BioC 2.14: CHECK report for gwascat on zin2

Package: gwascat

Version: 1.8.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings gwascat_1.8.0.tar.gz

StartedAt: 2014-10-08 00:20:14 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:25:30 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 316.1 seconds

RetCode: 0

Status:  OK

CheckDir: gwascat.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 gwascat_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/gwascat.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 ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘1.8.0’
* 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 ‘gwascat’ can be installed ... [48s/48s] OK
* checking installed package size ... NOTE
  installed size is 28.9Mb
  sub-directories of 1Mb or more:
    data  25.5Mb
    obo    1.3Mb
    tab    1.1Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addSeqlengths: no visible global function definition for ‘transcripts’
addSeqlengths: no visible global function definition for ‘seqlengths’
addSeqlengths: no visible global function definition for ‘seqlengths<-’
bindcadd_snv: no visible global function definition for ‘seqlevels<-’
bindcadd_snv: no visible global function definition for ‘findOverlaps’
bindcadd_snv: no visible global function definition for ‘queryHits’
bindcadd_snv: no visible global function definition for ‘subjectHits’
chklocs: no visible global function definition for ‘getSNPlocs’
gwcex2gviz: no visible global function definition for ‘exons’
makeConsecChrs: no visible global function definition for ‘seqlevels<-’
makeConsecChrs: no visible global function definition for ‘seqinfo<-’
snpGenos: no visible global function definition for ‘getSNPlocs’
traitsManh: no visible binding for global variable ‘Pvalue_mlog’
* 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
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
gwcex2gviz 8.009  0.128    8.19
* 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 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/gwascat.Rcheck/00check.log’
for details.

* installing *source* package ‘gwascat’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gwascat)

name	user	system	elapsed
bindcadd_snv	0.000	0.000	0.001
gwascat-package	0	0	0
gwastagger	2.268	0.028	2.299
gwaswloc-class	0.004	0.000	0.002
gwcex2gviz	8.009	0.128	8.190
gwdf_2012_02_02	0	0	0
locon6	0.012	0.000	0.013
makeCurrentGwascat	0	0	0
riskyAlleleCount	3.236	0.104	3.348
topTraits	0.008	0.000	0.007
traitsManh	2.092	0.028	2.123