BioC 2.13: CHECK report for vtpnet on perceval

Package: vtpnet

Version: 0.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch vtpnet_0.2.0.tar.gz

StartedAt: 2014-04-05 04:55:40 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:06:28 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 648.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: vtpnet.Rcheck

Warnings: 4

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/vtpnet.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vtpnet/DESCRIPTION’ ... OK
* this is package ‘vtpnet’ version ‘0.2.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘vtpnet’ can be installed ... [12s/12s] OK
* checking installed package size ... NOTE
  installed size is 30.7Mb
  sub-directories of 1Mb or more:
    data  30.5Mb
* 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 ... OK
* 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 dependencies in R code ... WARNING
‘library’ or ‘require’ calls not declared from:
  ‘doParallel’ ‘foreach’ ‘gwascat’
‘library’ or ‘require’ call to ‘GenomicRanges’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘GenomicRanges’ ‘graph’
  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
rng2facHits: warning in dir(patt = "rda$"): partial argument match of
  'patt' to 'pattern'
runfimo: warning in dir(patt = "_out"): partial argument match of
  'patt' to 'pattern'
gwMatchPWM: no visible binding for global variable ‘Hsapiens’
gwMatchPWM: no visible global function definition for ‘%dopar%’
gwMatchPWM: no visible global function definition for ‘foreach’
gwMatchPWM: no visible binding for global variable ‘i’
rng2facHits : <anonymous>: no visible global function definition for
  ‘makeCurrentGwascat’
rng2facHits: no visible global function definition for
  ‘registerDoParallel’
rng2facHits: no visible global function definition for ‘%dopar%’
rng2facHits: no visible global function definition for ‘foreach’
rng2facHits: no visible binding for global variable ‘i’
runfimo: no visible global function definition for ‘%dopar%’
runfimo: no visible global function definition for ‘foreach’
runfimo: no visible binding for global variable ‘i’
setupGWPM: no visible global function definition for
  ‘registerDoParallel’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘filterGWASbyMap’ ‘getMtags’ ‘getOneHits’ ‘gwMatchPWM’ ‘matrc’
  ‘MdbSearchToDisk’ ‘rng2facHits’ ‘runfimo’ ‘setupGWPM’
Undocumented data sets:
  ‘cancerMap’ ‘maurGWAS’ ‘pax4_75’ ‘pax4_85’ ‘pax4’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
no parsed files found
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
               old_size new_size compress
  maurGWAS.rda    103Kb     76Kb       xz
  pax4.rda       25.9Mb   17.5Mb       xz
  pax4_75.rda     4.5Mb    2.3Mb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ calls not declared from:
  ‘gwascat’ ‘ShortRead’
* 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

WARNING: There were 4 warnings.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/vtpnet.Rcheck/00check.log’
for details.

* installing *source* package ‘vtpnet’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
No man pages found in package  ‘vtpnet’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (vtpnet)