David L Gibbs
| Snapshot Date: 2018-09-10 16:45:13 -0400 (Mon, 10 Sep 2018) |
| URL: https://git.bioconductor.org/packages/ProCoNA |
| Branch: master |
| Last Commit: f06425e |
| Last Changed Date: 2018-04-30 10:41:39 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2018-09-11 11:11:14 -0400 (Tue, 11 Sep 2018).
| Package 1156/1598 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ProCoNA 1.19.0 David L Gibbs
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ProCoNA |
| Version: 1.19.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ProCoNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ProCoNA_1.19.0.tar.gz |
| StartedAt: 2018-09-11 01:47:56 -0400 (Tue, 11 Sep 2018) |
| EndedAt: 2018-09-11 01:52:04 -0400 (Tue, 11 Sep 2018) |
| EllapsedTime: 248.3 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 --install=check:ProCoNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ProCoNA_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ProCoNA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.19.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
bootstrapProconaNetwork 7.324 0.083 7.417
correlationWithPhenotypesHeatMap 5.554 0.130 5.698
* 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-3.8-bioc/meat/ProCoNA.Rcheck/00check.log’
for details.
ProCoNA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ProCoNA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * 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=24 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=24 * * 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=24 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=24 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== * DONE (ProCoNA)
ProCoNA.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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=24
*
* To set the environment variable in linux bash shell, type
*
* export ALLOW_WGCNA_THREADS=24
*
* 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 2.7.4
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: 0.027"
[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: 0.005"
[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 01:51:59 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
14.871 1.127 16.005
ProCoNA.Rcheck/ProCoNA-Ex.timings
| name | user | system | elapsed | |
| MMvsPS | 0.262 | 0.015 | 0.278 | |
| MMvsPSallModules | 0.002 | 0.001 | 0.002 | |
| accessors | 0.762 | 0.016 | 0.782 | |
| bootstrapProconaNetwork | 7.324 | 0.083 | 7.417 | |
| buildProconaNetwork | 2.904 | 0.115 | 3.025 | |
| compareNetworksWithFishersExactTest | 0.002 | 0.001 | 0.002 | |
| compareNetworksWithFishersExactTestProcona | 0.001 | 0.000 | 0.001 | |
| corBootstrap | 1.527 | 0.022 | 1.551 | |
| correlationWithPhenotypesHeatMap | 5.554 | 0.130 | 5.698 | |
| getFisherMatrix | 0.355 | 0.018 | 0.375 | |
| goStatTest | 0.001 | 0.000 | 0.001 | |
| hclust | 0.003 | 0.000 | 0.004 | |
| moduleMemberCorrelations | 0.439 | 0.018 | 0.456 | |
| modulePhenotypeCorrelations | 0.231 | 0.013 | 0.244 | |
| peptideConnectivityTest | 1.794 | 0.102 | 1.898 | |
| peptideCorrelationTest | 3.076 | 0.088 | 3.177 | |
| plotNet | 0.223 | 0.015 | 0.239 | |
| ppiPermTest | 0.356 | 0.017 | 0.374 | |
| printNet | 0.002 | 0.000 | 0.002 | |
| subsetPeptideData | 0.402 | 0.154 | 0.556 | |
| toPermTest | 0.409 | 0.054 | 0.463 | |
| utri | 0.001 | 0.000 | 0.001 | |