BioC 3.3: CHECK report for goseq on oaxaca

Package: goseq

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings goseq_1.24.0.tar.gz

StartedAt: 2016-10-13 02:17:15 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:24:37 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 442.5 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 goseq_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/goseq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘goseq/DESCRIPTION’ ... OK
* this is package ‘goseq’ version ‘1.24.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
getgo: no visible global function definition for ‘toTable’
getlength: no visible global function definition for
  ‘installed.packages’
getlength: no visible global function definition for ‘tail’
getlength: no visible global function definition for ‘toTable’
getlength: no visible global function definition for
  ‘transcriptLengths’
getlength: no visible global function definition for ‘browserSession’
getlength: no visible global function definition for ‘genome<-’
getlength: no visible global function definition for ‘ucscTableQuery’
getlength: no visible global function definition for ‘getTable’
supportedOrganisms: no visible global function definition for
  ‘ucscGenomes’
Undefined global functions or variables:
  browserSession genome<- getTable installed.packages tail toTable
  transcriptLengths ucscGenomes ucscTableQuery
Consider adding
  importFrom("utils", "installed.packages", "tail")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
goseq     27.302  2.327  42.148
getgo     12.852  1.811 160.804
nullp      5.792  0.519  50.506
plotPWF    5.486  0.383   5.881
getlength  3.937  0.212  11.382
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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	0.014	0.001	0.015
getgo	12.852	1.811	160.804
getlength	3.937	0.212	11.382
goseq	27.302	2.327	42.148
makespline	0.058	0.002	0.091
nullp	5.792	0.519	50.506
plotPWF	5.486	0.383	5.881
supportedOrganisms	0.664	0.011	0.875