BioC 3.5: CHECK report for ldblock on malbec2

Package: ldblock

Version: 1.6.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ldblock_1.6.0.tar.gz

StartedAt: 2017-08-16 00:09:56 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:14:40 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 284.0 seconds

RetCode: 0

Status:  OK

CheckDir: ldblock.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ldblock_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ldblock.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ldblock/DESCRIPTION’ ... OK
* this is package ‘ldblock’ version ‘1.6.0’
* 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 ‘ldblock’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 40.4Mb
  sub-directories of 1Mb or more:
    hapmap  39.9Mb
* 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
Package in Depends field not imported from: ‘Homo.sapiens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
downloadPopByChr: no visible global function definition for
  ‘download.file’
hmld: no visible global function definition for ‘read.delim’
stack1kg: no visible global function definition for ‘seqinfo<-’
stack1kg: no visible global function definition for ‘seqinfo’
Undefined global functions or variables:
  download.file read.delim seqinfo seqinfo<-
Consider adding
  importFrom("utils", "download.file", "read.delim")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: downloadPopByChr.Rd:49-51: 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
expandSnpSet 32.508  2.836  35.371
ldByGene      3.420  1.768   5.636
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘ldblock_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocStyle’
'library' or 'require' call not declared from: ‘gwascat’
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/ldblock.Rcheck/00check.log’
for details.

* installing *source* package ‘ldblock’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (ldblock)

name	user	system	elapsed
downloadPopByChr	0.000	0.000	0.001
expandSnpSet	32.508	2.836	35.371
hmld	0.000	0.000	0.001
ldByGene	3.420	1.768	5.636
ldblock-package	0.004	0.000	0.000
ldstruct-class	0.000	0.000	0.001
s3_1kg	0.012	0.004	0.014