BioC 2.12: CHECK report for TDARACNE on moscato2

Package: TDARACNE

Version: 1.10.0

Command: E:\biocbld\bbs-2.12-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings TDARACNE_1.10.0.tar.gz

StartedAt: 2013-10-09 04:24:49 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:26:20 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 91.4 seconds

RetCode: 0

Status:  OK

CheckDir: TDARACNE.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/TDARACNE.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TDARACNE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TDARACNE' version '1.10.0'
* 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 whether package 'TDARACNE' can be installed ... [5s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... 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 examples ... [38s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
TDARACNEdataPublished 30.8   0.11   31.37
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.12-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	4.22	0.03	4.26
TDARACNEdataPublished	30.80	0.11	31.37