Panos Balomenos
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CHRONOS |
| Branch: RELEASE_3_9 |
| Last Commit: 6fbd5ff |
| Last Changed Date: 2019-05-02 11:54:02 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:35:49 -0400 (Wed, 16 Oct 2019).
| Package 276/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CHRONOS 1.12.0 Panos Balomenos
| 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: CHRONOS |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CHRONOS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CHRONOS_1.12.0.tar.gz |
| StartedAt: 2019-10-16 02:40:24 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:43:42 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 198.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CHRONOS.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CHRONOS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CHRONOS_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CHRONOS.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 'CHRONOS/DESCRIPTION' ... OK * this is package 'CHRONOS' version '1.12.0' * 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 'CHRONOS' can be installed ... OK * checking installed package size ... OK * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * 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: OK
CHRONOS.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/CHRONOS_1.12.0.tar.gz && rm -rf CHRONOS.buildbin-libdir && mkdir CHRONOS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CHRONOS.buildbin-libdir CHRONOS_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CHRONOS_1.12.0.zip && rm CHRONOS_1.12.0.tar.gz CHRONOS_1.12.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
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install for i386
* installing *source* package 'CHRONOS' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CHRONOS'
finding HTML links ... done
CHRONOSrun html
convertMiRNANomenclature html
convertNomenclature html
createPathwayGraphs html
downloadKEGGPathwayList html
downloadMiRecords html
downloadPathways html
extractLinearSubpathways html
extractNonLinearSubpathways html
getEdgeTypes html
importExpressions html
pathwayMeasures html
scoreSubpathways html
subpathwayKEGGmap html
subpathwayMiRNAs html
visualizeResults html
** building package indices
** installing vignettes
** 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 'CHRONOS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CHRONOS' as CHRONOS_1.12.0.zip
* DONE (CHRONOS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CHRONOS' successfully unpacked and MD5 sums checked
|
CHRONOS.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage('CHRONOS')
Testing test_CHRONOSrun...Importing entrezgene data...done.
Importing miRNA data...done.
Downloading files...done.
Creating adjacency matrices...done.
Extracting Linear Subpathways...done.
#98 subpathways initially
Calculating subscores...done.
#21 subpathways after subscore.
Calculating mirscores......end.
Extracting Non Linear Subpathways...done.
#24 subpathways initially
Calculating subscores...done.
#19 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_pathwayToGraph...Creating adjacency matrices...done.
done.
Testing test_subExtractionLinear...Importing entrezgene data...done.
Extracting Linear Subpathways...done.
done.
Testing test_subExtractionNonLinear...Importing entrezgene data...done.
Extracting Non Linear Subpathways...done.
done.
Testing test_subRefinement...Importing entrezgene data...done.
Importing miRNA data...done.
#98 subpathways initially
Calculating subscores...done.
#21 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_subVisualization...Importing entrezgene data...done.
Summarising scores...Note: zip::zip() is deprecated, please use zip::zipr() instead
done.
Summarising scores...done.
done.
RUNIT TEST PROTOCOL -- Wed Oct 16 02:43:20 2019
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
CHRONOS RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
>
>
> proc.time()
user system elapsed
8.90 0.85 16.40
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CHRONOS.Rcheck/tests_x64/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage('CHRONOS')
Testing test_CHRONOSrun...Importing entrezgene data...done.
Importing miRNA data...done.
Downloading files...done.
Creating adjacency matrices...done.
Extracting Linear Subpathways...done.
#98 subpathways initially
Calculating subscores...done.
#21 subpathways after subscore.
Calculating mirscores......end.
Extracting Non Linear Subpathways...done.
#24 subpathways initially
Calculating subscores...done.
#19 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_pathwayToGraph...Creating adjacency matrices...done.
done.
Testing test_subExtractionLinear...Importing entrezgene data...done.
Extracting Linear Subpathways...done.
done.
Testing test_subExtractionNonLinear...Importing entrezgene data...done.
Extracting Non Linear Subpathways...done.
done.
Testing test_subRefinement...Importing entrezgene data...done.
Importing miRNA data...done.
#98 subpathways initially
Calculating subscores...done.
#21 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_subVisualization...Importing entrezgene data...done.
Summarising scores...Note: zip::zip() is deprecated, please use zip::zipr() instead
done.
Summarising scores...done.
done.
RUNIT TEST PROTOCOL -- Wed Oct 16 02:43:38 2019
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
CHRONOS RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
>
>
> proc.time()
user system elapsed
8.89 0.73 17.17
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CHRONOS.Rcheck/examples_i386/CHRONOS-Ex.timings
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CHRONOS.Rcheck/examples_x64/CHRONOS-Ex.timings
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