BioC 3.1: CHECK report for cytofkit on moscato2
This page was generated on 2015-10-09 09:32:01 -0700 (Fri, 09 Oct 2015).
cytofkit 1.1.0
Jinmiao Chen
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/cytofkit | | Last Changed Rev: 108228 / Revision: 109384 | | Last Changed Date: 2015-09-06 18:18:42 -0700 (Sun, 06 Sep 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: cytofkit
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| Version: 1.1.0
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| Command: rm -rf cytofkit.buildbin-libdir cytofkit.Rcheck && mkdir cytofkit.buildbin-libdir cytofkit.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cytofkit.buildbin-libdir cytofkit_1.1.0.tar.gz >cytofkit.Rcheck\00install.out 2>&1 && cp cytofkit.Rcheck\00install.out cytofkit-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=cytofkit.buildbin-libdir --install="check:cytofkit-install.out" --force-multiarch --no-vignettes --timings cytofkit_1.1.0.tar.gz
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| StartedAt: 2015-10-09 00:55:19 -0700 (Fri, 09 Oct 2015)
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| EndedAt: 2015-10-09 01:02:04 -0700 (Fri, 09 Oct 2015)
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| EllapsedTime: 405.0 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: cytofkit.Rcheck
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| Warnings: 0
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Command output
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###
### Running command:
###
### rm -rf cytofkit.buildbin-libdir cytofkit.Rcheck && mkdir cytofkit.buildbin-libdir cytofkit.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cytofkit.buildbin-libdir cytofkit_1.1.0.tar.gz >cytofkit.Rcheck\00install.out 2>&1 && cp cytofkit.Rcheck\00install.out cytofkit-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=cytofkit.buildbin-libdir --install="check:cytofkit-install.out" --force-multiarch --no-vignettes --timings cytofkit_1.1.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/cytofkit.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 'cytofkit/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cytofkit' version '1.1.0'
* 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 'cytofkit' 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [128s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
densVM_cluster 120.17 0.22 120.5
** running examples for arch 'x64' ... [130s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
densVM_cluster 120.73 0.35 121.66
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [5s]
[5s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [8s]
[8s] 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
cytofkit.Rcheck/00install.out:
install for i386
* installing *source* package 'cytofkit' ...
** R
** 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 'cytofkit' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cytofkit' as cytofkit_1.1.0.zip
* DONE (cytofkit)
cytofkit.Rcheck/examples_i386/cytofkit-Ex.timings:
| name | user | system | elapsed
|
| clust_mean_heatmap | 0.05 | 0.00 | 0.05 |
|
| clust_percentage_heatmap | 0.17 | 0.00 | 0.17 |
|
| clust_state | 0.02 | 0.00 | 0.02 |
|
| cluster_gridPlot | 0.47 | 0.00 | 0.47 |
|
| cluster_plot | 0.33 | 0.00 | 0.33 |
|
| cytof_dimReduction | 1.76 | 0.00 | 1.79 |
|
| cytof_tsne_densvm | 0 | 0 | 0 |
|
| cytof_tsne_densvm_GUI | 0 | 0 | 0 |
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| cytof_write_results | 0 | 0 | 0 |
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| cytofkit | 0 | 0 | 0 |
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| densVM_cluster | 120.17 | 0.22 | 120.50 |
|
| fcs_lgcl | 0.25 | 0.00 | 0.25 |
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| fcs_lgcl_merge | 0.28 | 0.00 | 0.28 |
|
| peaksGamma_plot | 0.14 | 0.00 | 0.14 |
|
cytofkit.Rcheck/examples_x64/cytofkit-Ex.timings:
| name | user | system | elapsed
|
| clust_mean_heatmap | 0.24 | 0.01 | 0.27 |
|
| clust_percentage_heatmap | 0.05 | 0.00 | 0.04 |
|
| clust_state | 0.02 | 0.00 | 0.02 |
|
| cluster_gridPlot | 0.49 | 0.03 | 0.52 |
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| cluster_plot | 0.39 | 0.00 | 0.39 |
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| cytof_dimReduction | 1.42 | 0.00 | 2.32 |
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| cytof_tsne_densvm | 0 | 0 | 0 |
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| cytof_tsne_densvm_GUI | 0 | 0 | 0 |
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| cytof_write_results | 0 | 0 | 0 |
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| cytofkit | 0 | 0 | 0 |
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| densVM_cluster | 120.73 | 0.35 | 121.66 |
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| fcs_lgcl | 0.23 | 0.00 | 0.24 |
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| fcs_lgcl_merge | 0.24 | 0.01 | 0.25 |
|
| peaksGamma_plot | 0.14 | 0.00 | 0.14 |
|