BioC 3.3: CHECK report for ProCoNA on moscato2

Package: ProCoNA

Version: 1.10.0

Command: rm -rf ProCoNA.buildbin-libdir ProCoNA.Rcheck && mkdir ProCoNA.buildbin-libdir ProCoNA.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProCoNA.buildbin-libdir ProCoNA_1.10.0.tar.gz >ProCoNA.Rcheck\00install.out 2>&1 && cp ProCoNA.Rcheck\00install.out ProCoNA-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ProCoNA.buildbin-libdir --install="check:ProCoNA-install.out" --force-multiarch --no-vignettes --timings ProCoNA_1.10.0.tar.gz

StartedAt: 2016-10-13 07:32:07 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:39:46 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 459.3 seconds

RetCode: 0

Status:  OK

CheckDir: ProCoNA.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf ProCoNA.buildbin-libdir ProCoNA.Rcheck && mkdir ProCoNA.buildbin-libdir ProCoNA.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProCoNA.buildbin-libdir ProCoNA_1.10.0.tar.gz >ProCoNA.Rcheck\00install.out 2>&1 && cp ProCoNA.Rcheck\00install.out ProCoNA-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ProCoNA.buildbin-libdir --install="check:ProCoNA-install.out" --force-multiarch --no-vignettes --timings ProCoNA_1.10.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/ProCoNA.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.10.0'
* 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
  'as.dist'
bootstrapProconaNetwork: no visible global function definition for
  'cutreeDynamic'
buildProconaNetwork: no visible global function definition for
  'as.dist'
buildProconaNetwork: no visible global function definition for
  'cutreeDynamic'
MMvsPSallModules,proconaNet-matrix-numeric-character: no visible global
  function definition for 'pdf'
MMvsPSallModules,proconaNet-matrix-numeric-character: no visible global
  function definition for 'dev.off'
correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric:
  no visible global function definition for 'par'
correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric:
  no visible global function definition for 'pdf'
correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric:
  no visible global function definition for 'dev.off'
getFisherMatrix,character-character-numeric-numeric: no visible global
  function definition for 'fisher.test'
peptideConnectivityTest,proconaNet-data.frame-character-character-numeric:
  no visible global function definition for 't.test'
peptideCorrelationTest,matrix-data.frame-character-character: no
  visible global function definition for 't.test'
Undefined global functions or variables:
  as.dist cutreeDynamic dev.off fisher.test par pdf t.test
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "as.dist", "fisher.test", "t.test")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapProconaNetwork 6.62   0.13    6.74
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapProconaNetwork 8.44   0.09    8.64
peptideCorrelationTest  5.49   0.03    5.52
buildProconaNetwork     5.09   0.02    5.10
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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-3.3-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 1.51 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 1.51 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 1.51 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_1.10.0.zip
* DONE (ProCoNA)

name	user	system	elapsed
MMvsPS	0.50	0.02	0.55
MMvsPSallModules	0	0	0
accessors	0.39	0.01	0.40
bootstrapProconaNetwork	6.62	0.13	6.74
buildProconaNetwork	3.63	0.03	3.67
compareNetworksWithFishersExactTest	0	0	0
compareNetworksWithFishersExactTestProcona	0	0	0
corBootstrap	1.54	0.03	1.58
correlationWithPhenotypesHeatMap	2.25	0.02	2.27
getFisherMatrix	0.73	0.00	0.74
goStatTest	0	0	0
hclust	0	0	0
moduleMemberCorrelations	0.30	0.01	0.31
modulePhenotypeCorrelations	0.31	0.03	0.34
peptideConnectivityTest	1.58	0.00	1.58
peptideCorrelationTest	3.77	0.01	3.80
plotNet	0.38	0.00	0.37
ppiPermTest	0.64	0.00	0.64
printNet	0	0	0
subsetPeptideData	0.42	0.02	0.44
toPermTest	0.68	0.00	0.68
utri	0	0	0

name	user	system	elapsed
MMvsPS	0.52	0.00	0.53
MMvsPSallModules	0	0	0
accessors	0.36	0.02	0.37
bootstrapProconaNetwork	8.44	0.09	8.64
buildProconaNetwork	5.09	0.02	5.10
compareNetworksWithFishersExactTest	0	0	0
compareNetworksWithFishersExactTestProcona	0	0	0
corBootstrap	1.73	0.00	1.73
correlationWithPhenotypesHeatMap	2.79	0.01	2.83
getFisherMatrix	0.58	0.02	0.59
goStatTest	0	0	0
hclust	0	0	0
moduleMemberCorrelations	0.35	0.03	0.39
modulePhenotypeCorrelations	0.33	0.00	0.33
peptideConnectivityTest	1.84	0.01	1.86
peptideCorrelationTest	5.49	0.03	5.52
plotNet	0.33	0.02	0.34
ppiPermTest	0.47	0.02	0.48
printNet	0	0	0
subsetPeptideData	0.53	0.01	0.55
toPermTest	0.52	0.03	0.55
utri	0	0	0