BioC 3.2: CHECK report for InPAS on windows1.bioconductor.org
This page was generated on 2015-10-27 17:32:05 -0400 (Tue, 27 Oct 2015).
InPAS 1.2.0
Jianhong Ou
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/InPAS | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 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: InPAS
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| Version: 1.2.0
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| Command: rm -rf InPAS.buildbin-libdir InPAS.Rcheck && mkdir InPAS.buildbin-libdir InPAS.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=InPAS.buildbin-libdir InPAS_1.2.0.tar.gz >InPAS.Rcheck\00install.out 2>&1 && cp InPAS.Rcheck\00install.out InPAS-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=InPAS.buildbin-libdir --install="check:InPAS-install.out" --force-multiarch --no-vignettes --timings InPAS_1.2.0.tar.gz
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| StartedAt: 2015-10-27 02:51:43 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 02:57:56 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 372.8 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: InPAS.Rcheck
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| Warnings: 0
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Command output
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### Running command:
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### rm -rf InPAS.buildbin-libdir InPAS.Rcheck && mkdir InPAS.buildbin-libdir InPAS.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=InPAS.buildbin-libdir InPAS_1.2.0.tar.gz >InPAS.Rcheck\00install.out 2>&1 && cp InPAS.Rcheck\00install.out InPAS-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=InPAS.buildbin-libdir --install="check:InPAS-install.out" --force-multiarch --no-vignettes --timings InPAS_1.2.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/InPAS.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'InPAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'InPAS' version '1.2.0'
* 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 'InPAS' 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 ... 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 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' ... [27s] OK
** running examples for arch 'x64' ... [30s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
testUsage 5.38 0.02 5.39
filterRes 5.01 0.03 5.04
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [16s]
[16s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [19s]
[19s] 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
InPAS.Rcheck/00install.out:
install for i386
* installing *source* package 'InPAS' ...
** 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 'InPAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'InPAS' as InPAS_1.2.0.zip
* DONE (InPAS)
InPAS.Rcheck/examples_i386/InPAS-Ex.timings:
| name | user | system | elapsed
|
| CPsites | 0 | 0 | 0 |
|
| coverageFromBedGraph | 0 | 0 | 0 |
|
| filterRes | 4.92 | 0.05 | 4.97 |
|
| fisher.exact.test | 0.04 | 0.00 | 0.05 |
|
| getUTR3eSet | 3.80 | 0.01 | 3.81 |
|
| inPAS | 0 | 0 | 0 |
|
| limmaAnalyze | 0.04 | 0.00 | 0.05 |
|
| prepare4GSEA | 0.12 | 0.00 | 0.13 |
|
| singleGroupAnalyze | 0.02 | 0.00 | 0.01 |
|
| singleSampleAnalyze | 0 | 0 | 0 |
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| testUsage | 3.71 | 0.03 | 3.75 |
|
| usage4plot | 1.84 | 0.05 | 1.89 |
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| utr3.hg19 | 0.75 | 0.02 | 0.76 |
|
| utr3.mm10 | 0.89 | 0.01 | 0.91 |
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| utr3Annotation | 0 | 0 | 0 |
|
| utr3UsageEstimation | 0.00 | 0.02 | 0.02 |
|
InPAS.Rcheck/examples_x64/InPAS-Ex.timings:
| name | user | system | elapsed
|
| CPsites | 0 | 0 | 0 |
|
| coverageFromBedGraph | 0 | 0 | 0 |
|
| filterRes | 5.01 | 0.03 | 5.04 |
|
| fisher.exact.test | 0.08 | 0.00 | 0.08 |
|
| getUTR3eSet | 4.28 | 0.02 | 4.30 |
|
| inPAS | 0 | 0 | 0 |
|
| limmaAnalyze | 0.03 | 0.01 | 0.04 |
|
| prepare4GSEA | 0.07 | 0.02 | 0.08 |
|
| singleGroupAnalyze | 0.01 | 0.00 | 0.02 |
|
| singleSampleAnalyze | 0 | 0 | 0 |
|
| testUsage | 5.38 | 0.02 | 5.39 |
|
| usage4plot | 2.52 | 0.00 | 2.52 |
|
| utr3.hg19 | 0.46 | 0.00 | 0.45 |
|
| utr3.mm10 | 0.45 | 0.00 | 0.45 |
|
| utr3Annotation | 0 | 0 | 0 |
|
| utr3UsageEstimation | 0 | 0 | 0 |
|