BioC experimental data: CHECK report for RTCGA.clinical on morelia

Package: RTCGA.clinical

Version: 20150821.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTCGA.clinical_20150821.1.2.tar.gz

StartedAt: 2015-11-25 11:13:39 -0800 (Wed, 25 Nov 2015)

EndedAt: 2015-11-25 11:17:33 -0800 (Wed, 25 Nov 2015)

EllapsedTime: 234.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RTCGA.clinical.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTCGA.clinical_20150821.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/RTCGA.clinical.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCGA.clinical/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTCGA.clinical’ version ‘20150821.1.2’
* 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 ‘RTCGA.clinical’ can be installed ... [82s/103s] OK
* checking installed package size ... NOTE
  installed size is 33.0Mb
  sub-directories of 1Mb or more:
    data  32.9Mb
* 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 loading without being on the library search path ... OK
* checking 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘PRAD.clinical’ ‘SARC.clinical’
Undocumented data sets:
  ‘PRAD.clinical’ ‘SARC.clinical’
All user-level objects in a package should have documentation entries.
See 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 ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... WARNING
  Warning: found non-ASCII strings
  '5-fluorouracil<e2><80><8e>' in object 'PAAD.clinical'
  'radical<c2><a0>pancreaticoduodenectomy' in object 'PAAD.clinical'
  'interferon-<ce><b1>2' in object 'SKCM.clinical'
  'pozna<c5><84>' in object 'STAD.clinical'
  'pozna<c5><84>' in object 'STES.clinical'
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/RTCGA.clinical.Rcheck/00check.log’
for details.

* installing *source* package ‘RTCGA.clinical’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RTCGA.clinical)