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BioC 3.5: CHECK report for anamiR on tokay2

This page was generated on 2017-08-16 13:26:20 -0400 (Wed, 16 Aug 2017).

Package 42/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
anamiR 1.4.2
Ti-Tai Wang
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/anamiR
Last Changed Rev: 130930 / Revision: 131943
Last Changed Date: 2017-07-04 04:09:54 -0400 (Tue, 04 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ TIMEOUT ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: anamiR
Version: 1.4.2
Command: rm -rf anamiR.buildbin-libdir anamiR.Rcheck && mkdir anamiR.buildbin-libdir anamiR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=anamiR.buildbin-libdir anamiR_1.4.2.tar.gz >anamiR.Rcheck\00install.out 2>&1 && cp anamiR.Rcheck\00install.out anamiR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=anamiR.buildbin-libdir --install="check:anamiR-install.out" --force-multiarch --no-vignettes --timings anamiR_1.4.2.tar.gz
StartedAt: 2017-08-15 21:57:57 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:37:57 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 2400.4 seconds
RetCode: None
Status:  TIMEOUT  
CheckDir: anamiR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf anamiR.buildbin-libdir anamiR.Rcheck && mkdir anamiR.buildbin-libdir anamiR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=anamiR.buildbin-libdir anamiR_1.4.2.tar.gz >anamiR.Rcheck\00install.out 2>&1 && cp anamiR.Rcheck\00install.out anamiR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=anamiR.buildbin-libdir --install="check:anamiR-install.out" --force-multiarch --no-vignettes --timings anamiR_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/anamiR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'anamiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'anamiR' version '1.4.2'
* 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 'anamiR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 22.0Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata  19.6Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'SummarizedExperiment'
A package should be listed in only one of these fields.
* 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
GSEA_ana: no visible binding for global variable 'msigdb.gs'
Undefined global functions or variables:
  msigdb.gs
* 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' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
GSEA_ana         448.92   5.78  546.75
GSEA_res           8.66   0.06  165.29
enrichment         5.51   3.06  466.74
heat_vis           1.63   0.03    6.48
database_support   1.09   0.02   30.23
** running examples for arch 'x64' ...

anamiR.Rcheck/00install.out:


install for i386

* installing *source* package 'anamiR' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'anamiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'anamiR' as anamiR_1.4.2.zip
* DONE (anamiR)

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

nameusersystemelapsed
GSEA_ana448.92 5.78546.75
GSEA_res 8.66 0.06165.29
database_support 1.09 0.0230.23
differExp_continuous0.050.000.05
differExp_discrete0.030.000.03
enrichment 5.51 3.06466.74
heat_vis1.630.036.48
miR_converter0.010.004.67
multi_Differ0.020.000.02
negative_cor0.890.000.89
normalization0.020.020.03

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

nameusersystemelapsed
GSEA_ana591.58 2.23688.33