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BioC 3.4: CHECK report for RefNet on moscato1

This page was generated on 2016-09-21 03:45:49 -0700 (Wed, 21 Sep 2016).

Package 1002/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RefNet 1.9.0
Paul Shannon
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RefNet
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RefNet
Version: 1.9.0
Command: rm -rf RefNet.buildbin-libdir RefNet.Rcheck && mkdir RefNet.buildbin-libdir RefNet.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefNet.buildbin-libdir RefNet_1.9.0.tar.gz >RefNet.Rcheck\00install.out 2>&1 && cp RefNet.Rcheck\00install.out RefNet-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RefNet.buildbin-libdir --install="check:RefNet-install.out" --force-multiarch --no-vignettes --timings RefNet_1.9.0.tar.gz
StartedAt: 2016-09-20 15:05:23 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:12:22 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 418.8 seconds
RetCode: 0
Status:  OK  
CheckDir: RefNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RefNet.buildbin-libdir RefNet.Rcheck && mkdir RefNet.buildbin-libdir RefNet.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefNet.buildbin-libdir RefNet_1.9.0.tar.gz >RefNet.Rcheck\00install.out 2>&1 && cp RefNet.Rcheck\00install.out RefNet-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RefNet.buildbin-libdir --install="check:RefNet-install.out" --force-multiarch --no-vignettes --timings RefNet_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/RefNet.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RefNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RefNet' version '1.9.0'
* 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 'RefNet' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
RefNet-class    21.20   0.76   48.61
interactions    16.88   0.74   19.58
providers       15.96   0.58   18.35
providerClasses 15.70   0.54   17.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
RefNet-class    16.91   0.70   19.37
providerClasses 14.71   0.53   18.08
providers       14.40   0.45   16.69
interactions    14.37   0.45   16.70
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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-3.4-bioc/meat/RefNet.Rcheck/00check.log'
for details.


RefNet.Rcheck/00install.out:


install for i386

* installing *source* package 'RefNet' ...
** 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 'RefNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RefNet' as RefNet_1.9.0.zip
* DONE (RefNet)

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

nameusersystemelapsed
RefNet-class21.20 0.7648.61
detectDuplicateInteractions0.030.000.03
interactions16.88 0.7419.58
pickBestFromDupGroup0.010.000.02
providerClasses15.70 0.5417.92
providers15.96 0.5818.35
pubmedAbstract0.000.000.38

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

nameusersystemelapsed
RefNet-class16.91 0.7019.37
detectDuplicateInteractions0.030.000.03
interactions14.37 0.4516.70
pickBestFromDupGroup0.020.000.01
providerClasses14.71 0.5318.08
providers14.40 0.4516.69
pubmedAbstract0.000.000.41