BioC 3.1: CHECK report for ProCoNA on moscato2

Package: ProCoNA

Version: 1.6.0

Command: rm -rf ProCoNA.buildbin-libdir ProCoNA.Rcheck && mkdir ProCoNA.buildbin-libdir ProCoNA.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProCoNA.buildbin-libdir ProCoNA_1.6.0.tar.gz >ProCoNA.Rcheck\00install.out 2>&1 && cp ProCoNA.Rcheck\00install.out ProCoNA-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ProCoNA.buildbin-libdir --install="check:ProCoNA-install.out" --force-multiarch --no-vignettes --timings ProCoNA_1.6.0.tar.gz

StartedAt: 2015-10-09 04:59:18 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:06:09 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 410.6 seconds

RetCode: 0

Status:  OK

CheckDir: ProCoNA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ProCoNA.buildbin-libdir ProCoNA.Rcheck && mkdir ProCoNA.buildbin-libdir ProCoNA.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProCoNA.buildbin-libdir ProCoNA_1.6.0.tar.gz >ProCoNA.Rcheck\00install.out 2>&1 && cp ProCoNA.Rcheck\00install.out ProCoNA-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ProCoNA.buildbin-libdir --install="check:ProCoNA-install.out" --force-multiarch --no-vignettes --timings ProCoNA_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/ProCoNA.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 'ProCoNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ProCoNA' version '1.6.0'
* 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 ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* 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 ... 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 'exprs'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [32s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapProconaNetwork  5.9   0.06    5.98
** running examples for arch 'x64' ... [31s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapProconaNetwork 5.98   0.03    6.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [17s]
 [18s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [19s]
 [19s] 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

Status: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/ProCoNA.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ProCoNA' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
==========================================================================
*
*  Package WGCNA 1.47 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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
==========================================================================
*
*  Package WGCNA 1.47 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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
==========================================================================
*
*  Package WGCNA 1.47 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_1.6.0.zip
* DONE (ProCoNA)

name	user	system	elapsed
MMvsPS	0.38	0.00	0.38
MMvsPSallModules	0	0	0
accessors	0.26	0.00	0.26
bootstrapProconaNetwork	5.90	0.06	5.98
buildProconaNetwork	3.70	0.04	3.73
compareNetworksWithFishersExactTest	0	0	0
compareNetworksWithFishersExactTestProcona	0	0	0
corBootstrap	1.28	0.00	1.28
correlationWithPhenotypesHeatMap	0.87	0.01	0.90
getFisherMatrix	0.76	0.02	0.78
goStatTest	0	0	0
hclust	0	0	0
moduleMemberCorrelations	0.36	0.01	0.38
modulePhenotypeCorrelations	0.36	0.00	0.35
peptideConnectivityTest	1.65	0.00	1.66
peptideCorrelationTest	3.86	0.02	3.87
plotNet	0.4	0.0	0.4
ppiPermTest	0.39	0.01	0.41
printNet	0	0	0
subsetPeptideData	0.33	0.08	0.40
toPermTest	0.56	0.02	0.58
utri	0	0	0

name	user	system	elapsed
MMvsPS	0.35	0.00	0.36
MMvsPSallModules	0	0	0
accessors	0.23	0.00	0.24
bootstrapProconaNetwork	5.98	0.03	6.02
buildProconaNetwork	3.74	0.00	4.07
compareNetworksWithFishersExactTest	0	0	0
compareNetworksWithFishersExactTestProcona	0	0	0
corBootstrap	1.22	0.01	1.23
correlationWithPhenotypesHeatMap	0.95	0.00	1.52
getFisherMatrix	0.72	0.00	0.71
goStatTest	0	0	0
hclust	0	0	0
moduleMemberCorrelations	0.24	0.02	0.25
modulePhenotypeCorrelations	0.23	0.00	0.23
peptideConnectivityTest	1.14	0.00	1.14
peptideCorrelationTest	3.82	0.05	3.87
plotNet	0.22	0.01	0.24
ppiPermTest	0.34	0.00	0.34
printNet	0	0	0
subsetPeptideData	0.36	0.00	0.36
toPermTest	0.5	0.0	0.5
utri	0	0	0