BioC 3.2: CHECK report for mirIntegrator on moscato1
This page was generated on 2015-08-20 13:24:18 -0700 (Thu, 20 Aug 2015).
mirIntegrator 0.99.5
Diana Diaz
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mirIntegrator | | Last Changed Rev: 104760 / Revision: 107602 | | Last Changed Date: 2015-06-09 14:33:49 -0700 (Tue, 09 Jun 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: mirIntegrator
|
| Version: 0.99.5
|
| Command: rm -rf mirIntegrator.buildbin-libdir mirIntegrator.Rcheck && mkdir mirIntegrator.buildbin-libdir mirIntegrator.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mirIntegrator.buildbin-libdir mirIntegrator_0.99.5.tar.gz >mirIntegrator.Rcheck\00install.out 2>&1 && cp mirIntegrator.Rcheck\00install.out mirIntegrator-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=mirIntegrator.buildbin-libdir --install="check:mirIntegrator-install.out" --force-multiarch --no-vignettes --timings mirIntegrator_0.99.5.tar.gz
|
| StartedAt: 2015-08-20 07:19:47 -0700 (Thu, 20 Aug 2015)
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| EndedAt: 2015-08-20 07:24:34 -0700 (Thu, 20 Aug 2015)
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| EllapsedTime: 287.1 seconds
|
| RetCode: 0
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| Status: OK
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| CheckDir: mirIntegrator.Rcheck
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| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf mirIntegrator.buildbin-libdir mirIntegrator.Rcheck && mkdir mirIntegrator.buildbin-libdir mirIntegrator.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mirIntegrator.buildbin-libdir mirIntegrator_0.99.5.tar.gz >mirIntegrator.Rcheck\00install.out 2>&1 && cp mirIntegrator.Rcheck\00install.out mirIntegrator-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=mirIntegrator.buildbin-libdir --install="check:mirIntegrator-install.out" --force-multiarch --no-vignettes --timings mirIntegrator_0.99.5.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/mirIntegrator.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mirIntegrator/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mirIntegrator' version '0.99.5'
* 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 'mirIntegrator' 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
** checking loading without being on the library search path ... 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 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
plotLines: no visible binding for global variable 'x'
plotLines: no visible binding for global variable 'y'
* 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' ... [28s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pathways2pdf 9.39 0.05 9.53
** running examples for arch 'x64' ... [27s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pathways2pdf 8.76 0.23 9
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [9s]
[10s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [13s]
[14s] 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: 1 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/mirIntegrator.Rcheck/00check.log'
for details.
mirIntegrator.Rcheck/00install.out:
install for i386
* installing *source* package 'mirIntegrator' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'mirIntegrator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mirIntegrator' as mirIntegrator_0.99.5.zip
* DONE (mirIntegrator)
mirIntegrator.Rcheck/examples_i386/mirIntegrator-Ex.timings:
| name | user | system | elapsed
|
| GSE43592_mRNA | 0.18 | 0.00 | 0.18 |
|
| GSE43592_miRNA | 0.01 | 0.00 | 0.01 |
|
| augmented_pathways | 1.06 | 0.00 | 1.06 |
|
| integrate_mir | 4.81 | 0.02 | 4.82 |
|
| kegg_pathways | 0.39 | 0.00 | 0.39 |
|
| mirTarBase | 0.09 | 0.00 | 0.43 |
|
| names_pathways | 0.00 | 0.01 | 0.02 |
|
| pathways2pdf | 9.39 | 0.05 | 9.53 |
|
| plot_augmented_pathway | 2.67 | 0.04 | 2.81 |
|
| plot_change | 1.68 | 0.00 | 1.68 |
|
| smallest_pathway | 0.89 | 0.02 | 0.91 |
|
mirIntegrator.Rcheck/examples_x64/mirIntegrator-Ex.timings:
| name | user | system | elapsed
|
| GSE43592_mRNA | 0.15 | 0.00 | 0.15 |
|
| GSE43592_miRNA | 0.02 | 0.00 | 0.02 |
|
| augmented_pathways | 1.09 | 0.02 | 1.11 |
|
| integrate_mir | 4.63 | 0.03 | 4.66 |
|
| kegg_pathways | 0.3 | 0.0 | 0.3 |
|
| mirTarBase | 0.12 | 0.00 | 0.12 |
|
| names_pathways | 0.00 | 0.02 | 0.02 |
|
| pathways2pdf | 8.76 | 0.23 | 9.00 |
|
| plot_augmented_pathway | 3.16 | 0.00 | 3.17 |
|
| plot_change | 1.33 | 0.00 | 1.32 |
|
| smallest_pathway | 0.81 | 0.00 | 0.81 |
|