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BioC 3.0: CHECK report for CoRegNet on zin1

This page was generated on 2015-04-10 09:42:46 -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: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings CoRegNet_1.1.2.tar.gz
StartedAt: 2015-04-09 22:55:47 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:57:47 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 119.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CoRegNet.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings CoRegNet_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/CoRegNet.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ... [8s/8s] 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:
  ‘RColorBrewer’ ‘gplots’
  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 ... [45s/26s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
hLICORN         27.345  0.788  14.501
masterRegulator 10.265  0.228   5.518
* checking for unstated dependencies in tests ... WARNING
'::' or ':::' import not declared from: ‘BiocGenerics’
* checking tests ...
  Running ‘runTests.R’ [9s/8s]
 [9s/8s] 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
  ‘/home/biocbuild/bbs-3.0-bioc/meat/CoRegNet.Rcheck/00check.log’
for details.

CoRegNet.Rcheck/00install.out:

* installing *source* package ‘CoRegNet’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c comblicorn.c -o comblicorn.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o CoRegNet.so comblicorn.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/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
HumanDataExamples0.0240.0000.024
HumanTF0.0080.0000.008
addEvidences0.2040.1200.261
coregnet0.0320.0520.062
coregulators0.5000.1520.459
discretizeExpressionData0.0440.0040.048
display0.0680.0800.274
hLICORN27.345 0.78814.501
masterRegulator10.265 0.228 5.518
refine0.4080.2640.515
regulatorInfluence0.0600.0960.279
regulators0.3200.1360.085
summary0.0520.0400.070