BioC experimental data: CHECK report for HSMMSingleCell on perceval

Package: HSMMSingleCell

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HSMMSingleCell_1.0.0.tar.gz

StartedAt: 2015-04-08 10:08:54 -0700 (Wed, 08 Apr 2015)

EndedAt: 2015-04-08 10:12:44 -0700 (Wed, 08 Apr 2015)

EllapsedTime: 230.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: HSMMSingleCell.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HSMMSingleCell_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/HSMMSingleCell.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HSMMSingleCell/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HSMMSingleCell’ version ‘1.0.0’
* 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 ‘HSMMSingleCell’ can be installed ... [3s/3s] OK
* checking installed package size ... NOTE
  installed size is 32.6Mb
  sub-directories of 1Mb or more:
    data  32.5Mb
* 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 ... 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 ... NOTE
Package in Depends field not imported from: ‘VGAM’
  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 ... OK
* 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 ... NOTE
  Error in .requirePackage(package) : 
    unable to find required package 'monocle'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... WARNING
  Warning: namespace ‘monocle’ is not available and has been replaced
  by .GlobalEnv when processing object ‘HSMM’
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  HSMM.rda   32.5Mb   18.3Mb       xz
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘HSMMSingleCell-vignette.bbl’, ‘HSMMSingleCell-vignette.log’,
  ‘HSMMSingleCell-vignette.toc’
Please remove them from your package.
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/HSMMSingleCell.Rcheck/00check.log’
for details.

* installing *source* package ‘HSMMSingleCell’ ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HSMMSingleCell)