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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-09-11 10:44:41 -0400 (Tue, 11 Sep 2018).
| Package 1128/1560 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ProCoNA 1.18.0 David L Gibbs
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
##############################################################################
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###
### 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
###
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* 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.
ProCoNA.Rcheck/00install.out
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###
### 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
###
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% 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
|
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
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ProCoNA.Rcheck/examples_i386/ProCoNA-Ex.timings
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ProCoNA.Rcheck/examples_x64/ProCoNA-Ex.timings
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