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CHECK report for ProCoNA on tokay2

This page was generated on 2018-09-11 10:44:41 -0400 (Tue, 11 Sep 2018).

Package 1128/1560HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProCoNA 1.18.0
David L Gibbs
Snapshot Date: 2018-09-10 16:45:09 -0400 (Mon, 10 Sep 2018)
URL: https://git.bioconductor.org/packages/ProCoNA
Branch: RELEASE_3_7
Last Commit: b9b2d27
Last Changed Date: 2018-04-30 10:35:31 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ProCoNA
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ProCoNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ProCoNA_1.18.0.tar.gz
StartedAt: 2018-09-11 03:55:02 -0400 (Tue, 11 Sep 2018)
EndedAt: 2018-09-11 04:00:57 -0400 (Tue, 11 Sep 2018)
EllapsedTime: 355.3 seconds
RetCode: 0
Status:  OK  
CheckDir: ProCoNA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ProCoNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ProCoNA_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ProCoNA.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.18.0'
* 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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
bootstrapProconaNetwork          8.28   0.09    8.52
correlationWithPhenotypesHeatMap 4.73   0.37    5.27
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
bootstrapProconaNetwork          9.28   0.09    9.48
correlationWithPhenotypesHeatMap 5.69   0.03    5.71
* 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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/ProCoNA.Rcheck/00check.log'
for details.



Installation output

ProCoNA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ProCoNA_1.18.0.tar.gz && rm -rf ProCoNA.buildbin-libdir && mkdir ProCoNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ProCoNA.buildbin-libdir ProCoNA_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ProCoNA_1.18.0.zip && rm ProCoNA_1.18.0.tar.gz ProCoNA_1.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2414k  100 2414k    0     0  5767k      0 --:--:-- --:--:-- --:--:-- 5846k

install for i386

* installing *source* package 'ProCoNA' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
==========================================================================
*
*  Package WGCNA 1.63 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=20
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=20
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


** help
*** installing help indices
  converting help for package 'ProCoNA'
    finding HTML links ... done
    MMvsPS                                  html  
    MMvsPSallModules                        html  
    ProCoNA_Data                            html  
    accessors                               html  
    bootstrapProconaNetwork                 html  
    buildProconaNetwork                     html  
    c2i                                     html  
    compareNetworksWithFishersExactTest     html  
    compareNetworksWithFishersExactTestProcona
                                            html  
    corBootstrap                            html  
    correlationWithPhenotypesHeatMap        html  
    getFisherMatrix                         html  
    getPeptideNAs                           html  
    goStatTest                              html  
    hclust                                  html  
    i2c                                     html  
    i2col                                   html  
    moduleMemberCorrelations                html  
    modulePhenotypeCorrelations             html  
    orderMatrixIndex                        html  
    peptideConnectivityTest                 html  
    peptideCorrelationTest                  html  
    plotNet                                 html  
    ppiPermTest                             html  
    printNet                                html  
    procona-package                         html  
    proconaNet-class                        html  
    proconaVersionFun                       html  
    runningStats                            html  
    subsetModCors                           html  
    subsetPeptideData                       html  
    toPermTest                              html  
    utri                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
==========================================================================
*
*  Package WGCNA 1.63 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=20
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=20
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


In R CMD INSTALL

install for x64

* installing *source* package 'ProCoNA' ...
** testing if installed package can be loaded
==========================================================================
*
*  Package WGCNA 1.63 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=20
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=20
*
*     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_1.18.0.zip
* DONE (ProCoNA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ProCoNA' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

ProCoNA.Rcheck/tests_i386/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("ProCoNA") || stop("unable to load MyPackage")
Loading required package: ProCoNA
Loading required package: WGCNA
Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust


==========================================================================
*
*  Package WGCNA 1.63 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=20
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=20
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================



Attaching package: 'WGCNA'

The following object is masked from 'package:stats':

    cor

Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 2.6.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws

Loading required package: flashClust

Attaching package: 'flashClust'

The following object is masked from 'package:fastcluster':

    hclust

The following object is masked from 'package:stats':

    hclust


Attaching package: 'ProCoNA'

The following object is masked from 'package:ProtGenerics':

    peptides

The following object is masked from 'package:Biobase':

    samples

[1] TRUE
> BiocGenerics:::testPackage("ProCoNA")
Constructing New ProCoNA Network Object
Using power: 1

Computing adjacency
Computing TOM
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
Clustering
 ..cutHeight not given, setting it to 0.461  ===>  99% of the (truncated) height range in dendro.
 ..done.

  0   1   2   3   4 
  4 174 127  92  77 
Merging modules
 mergeCloseModules: Merging modules whose distance is less than 0.1
   .. will look for grey label ME0
   multiSetMEs: Calculating module MEs.
     Working on set 1 ...
     moduleEigengenes : Working on ME for module 1
     moduleEigengenes : Working on ME for module 2
     moduleEigengenes : Working on ME for module 3
     moduleEigengenes : Working on ME for module 4
    Changing original colors:
        1 to  1
        2 to  2
        3 to  3
        4 to  4
   Calculating new MEs...
   multiSetMEs: Calculating module MEs.
     Working on set 1 ...
     moduleEigengenes : Working on ME for module 0
     moduleEigengenes : Working on ME for module 1
     moduleEigengenes : Working on ME for module 2
     moduleEigengenes : Working on ME for module 3
     moduleEigengenes : Working on ME for module 4
Topological Overlap Permutation Test On Modules
Permuting module: 1

   dim of TOM: 174174

Permuting module: 2

   dim of TOM: 127127

Permuting module: 3

   dim of TOM: 9292

Permuting module: 4

   dim of TOM: 7777

DONE!
[1] "module analysis:  1"
[1] "probes that pass Kme and are within module: 122"
[1] "of these, 26 are relevant to our PI network..."
[1] "found  4  in the first column"
[1] "found  3  in the second column"
[1] "1  observed edges"
[1] "pvalue:  0.023"
[1] "*****"
[1] "module analysis:  2"
[1] "probes that pass Kme and are within module: 123"
[1] "of these, 65 are relevant to our PI network..."
[1] "found  6  in the first column"
[1] "found  8  in the second column"
[1] "6  observed edges"
[1] "pvalue:  0"
[1] "*****"
[1] "module analysis:  3"
[1] "probes that pass Kme and are within module: 92"
[1] "of these, 0 are relevant to our PI network..."
[1] "ERROR: no probes meet Kme threshold within module"
[1] "module analysis:  0"
[1] "probes that pass Kme and are within module: 4"
[1] "of these, 0 are relevant to our PI network..."
[1] "ERROR: no probes meet Kme threshold within module"
[1] "module analysis:  4"
[1] "probes that pass Kme and are within module: 74"
[1] "of these, 8 are relevant to our PI network..."
[1] "found  2  in the first column"
[1] "found  1  in the second column"
[1] "1  observed edges"
[1] "pvalue:  0.006"
[1] "*****"
Permuting module: 1

   dim of TOM: 100100

Permuting module: 2

   dim of TOM: 100100

Permuting module: 3

   dim of TOM: 100100

Permuting module: 4

   dim of TOM: 100100

Permuting module: 5

   dim of TOM: 100100



RUNIT TEST PROTOCOL -- Tue Sep 11 04:00:32 2018 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ProCoNA RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  13.51    0.93   14.59 

ProCoNA.Rcheck/tests_x64/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("ProCoNA") || stop("unable to load MyPackage")
Loading required package: ProCoNA
Loading required package: WGCNA
Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust


==========================================================================
*
*  Package WGCNA 1.63 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=20
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=20
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================



Attaching package: 'WGCNA'

The following object is masked from 'package:stats':

    cor

Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 2.6.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws

Loading required package: flashClust

Attaching package: 'flashClust'

The following object is masked from 'package:fastcluster':

    hclust

The following object is masked from 'package:stats':

    hclust


Attaching package: 'ProCoNA'

The following object is masked from 'package:ProtGenerics':

    peptides

The following object is masked from 'package:Biobase':

    samples

[1] TRUE
> BiocGenerics:::testPackage("ProCoNA")
Constructing New ProCoNA Network Object
Using power: 1

Computing adjacency
Computing TOM
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
Clustering
 ..cutHeight not given, setting it to 0.461  ===>  99% of the (truncated) height range in dendro.
 ..done.

  0   1   2   3   4 
  4 174 127  92  77 
Merging modules
 mergeCloseModules: Merging modules whose distance is less than 0.1
   .. will look for grey label ME0
   multiSetMEs: Calculating module MEs.
     Working on set 1 ...
     moduleEigengenes : Working on ME for module 1
     moduleEigengenes : Working on ME for module 2
     moduleEigengenes : Working on ME for module 3
     moduleEigengenes : Working on ME for module 4
    Changing original colors:
        1 to  1
        2 to  2
        3 to  3
        4 to  4
   Calculating new MEs...
   multiSetMEs: Calculating module MEs.
     Working on set 1 ...
     moduleEigengenes : Working on ME for module 0
     moduleEigengenes : Working on ME for module 1
     moduleEigengenes : Working on ME for module 2
     moduleEigengenes : Working on ME for module 3
     moduleEigengenes : Working on ME for module 4
Topological Overlap Permutation Test On Modules
Permuting module: 1

   dim of TOM: 174174

Permuting module: 2

   dim of TOM: 127127

Permuting module: 3

   dim of TOM: 9292

Permuting module: 4

   dim of TOM: 7777

DONE!
[1] "module analysis:  1"
[1] "probes that pass Kme and are within module: 122"
[1] "of these, 26 are relevant to our PI network..."
[1] "found  4  in the first column"
[1] "found  3  in the second column"
[1] "1  observed edges"
[1] "pvalue:  0.035"
[1] "*****"
[1] "module analysis:  2"
[1] "probes that pass Kme and are within module: 123"
[1] "of these, 65 are relevant to our PI network..."
[1] "found  6  in the first column"
[1] "found  8  in the second column"
[1] "6  observed edges"
[1] "pvalue:  0"
[1] "*****"
[1] "module analysis:  3"
[1] "probes that pass Kme and are within module: 92"
[1] "of these, 0 are relevant to our PI network..."
[1] "ERROR: no probes meet Kme threshold within module"
[1] "module analysis:  0"
[1] "probes that pass Kme and are within module: 4"
[1] "of these, 0 are relevant to our PI network..."
[1] "ERROR: no probes meet Kme threshold within module"
[1] "module analysis:  4"
[1] "probes that pass Kme and are within module: 74"
[1] "of these, 8 are relevant to our PI network..."
[1] "found  2  in the first column"
[1] "found  1  in the second column"
[1] "1  observed edges"
[1] "pvalue:  0.01"
[1] "*****"
Permuting module: 1

   dim of TOM: 100100

Permuting module: 2

   dim of TOM: 100100

Permuting module: 3

   dim of TOM: 100100

Permuting module: 4

   dim of TOM: 100100

Permuting module: 5

   dim of TOM: 100100



RUNIT TEST PROTOCOL -- Tue Sep 11 04:00:52 2018 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ProCoNA RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  19.09    0.59   19.81 

Example timings

ProCoNA.Rcheck/examples_i386/ProCoNA-Ex.timings

nameusersystemelapsed
MMvsPS0.470.060.63
MMvsPSallModules000
accessors0.300.020.31
bootstrapProconaNetwork8.280.098.52
buildProconaNetwork3.300.143.44
compareNetworksWithFishersExactTest000
compareNetworksWithFishersExactTestProcona000
corBootstrap1.710.021.72
correlationWithPhenotypesHeatMap4.730.375.27
getFisherMatrix0.620.060.69
goStatTest000
hclust000
moduleMemberCorrelations0.360.000.36
modulePhenotypeCorrelations0.280.000.28
peptideConnectivityTest1.550.181.72
peptideCorrelationTest2.780.002.78
plotNet0.370.010.39
ppiPermTest0.390.020.40
printNet000
subsetPeptideData0.390.060.46
toPermTest0.460.000.45
utri000

ProCoNA.Rcheck/examples_x64/ProCoNA-Ex.timings

nameusersystemelapsed
MMvsPS0.210.040.26
MMvsPSallModules000
accessors0.190.020.20
bootstrapProconaNetwork9.280.099.48
buildProconaNetwork3.050.053.10
compareNetworksWithFishersExactTest000
compareNetworksWithFishersExactTestProcona000
corBootstrap1.790.001.80
correlationWithPhenotypesHeatMap5.690.035.71
getFisherMatrix0.270.030.32
goStatTest000
hclust000
moduleMemberCorrelations0.210.000.22
modulePhenotypeCorrelations0.190.030.21
peptideConnectivityTest0.830.020.85
peptideCorrelationTest3.450.003.45
plotNet0.250.030.28
ppiPermTest0.440.010.46
printNet000
subsetPeptideData0.360.070.42
toPermTest0.330.000.34
utri000