BioC 3.5: CHECK report for gQTLBase on veracruz2

Package: gQTLBase

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gQTLBase_1.8.0.tar.gz

StartedAt: 2017-10-18 04:31:52 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:36:52 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 300.6 seconds

RetCode: 0

Status:  OK

CheckDir: gQTLBase.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gQTLBase_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/gQTLBase.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gQTLBase/DESCRIPTION’ ... OK
* this is package ‘gQTLBase’ 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 ‘gQTLBase’ can be installed ... OK
* checking installed package size ... OK
* 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
.describeStore: no visible global function definition for ‘getJobInfo’
.extractByProbes: no visible binding for global variable ‘x’
.extractByRanges: no visible global function definition for
  ‘subsetByOverlaps’
.extractByRanges: no visible binding for global variable ‘x’
DFstoreToFf: no visible binding for global variable ‘x’
cb2range: no visible global function definition for ‘select’
cb2range: no visible global function definition for ‘IRanges’
dendroReduce.bj: no visible global function definition for ‘batchMap’
dendroReduce.fe: no visible binding for global variable ‘i’
describeStore.old: no visible global function definition for ‘hist’
ffapp2: no visible global function definition for ‘as.ff’
ffapp2: no visible global function definition for ‘appendLevels’
ffapp2: no visible global function definition for ‘as.which’
mergeGWhits: no visible global function definition for ‘genome’
storeApply: no visible binding for global variable ‘x’
storeApply2: no visible binding for global variable ‘x’
storeToFf: no visible binding for global variable ‘x’
show,storeDescription: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  IRanges appendLevels as.ff as.which batchMap genome getJobInfo hist i
  median select subsetByOverlaps x
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: ufeatByTiling.Rd:50-52: Dropping empty section \seealso
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
storeApply      23.000  0.796  24.737
mergeCIstates    7.665  0.265   8.886
extractByProbes  6.763  0.223   7.264
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘BiocParallel’
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/gQTLBase.Rcheck/00check.log’
for details.

* installing *source* package ‘gQTLBase’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gQTLBase)

name	user	system	elapsed
ciseStore-class	0.506	0.030	0.550
describeStore	0.000	0.000	0.001
extractByProbes	6.763	0.223	7.264
mergeCIstates	7.665	0.265	8.886
storeApply	23.000	0.796	24.737
storeMapResults	0	0	0
storeToFf	0.621	0.026	0.662
ufeatByTiling	0	0	0