BioC 3.3: CHECK report for gwascat on zin2

Package: gwascat

Version: 2.4.2

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings gwascat_2.4.2.tar.gz

StartedAt: 2016-10-13 03:04:05 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:09:39 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 334.1 seconds

RetCode: 0

Status:  OK

CheckDir: gwascat.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings gwascat_2.4.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/gwascat.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘2.4.2’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 38.7Mb
  sub-directories of 1Mb or more:
    data     30.9Mb
    obo       3.1Mb
    olddata   2.2Mb
    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
buildq: no visible global function definition for 'read.delim'
chklocs: no visible binding for global variable 'gwrngs19'
chklocs: no visible global function definition for 'getSNPlocs'
lo38to19: no visible global function definition for 'sessionInfo'
lo38to19: no visible global function definition for 'data'
lo38to19: no visible binding for global variable 'si.hs.37'
makeCurrentGwascat: no visible global function definition for
  'read.delim'
makeCurrentGwascat: no visible global function definition for 'data'
makeCurrentGwascat: no visible binding for global variable 'si.hs.38'
makeCurrentGwascat: no visible global function definition for
  'sessionInfo'
makeCurrentGwascat.legacy: no visible global function definition for
  'read.delim'
makeCurrentGwascat.legacy: no visible global function definition for
  'data'
makeCurrentGwascat.legacy: no visible binding for global variable
  'si.hs.38'
snpGenos: no visible global function definition for 'getSNPlocs'
tfilt: no visible binding for global variable 'phr'
tpad: no visible binding for global variable 'phr'
traitsManh: no visible binding for global variable 'PVALUE_MLOG'
variantProps: no visible binding for global variable 'gwrngs'
Undefined global functions or variables:
  PVALUE_MLOG data getSNPlocs gwrngs gwrngs19 phr read.delim
  sessionInfo si.hs.37 si.hs.38
Consider adding
  importFrom("utils", "data", "read.delim", "sessionInfo")
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 ... NOTE
  Note: found 6 marked Latin-1 strings
  Note: found 1 marked UTF-8 string
* 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
riskyAlleleCount 10.049  0.028  10.085
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocStyle’
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/gwascat.Rcheck/00check.log’
for details.

* installing *source* package ‘gwascat’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
* DONE (gwascat)

name	user	system	elapsed
bindcadd_snv	0	0	0
gwascat-package	0.001	0.000	0.001
gwastagger	2.371	0.044	2.418
gwaswloc-class	0.002	0.000	0.002
gwcex2gviz	4.831	0.116	4.957
gwdf_2012_02_02	0.000	0.000	0.001
ldtagr	0.680	0.016	0.714
locon6	0.028	0.000	0.028
makeCurrentGwascat	0.001	0.000	0.001
obo2graphNEL	0.21	0.00	0.21
riskyAlleleCount	10.049	0.028	10.085
topTraits	0.324	0.000	0.324
traitsManh	0.720	0.004	0.725