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BioC 3.5: CHECK report for ldblock on malbec2

This page was generated on 2017-08-16 13:16:54 -0400 (Wed, 16 Aug 2017).

Package 709/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ldblock 1.6.0
VJ Carey
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ldblock
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


ldblock.Rcheck/00install.out:

* 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)

ldblock.Rcheck/ldblock-Ex.timings:

nameusersystemelapsed
downloadPopByChr0.0000.0000.001
expandSnpSet32.508 2.83635.371
hmld0.0000.0000.001
ldByGene3.4201.7685.636
ldblock-package0.0040.0000.000
ldstruct-class0.0000.0000.001
s3_1kg0.0120.0040.014