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BioC 3.0: CHECK report for CoRegNet on perceval

This page was generated on 2015-04-10 10:00:38 -0700 (Fri, 10 Apr 2015).

Package 199/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoRegNet 1.1.2
Remy Nicolle
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/CoRegNet
Last Changed Rev: 101149 / Revision: 102249
Last Changed Date: 2015-03-25 08:03:54 -0700 (Wed, 25 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: CoRegNet
Version: 1.1.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CoRegNet_1.1.2.tar.gz
StartedAt: 2015-04-10 00:22:02 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:26:26 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 264.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CoRegNet.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CoRegNet_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/CoRegNet.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoRegNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoRegNet’ version ‘1.1.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CoRegNet’ can be installed ... [14s/39s] OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.4Mb
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/unitTests/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘gplots’ ‘RColorBrewer’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
.descriptionUpdate: no visible global function definition for ‘vcount’
.heatplot: no visible global function definition for ‘heatmap.2’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [88s/52s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
hLICORN         48.645  3.779  26.957
masterRegulator 21.321  1.314  12.242
* checking for unstated dependencies in tests ... WARNING
'::' or ':::' import not declared from: ‘BiocGenerics’
* checking tests ...
  Running ‘runTests.R’ [21s/19s]
 [22s/20s] 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

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/CoRegNet.Rcheck/00check.log’
for details.

CoRegNet.Rcheck/00install.out:

* installing *source* package ‘CoRegNet’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c comblicorn.c -o comblicorn.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o CoRegNet.so comblicorn.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/CoRegNet.Rcheck/CoRegNet/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CoRegNet)

CoRegNet.Rcheck/CoRegNet-Ex.timings:

nameusersystemelapsed
HumanDataExamples0.0370.0070.278
HumanTF0.0080.0010.009
addEvidences0.6120.5041.076
coregnet0.0760.1760.190
coregulators0.1770.2720.351
discretizeExpressionData0.0530.0170.128
display0.1150.2580.592
hLICORN48.645 3.77926.957
masterRegulator21.321 1.31412.242
refine0.7131.1051.287
regulatorInfluence0.3180.3940.643
regulators0.3130.3870.289
summary0.0750.1770.196