BioC 3.2: CHECK report for TDARACNE on moscato1

Package: TDARACNE

Version: 1.20.0

Command: D:\biocbld\bbs-3.2-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings TDARACNE_1.20.0.tar.gz

StartedAt: 2016-04-23 08:08:45 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 08:10:06 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 80.7 seconds

RetCode: 0

Status:  OK

CheckDir: TDARACNE.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbld\bbs-3.2-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings TDARACNE_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/TDARACNE.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.20.0'
* 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 ... [6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CalcMI_time2: no visible global function definition for 'dpik'
CalcMI_time2: no visible global function definition for 'KernSec'
CalcMI_time2: no visible global function definition for 'KernSur'
TDARACNE: no visible global function definition for 'exprs'
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 ... [27s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
TDARACNEdataPublished 22.59   0.06   22.65
* 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

Status: 5 NOTEs
See
  'D:/biocbld/bbs-3.2-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	2.68	0.00	2.69
TDARACNEdataPublished	22.59	0.06	22.65