BioC experimental data: CHECK report for ggtut on zin1

Package: ggtut

Version: 0.3.2

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ggtut_0.3.2.tar.gz

StartedAt: 2015-04-08 08:23:38 -0700 (Wed, 08 Apr 2015)

EndedAt: 2015-04-08 08:31:19 -0700 (Wed, 08 Apr 2015)

EllapsedTime: 460.9 seconds

RetCode: 0

Status:  OK

CheckDir: ggtut.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ggtut_0.3.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-data-experiment/meat/ggtut.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggtut/DESCRIPTION’ ... OK
* this is package ‘ggtut’ version ‘0.3.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘GGtools’ ‘ff’ ‘GenomicRanges’ ‘snpStats’ ‘GGdata’ ‘GenomicFeatures’
  ‘ChIPpeakAnno’ ‘Rsamtools’ ‘cheung2010’
  ‘SNPlocs.Hsapiens.dbSNP.20120608’ ‘hmyriB36’
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 ‘ggtut’ can be installed ... [45s/49s] OK
* checking installed package size ... NOTE
  installed size is 189.4Mb
  sub-directories of 1Mb or more:
    bam          15.1Mb
    data         22.3Mb
    ffarchives  136.9Mb
    ffobjects     1.6Mb
    images       12.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicFeatures’ ‘ChIPpeakAnno’
A package should be listed in only one of these fields.
* 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' call to ‘TxDb.Hsapiens.UCSC.hg18.knownGene’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘ChIPpeakAnno’ ‘GGdata’ ‘GGtools’ ‘GenomicFeatures’ ‘GenomicRanges’
  ‘Rsamtools’ ‘SNPlocs.Hsapiens.dbSNP.20120608’ ‘cheung2010’ ‘ff’
  ‘hmyriB36’ ‘snpStats’
  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
getFixedBFL: no visible global function definition for ‘BamFileList’
getFixedBFL: no visible global function definition for ‘path’
hg18tx: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg18.knownGene’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [31s/31s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
rules.n43 4.928  0.072   5.116
* checking PDF version of manual ... OK
* DONE

NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-3.0-data-experiment/meat/ggtut.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
c17imp	1.164	0.028	1.263
g17rngsnr	0.620	0.004	0.623
ggtut-package	0.220	0.008	0.228
observed17ceu	0.172	0.012	0.188
rules.n43	4.928	0.072	5.116
snpgr17	1.052	0.024	1.133