Vinicius Jardim
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/BioNetStat |
| Branch: RELEASE_3_9 |
| Last Commit: 0ea1607 |
| Last Changed Date: 2019-09-11 14:40:08 -0400 (Wed, 11 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:41:17 -0400 (Wed, 16 Oct 2019).
| Package 165/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BioNetStat 1.4.3 Vinicius Jardim
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BioNetStat |
| Version: 1.4.3 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNetStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BioNetStat_1.4.3.tar.gz |
| StartedAt: 2019-10-16 02:16:19 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:21:52 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 333.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioNetStat.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNetStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BioNetStat_1.4.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BioNetStat.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BioNetStat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNetStat' version '1.4.3'
* package encoding: UTF-8
* 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 'BioNetStat' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
extdata 1.9Mb
shiny 1.6Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Namespaces in Imports field not imported from:
'BiocParallel' 'RColorBrewer' 'RJSONIO' 'ggplot2' 'knitr' 'pheatmap'
'plyr' 'stats' 'utils' 'whisker' 'yaml'
All declared Imports should be used.
Packages in Depends field not imported from:
'shiny' 'shinyBS'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
adjacencyMatrix : : no visible global function definition
for 'cor'
adjacencyMatrix : : no visible global function definition
for 'p.adjust'
betweennessCentralityTest: no visible global function definition for
'bplapply'
betweennessCentralityVertexTest: no visible global function definition
for 'bplapply'
betweennessEdgesCentrality: no visible global function definition for
'adjacencyMatrix1'
closenessCentralityTest: no visible global function definition for
'bplapply'
closenessCentralityVertexTest: no visible global function definition
for 'bplapply'
clusteringCoefficientTest : : no visible global function
definition for 'dist'
clusteringCoefficientTest : : : no visible
global function definition for 'dist'
clusteringCoefficientTest: no visible global function definition for
'bplapply'
clusteringCoefficientVertexTest: no visible global function definition
for 'bplapply'
degreeCentralityTest: no visible global function definition for
'bplapply'
degreeCentralityVertexTest: no visible global function definition for
'bplapply'
degreeDistributionTest: no visible global function definition for
'bplapply'
diffNetAnalysis: no visible binding for global variable 'expr'
diffNetAnalysis: no visible global function definition for 'p.adjust'
doLabels: no visible global function definition for 'read.csv'
edgeBetweennessEdgeTest: no visible global function definition for
'bplapply'
edgeBetweennessTest: no visible global function definition for
'bplapply'
edgesResInt : : no visible global function definition for
'dist'
eigenvectorCentralityTest: no visible global function definition for
'bplapply'
eigenvectorCentralityVertexTest: no visible global function definition
for 'bplapply'
gaussianDensity: no visible global function definition for 'bw.nrd0'
gaussianDensity: no visible global function definition for 'density'
pathPlot: no visible binding for global variable 'median'
readVarFile: no visible global function definition for 'read.table'
resInt : : no visible global function definition for 'dist'
retEdgesTable: no visible global function definition for 'p.adjust'
retTable: no visible global function definition for 'p.adjust'
spectralDistributionTest: no visible global function definition for
'bplapply'
spectralEntropyTest: no visible global function definition for
'bplapply'
var.list: no visible global function definition for 'aggregate'
Undefined global functions or variables:
adjacencyMatrix1 aggregate bplapply bw.nrd0 cor density dist expr
median p.adjust read.csv read.table
Consider adding
importFrom("stats", "aggregate", "bw.nrd0", "cor", "density", "dist",
"median", "p.adjust")
importFrom("utils", "read.csv", "read.table")
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
networkTest 14.14 0.25 14.39
centralityPathPlot 8.80 2.03 12.56
pathPlot 6.61 1.28 7.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
networkTest 12.46 0.06 12.52
centralityPathPlot 8.94 2.37 13.15
pathPlot 7.33 2.03 9.36
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/BioNetStat.Rcheck/00check.log'
for details.
BioNetStat.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/BioNetStat_1.4.3.tar.gz && rm -rf BioNetStat.buildbin-libdir && mkdir BioNetStat.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioNetStat.buildbin-libdir BioNetStat_1.4.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BioNetStat_1.4.3.zip && rm BioNetStat_1.4.3.tar.gz BioNetStat_1.4.3.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
100 2702k 100 2702k 0 0 28.9M 0 --:--:-- --:--:-- --:--:-- 31.4M
install for i386
* installing *source* package 'BioNetStat' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BioNetStat'
finding HTML links ... done
KLdegree html
KLspectrum html
adjacencyMatrix html
bnsDataTest html
centralityPathPlot html
diffNetAnalysis html
doLabels html
edgeTest html
labels html
nDegreeDensities html
nSpectralDensities html
networkFeature html
networkTest html
nodeScores html
nodeTest html
pathPlot html
readGmtFile html
readVarFile html
runBioNetStat html
varFile html
** building package indices
** installing vignettes
'BNS_tutorial_by_command_line.Rmd' using 'UTF-8'
'vignette.Rmd' using 'UTF-8'
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'BioNetStat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioNetStat' as BioNetStat_1.4.3.zip
* DONE (BioNetStat)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'BioNetStat' successfully unpacked and MD5 sums checked
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BioNetStat.Rcheck/examples_i386/BioNetStat-Ex.timings
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BioNetStat.Rcheck/examples_x64/BioNetStat-Ex.timings
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