Package: gwascat

Version: 2.19.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gwascat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gwascat_2.19.1.tar.gz

StartedAt: 2020-01-16 05:18:13 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 05:28:01 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 588.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gwascat.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gwascat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gwascat_2.19.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/gwascat.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘2.19.1’
* package encoding: UTF-8
* 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 36.7Mb
  sub-directories of 1Mb or more:
    data     28.7Mb
    obo       3.0Mb
    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 ... NOTE
Namespace in Imports field not imported from: 'BiocGenerics'
  All declared Imports should be used.
* 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 binding for global variable ‘gwrngs19’
chklocs: no visible global function definition for ‘snpsBySeqname’
chklocs: no visible global function definition for ‘start’
gwdf2GRanges: no visible global function definition for ‘new’
lo38to19: no visible global function definition for ‘liftOver’
lo38to19: no visible global function definition for ‘metadata’
lo38to19: no visible global function definition for ‘metadata<-’
lo38to19: no visible global function definition for ‘sessionInfo’
lo38to19: no visible global function definition for ‘seqinfo<-’
lo38to19: no visible binding for global variable ‘si.hs.37’
lo38to19: no visible global function definition for ‘new’
locs4trait: no visible global function definition for ‘new’
makeConsecChrs: no visible global function definition for ‘seqinfo’
makeConsecChrs: no visible global function definition for ‘seqinfo<-’
makeCurrentGwascat: no visible global function definition for
  ‘seqinfo<-’
makeCurrentGwascat: no visible binding for global variable ‘si.hs.38’
makeCurrentGwascat: no visible global function definition for
  ‘metadata<-’
makeCurrentGwascat: no visible global function definition for
  ‘sessionInfo’
makeCurrentGwascat.legacy: no visible global function definition for
  ‘seqinfo<-’
makeCurrentGwascat.legacy: no visible binding for global variable
  ‘si.hs.38’
obo2graphNEL: no visible global function definition for ‘new’
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’
[,gwaswloc-ANY-ANY-ANY: no visible global function definition for ‘new’
show,gwaswloc: no visible global function definition for ‘show’
Undefined global functions or variables:
  PVALUE_MLOG getSNPlocs gwrngs gwrngs19 liftOver metadata metadata<-
  new phr seqinfo seqinfo<- sessionInfo show si.hs.37 si.hs.38
  snpsBySeqname start
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "start")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘si.hs.37’ ‘ebicat37 ’ ‘ebicat37UCSC ’ ‘ebicat_b37 ’ ‘ebicat_b38’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
File ‘data/datalist’ contains malformed line(s):
  ‘ebicat37 ’ ‘ebicat37UCSC ’ ‘ebicat_b37 ’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
riskyAlleleCount 20.526  0.326  22.542
gwcex2gviz       19.349  1.311  21.941
ldtagr            7.099  0.583   8.172
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* 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: 2 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/gwascat.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gwascat
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘gwascat’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gwascat)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("gwascat")
gwascat loaded.  Use makeCurrentGwascat() to extract current image.
 from EBI.  The data folder of this package has some legacy extracts.


RUNIT TEST PROTOCOL -- Thu Jan 16 05:27:50 2020 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gwascat RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 20.707   1.727  23.304 

name	user	system	elapsed
bindcadd_snv	0.001	0.000	0.001
gwascat-package	1.058	0.098	1.216
gwastagger	1.906	0.143	2.142
gwaswloc-class	0.003	0.001	0.005
gwcex2gviz	19.349	1.311	21.941
gwdf_2012_02_02	0.001	0.001	0.000
ldtagr	7.099	0.583	8.172
locon6	0.047	0.008	0.055
makeCurrentGwascat	0.001	0.000	0.001
obo2graphNEL	0.354	0.021	0.375
riskyAlleleCount	20.526	0.326	22.542
topTraits	0.832	0.084	0.995
traitsManh	0.000	0.000	0.001