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BioC 3.2: CHECK report for ensemblVEP on zin1

This page was generated on 2016-04-23 10:12:48 -0700 (Sat, 23 Apr 2016).

Package 320/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ensemblVEP 1.10.3
Bioconductor Package Maintainer
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ensemblVEP
Last Changed Rev: 115246 / Revision: 116712
Last Changed Date: 2016-03-24 13:28:37 -0700 (Thu, 24 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ensemblVEP
Version: 1.10.3
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ensemblVEP_1.10.3.tar.gz
StartedAt: 2016-04-23 00:22:23 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:29:12 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 408.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ensemblVEP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ensemblVEP_1.10.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ensemblVEP.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ensemblVEP/DESCRIPTION’ ... OK
* this is package ‘ensemblVEP’ version ‘1.10.3’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ensemblVEP’ can be installed ... [17s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 loading without being on the library search path ... 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
parseCSQToGRanges,VCF : .local: no visible global function definition
  for ‘elementLengths’
parseCSQToGRanges,VCF : .local: no visible global function definition
  for ‘DataFrame’
parseCSQToGRanges,VCF : .local: no visible global function definition
  for ‘genome<-’
show,VEPParam: no visible global function definition for
  ‘elementLengths’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/117s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ensemblVEP        1.496  0.143  53.788
parseCSQToGRanges 1.231  0.177  54.385
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [13s/121s]
 [13s/121s] 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/ensemblVEP.Rcheck/00check.log’
for details.


ensemblVEP.Rcheck/00install.out:

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

ensemblVEP.Rcheck/ensemblVEP-Ex.timings:

nameusersystemelapsed
VEPParam-class0.0280.0040.032
ensemblVEP 1.496 0.14353.788
parseCSQToGRanges 1.231 0.17754.385
runtimeOptions0.0000.0000.001