiarch --no-vignettes --timings ProCoNA_1.0.2.tar.gz && mv ProCoNA.buildbin-libdir/* ProCoNA.Rcheck/ && rmdir ProCoNA.buildbin-libdir

StartedAt: 2014-04-05 05:58:41 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 06:06:33 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 471.3 seconds

RetCode: 0

Status:  OK

CheckDir: ProCoNA.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/ProCoNA.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.0.2'
* 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
* 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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'ProCoNA_Vignette.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [32s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapProconaNetwork  5.8   0.06    5.87
** running examples for arch 'x64' ... [38s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapProconaNetwork 7.47   0.04    7.52
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [21s]
 [21s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [27s]
 [27s] 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 were 2 notes.
See
  'D:/biocbld/bbs-2.13-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 1.34 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 1.34 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 1.34 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_1.0.2.zip
* DONE (ProCoNA)

name	user	system	elapsed
MMvsPS	0.35	0.00	0.35
MMvsPSallModules	0	0	0
accessors	0.27	0.02	0.28
bootstrapProconaNetwork	5.80	0.06	5.87
buildProconaNetwork	3.31	0.02	3.32
compareNetworksWithFishersExactTest	0	0	0
compareNetworksWithFishersExactTestProcona	0.01	0.00	0.02
corBootstrap	0.94	0.00	0.93
correlationWithPhenotypesHeatMap	1.18	0.00	1.20
getFisherMatrix	0.30	0.01	0.31
goStatTest	0	0	0
hclust	0	0	0
moduleMemberCorrelations	0.28	0.00	0.28
modulePhenotypeCorrelations	0.26	0.00	0.26
peptideConnectivityTest	1.78	0.00	1.78
peptideCorrelationTest	2.96	0.02	2.98
plotNet	0.28	0.00	0.28
ppiPermTest	0.59	0.01	0.60
printNet	0.02	0.00	0.02
subsetPeptideData	0.37	0.02	0.39
toPermTest	0.69	0.04	0.73
utri	0	0	0

name	user	system	elapsed
MMvsPS	0.31	0.01	0.33
MMvsPSallModules	0	0	0
accessors	0.25	0.02	0.26
bootstrapProconaNetwork	7.47	0.04	7.52
buildProconaNetwork	4.15	0.08	4.23
compareNetworksWithFishersExactTest	0	0	0
compareNetworksWithFishersExactTestProcona	0	0	0
corBootstrap	1.25	0.02	1.26
correlationWithPhenotypesHeatMap	1.79	0.01	1.82
getFisherMatrix	0.28	0.03	0.31
goStatTest	0.36	0.00	0.36
hclust	0.01	0.00	0.02
moduleMemberCorrelations	0.27	0.00	0.26
modulePhenotypeCorrelations	0.23	0.00	0.24
peptideConnectivityTest	1.95	0.01	1.97
peptideCorrelationTest	4.39	0.02	4.40
plotNet	0.25	0.00	0.25
ppiPermTest	0.38	0.00	0.38
printNet	0.01	0.00	0.01
subsetPeptideData	0.34	0.02	0.36
toPermTest	0.64	0.00	0.64
utri	0	0	0