BioC 3.0: CHECK report for goseq on perceval

Package: goseq

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch goseq_1.18.0.tar.gz

StartedAt: 2015-04-10 02:19:48 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:28:52 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 544.1 seconds

RetCode: 0

Status:  OK

CheckDir: goseq.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 goseq_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/goseq.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 ‘goseq/DESCRIPTION’ ... OK
* this is package ‘goseq’ version ‘1.18.0’
* 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 ‘goseq’ can be installed ... [41s/41s] 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘rtracklayer’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
getlength: no visible global function definition for ‘browserSession’
getlength: no visible global function definition for ‘ucscTableQuery’
getlength: no visible global function definition for ‘getTable’
* 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 ... [140s/145s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
goseq     44.956  3.852  49.167
getgo     36.919  2.251  39.224
nullp     10.206  1.277  15.641
plotPWF    9.474  1.146  10.667
getlength  7.930  0.844   8.866
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/goseq.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
genes	0.025	0.001	0.026
getgo	36.919	2.251	39.224
getlength	7.930	0.844	8.866
goseq	44.956	3.852	49.167
makespline	0.071	0.003	0.099
nullp	10.206	1.277	15.641
plotPWF	9.474	1.146	10.667