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BioC 3.2: CHECK report for cytofkit on moscato1

This page was generated on 2015-08-20 13:23:43 -0700 (Thu, 20 Aug 2015).

Package 242/1069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cytofkit 0.99.26
Jinmiao Chen
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cytofkit
Last Changed Rev: 106711 / Revision: 107602
Last Changed Date: 2015-07-23 17:53:15 -0700 (Thu, 23 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK NO, built version is LOWER than in internal repository!!!
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK NO, built version is LOWER than in internal repository!!!
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!

Summary

Package: cytofkit
Version: 0.99.26
Command: rm -rf cytofkit.buildbin-libdir cytofkit.Rcheck && mkdir cytofkit.buildbin-libdir cytofkit.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cytofkit.buildbin-libdir cytofkit_0.99.26.tar.gz >cytofkit.Rcheck\00install.out 2>&1 && cp cytofkit.Rcheck\00install.out cytofkit-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cytofkit.buildbin-libdir --install="check:cytofkit-install.out" --force-multiarch --no-vignettes --timings cytofkit_0.99.26.tar.gz
StartedAt: 2015-08-20 03:22:41 -0700 (Thu, 20 Aug 2015)
EndedAt: 2015-08-20 03:30:43 -0700 (Thu, 20 Aug 2015)
EllapsedTime: 481.9 seconds
RetCode: 0
Status:  OK  
CheckDir: cytofkit.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cytofkit.buildbin-libdir cytofkit.Rcheck && mkdir cytofkit.buildbin-libdir cytofkit.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cytofkit.buildbin-libdir cytofkit_0.99.26.tar.gz >cytofkit.Rcheck\00install.out 2>&1 && cp cytofkit.Rcheck\00install.out cytofkit-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cytofkit.buildbin-libdir --install="check:cytofkit-install.out" --force-multiarch --no-vignettes --timings cytofkit_0.99.26.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-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 '0.99.26'
* 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' ... [155s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
densVM_cluster 145.46   0.26  145.92
** running examples for arch 'x64' ... [157s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
densVM_cluster 145.19    0.2  146.95
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [6s]
 [6s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [6s]
 [6s] 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_0.99.26.zip
* DONE (cytofkit)

cytofkit.Rcheck/examples_i386/cytofkit-Ex.timings:

nameusersystemelapsed
clust_mean_heatmap0.090.000.09
clust_percentage_heatmap0.330.000.33
clust_state0.030.000.03
cluster_gridPlot0.750.020.77
cluster_plot0.340.000.34
cytof_dimReduction1.400.001.43
cytof_tsne_densvm0.020.000.02
cytof_tsne_densvm_GUI000
cytof_write_results000
cytofkit000
densVM_cluster145.46 0.26145.92
fcs_lgcl0.250.000.25
fcs_lgcl_merge0.290.000.29
peaksGamma_plot0.140.000.14

cytofkit.Rcheck/examples_x64/cytofkit-Ex.timings:

nameusersystemelapsed
clust_mean_heatmap0.060.010.07
clust_percentage_heatmap0.080.000.08
clust_state0.010.000.02
cluster_gridPlot0.740.000.73
cluster_plot0.580.020.59
cytof_dimReduction1.630.001.93
cytof_tsne_densvm000
cytof_tsne_densvm_GUI000
cytof_write_results000
cytofkit000
densVM_cluster145.19 0.20146.95
fcs_lgcl0.360.000.36
fcs_lgcl_merge0.340.020.36
peaksGamma_plot0.20.00.2