Package: ProCoNA

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ProCoNA_1.16.0.tar.gz

StartedAt: 2018-04-12 07:52:57 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 07:57:18 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 260.3 seconds

RetCode: 0

Status:  OK

CheckDir: ProCoNA.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ProCoNA_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ProCoNA.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ProCoNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ProCoNA’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
correlationWithPhenotypesHeatMap 5.986  0.131   6.188
bootstrapProconaNetwork          5.831  0.062   5.967
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/ProCoNA.Rcheck/00check.log’
for details.

* installing *source* package ‘ProCoNA’ ...
** R
** data
** inst
** preparing 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=8
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=8
*
*     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 1.63 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=8
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=8
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


* DONE (ProCoNA)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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=8
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=8
*
*     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, cbind, colMeans, colSums, colnames, 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 2.4.2 
  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:  0.034"
[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 -- Thu Apr 12 07:57:13 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 
 15.969   0.588  17.168 

name	user	system	elapsed
MMvsPS	0.353	0.015	0.379
MMvsPSallModules	0.001	0.000	0.001
accessors	0.181	0.008	0.191
bootstrapProconaNetwork	5.831	0.062	5.967
buildProconaNetwork	3.094	0.091	3.225
compareNetworksWithFishersExactTest	0.001	0.000	0.001
compareNetworksWithFishersExactTestProcona	0.000	0.000	0.001
corBootstrap	1.072	0.015	1.102
correlationWithPhenotypesHeatMap	5.986	0.131	6.188
getFisherMatrix	0.308	0.014	0.324
goStatTest	0.001	0.001	0.001
hclust	0.001	0.000	0.002
moduleMemberCorrelations	0.206	0.011	0.220
modulePhenotypeCorrelations	0.209	0.010	0.232
peptideConnectivityTest	1.809	0.157	1.993
peptideCorrelationTest	2.491	0.083	2.616
plotNet	0.188	0.010	0.198
ppiPermTest	0.250	0.010	0.261
printNet	0	0	0
subsetPeptideData	0.293	0.104	0.406
toPermTest	0.404	0.046	0.459
utri	0.001	0.000	0.001