BioC 2.14: CHECK report for TDARACNE on zin2

Package: TDARACNE

Version: 1.14.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings TDARACNE_1.14.0.tar.gz

StartedAt: 2014-10-08 03:13:01 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 03:13:53 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 52.1 seconds

RetCode: 0

Status:  OK

CheckDir: TDARACNE.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings TDARACNE_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/TDARACNE.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TDARACNE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TDARACNE’ version ‘1.14.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TDARACNE’ can be installed ... [3s/3s] 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/CITATION.txt
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 to packages already attached by Depends:
  ‘Biobase’ ‘GenKern’ ‘Rgraphviz’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘GenKern’ ‘Rgraphviz’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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
TDARACNEdataPublished: no visible binding for global variable
  ‘dataYeast’
TDARACNEdataPublished: no visible binding for global variable
  ‘threshYeast’
TDARACNEdataPublished: no visible binding for global variable
  ‘dataSOSmean’
TDARACNEdataPublished: no visible binding for global variable
  ‘threshSOSmean’
TDARACNEdataPublished: no visible binding for global variable
  ‘dataIRMAon’
TDARACNEdataPublished: no visible binding for global variable
  ‘threshIRMAon’
* 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 ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
TDARACNEdataPublished 15.641  0.008  15.712
* 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 4 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/TDARACNE.Rcheck/00check.log’
for details.

* installing *source* package ‘TDARACNE’ ...
** 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 (TDARACNE)

name	user	system	elapsed
TDARACNE	2.124	0.004	2.131
TDARACNEdataPublished	15.641	0.008	15.712