BioC experimental data: CHECK report for parathyroid on zin2

Package: parathyroid

Version: 1.0.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings parathyroid_1.0.0.tar.gz

StartedAt: 2014-10-04 09:35:20 -0700 (Sat, 04 Oct 2014)

EndedAt: 2014-10-04 09:38:03 -0700 (Sat, 04 Oct 2014)

EllapsedTime: 162.8 seconds

RetCode: 0

Status:  OK

CheckDir: parathyroid.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings parathyroid_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-data-experiment/meat/parathyroid.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘parathyroid/DESCRIPTION’ ... OK
* this is package ‘parathyroid’ 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 ‘parathyroid’ can be installed ... [17s/17s] OK
* checking installed package size ... NOTE
  installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data  13.8Mb
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘DESeq’ ‘DEXSeq’
  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
File ‘parathyroid/R/onloadmessage.R’:
  .onLoad calls:
    packageStartupMessage("NOTE:\nThe parathyroid data package is planning to be removed\nfrom Bioconductor 2.15 (October 2014).\n\nReason: The ExonCountSet class is being deprecated in DEXSeq v1.10,\nand DESeq2's DESeqDataSet serves as a replacement for DESeq's CountDataSet.\n\nThe parathyroidSE data package will remain, with SummarizedExperiment versions\nof the objects in the parathyroid data package.")

See section ‘Good practice’ in '?.onAttach'.
* 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
  'BiocParallel' did not register default BiocParallelParams
  Note: found 2 marked UTF-8 strings
* 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

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.14-data-experiment/meat/parathyroid.Rcheck/00check.log’
for details.

* installing *source* package ‘parathyroid’ ...
** 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 (parathyroid)