Package: gwascat

Version: 1.1.11

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gwascat_1.1.11.tar.gz

StartedAt: 2012-06-21 00:49:06 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 00:59:14 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 608.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gwascat.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/gwascat.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '1.1.11'
* 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 whether package 'gwascat' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.8Mb
  sub-directories of 1Mb or more:
    data  20.5Mb
    obo    1.3Mb
    tab    1.1Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
chklocs: no visible global function definition for 'getSNPlocs'
snpGenos: no visible global function definition for 'getSNPlocs'
traitsManh: no visible binding for global variable 'Pvalue_mlog'
traitsManh: no visible binding for global variable 'Trait'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'gwcex2gviz':
gwcex2gviz
  Code: function(basegr = gwrngs, contextGR = GRanges(seqnames =
                 "chr17", IRanges(start = 37500000, width = 1e+06)),
                 txrefpk = "TxDb.Hsapiens.UCSC.hg19.knownGene", genome
                 = "hg19", genesympk = "org.Hs.eg.db", plot.it = TRUE,
                 maxmlp = 25)
  Docs: function(contextGR = GRanges(seqnames = "chr17", IRanges(start
                 = 37500000, width = 1e+06)), txrefpk =
                 "TxDb.Hsapiens.UCSC.hg19.knownGene", genesympk =
                 "org.Hs.eg.db", genome = "hg19", plot.it = TRUE)
  Argument names in code not in docs:
    basegr maxmlp
  Mismatches in argument names (first 3):
    Position: 1 Code: basegr Docs: contextGR
    Position: 2 Code: contextGR Docs: txrefpk
    Position: 3 Code: txrefpk Docs: genesympk

* 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 examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'rtracklayer'
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/gwascat.Rcheck/00check.log'
for details.

* installing *source* package 'gwascat' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'gwascat.Rnw' 
** testing if installed package can be loaded

* DONE (gwascat)

name	user	system	elapsed
gwascat-package	0.001	0.000	0.000
gwaswloc-class	0.003	0.001	0.004
gwcex2gviz	15.035	2.554	18.378
gwdf_2012_02_02	0	0	0
locon6	0.056	0.004	0.061
makeCurrentGwascat	0	0	0
riskyAlleleCount	18.427	2.117	20.765
topTraits	3.524	2.050	5.661
traitsManh	7.567	2.184	9.899