BioC 3.0: CHECK report for COPDSexualDimorphism on oaxaca

Package: COPDSexualDimorphism

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch COPDSexualDimorphism_1.2.0.tar.gz

StartedAt: 2015-04-09 22:35:10 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:37:53 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 163.0 seconds

RetCode: 0

Status:  OK

CheckDir: COPDSexualDimorphism.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch COPDSexualDimorphism_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/COPDSexualDimorphism.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COPDSexualDimorphism/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COPDSexualDimorphism’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘COPDSexualDimorphism.data’ ‘NCBI2R’ ‘RColorBrewer’ ‘beeswarm’
  ‘limma’ ‘GenomicRanges’ ‘gplots’ ‘gtools’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘COPDSexualDimorphism’ can be installed ... [13s/14s] OK
* checking installed package size ... OK
* 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
'library' or 'require' calls to packages already attached by Depends:
  ‘GenomicRanges’ ‘NCBI2R’ ‘RColorBrewer’ ‘beeswarm’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘COPDSexualDimorphism.data’ ‘NCBI2R’ ‘RColorBrewer’ ‘gplots’ ‘limma’
  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
getNeighbors: no visible global function definition for ‘Rle’
getNeighbors: no visible global function definition for ‘IRanges’
my.smart.plot: no visible global function definition for ‘brewer.pal’
sdcd: no visible binding for global variable ‘chromosome_name’
sdcd.vmr: no visible global function definition for ‘GetNeighGenes’
sdcd.vmr: no visible binding for global variable ‘vmr’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/14s] OK
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/COPDSexualDimorphism.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
COPDSexualDimorphism-package	3.944	0.357	4.377
do.sdcd.boxplot	0.437	0.028	0.467
lgrc.sdcd.genes	0.024	0.001	0.025
sdcd	2.770	0.360	3.142