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BioC 2.13: CHECK report for FGNet on moscato1

This page was generated on 2014-04-05 09:51:33 -0700 (Sat, 05 Apr 2014).

Package 244/750HostnameOS / ArchBUILDCHECKBUILD BIN
FGNet 1.2.2
Sara Aibar
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/FGNet
Last Changed Rev: 87521 / Revision: 88450
Last Changed Date: 2014-03-17 11:51:28 -0700 (Mon, 17 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: FGNet
Version: 1.2.2
Command: rm -rf FGNet.buildbin-libdir && mkdir FGNet.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FGNet.buildbin-libdir FGNet_1.2.2.tar.gz >FGNet-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=FGNet.buildbin-libdir --install="check:FGNet-install.out" --force-multiarch --no-vignettes --timings FGNet_1.2.2.tar.gz && mv FGNet.buildbin-libdir/* FGNet.Rcheck/ && rmdir FGNet.buildbin-libdir
StartedAt: 2014-04-05 03:48:22 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:51:08 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 166.4 seconds
RetCode: 0
Status:  OK  
CheckDir: FGNet.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/FGNet.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FGNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FGNet' version '1.2.2'
* 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 'FGNet' 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
* 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 dependencies in R code ... NOTE
':::' call which should be '::': 'RCurl:::parseHTTPHeader'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotMetagroupsDistance: no visible global function definition for
  'brewer.pal'
query_david: no visible binding for global variable 'DAVIDWebService'
query_david: no visible global function definition for 'addList'
query_david : <anonymous>: no visible global function definition for
  'getIdTypes'
query_david: no visible global function definition for
  'setAnnotationCategories'
query_david : <anonymous>: no visible global function definition for
  'getAllAnnotationCategoryNames'
query_david: no visible global function definition for
  'getClusterReportFile'
* 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' ... [41s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
functionalNetwork      2.79   0.08    7.84
report                 0.73   0.22    5.97
toMatrix               0.43   0.01    5.66
plotMetagroupsDistance 0.11   0.03    6.60
** running examples for arch 'x64' ... [41s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getResults_david       3.73   0.01    5.46
functionalNetwork      3.01   0.14    7.54
report                 0.69   0.19    5.36
plotMetagroupsDistance 0.13   0.00    8.24
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [14s]
 [14s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [13s]
 [14s] 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/FGNet.Rcheck/00check.log'
for details.

FGNet.Rcheck/00install.out:


install for i386

* installing *source* package 'FGNet' ...
** 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 'FGNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FGNet' as FGNet_1.2.2.zip
* DONE (FGNet)

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

nameusersystemelapsed
FGNet-package0.020.000.02
functionalNetwork2.790.087.84
getResults_david3.120.064.87
getResults_gtLinker0.070.023.90
getTerms000
intersectionNetwork0.290.004.31
plotMetagroupsDistance0.110.036.60
query_david000
query_gtLinker000
report0.730.225.97
toMatrix0.430.015.66

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

nameusersystemelapsed
FGNet-package0.010.000.02
functionalNetwork3.010.147.54
getResults_david3.730.015.46
getResults_gtLinker0.010.003.94
getTerms000
intersectionNetwork0.230.024.15
plotMetagroupsDistance0.130.008.24
query_david0.010.000.01
query_gtLinker000
report0.690.195.36
toMatrix0.440.004.38