BioC experimental data: CHECK report for cgdv17 on morelia

Package: cgdv17

Version: 0.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cgdv17_0.9.0.tar.gz

StartedAt: 2015-11-25 10:11:38 -0800 (Wed, 25 Nov 2015)

EndedAt: 2015-11-25 10:16:00 -0800 (Wed, 25 Nov 2015)

EllapsedTime: 262.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cgdv17.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cgdv17_0.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/cgdv17.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cgdv17/DESCRIPTION’ ... OK
* this is package ‘cgdv17’ version ‘0.9.0’
* 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 ‘cgdv17’ can be installed ... [17s/36s] OK
* checking installed package size ... NOTE
  installed size is 240.1Mb
  sub-directories of 1Mb or more:
    data         5.6Mb
    rowranges  224.9Mb
    vcf          9.3Mb
* 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 ... NOTE
'library' or 'require' call to ‘org.Hs.eg.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘VariantAnnotation’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘VariantAnnotation::MatrixToSnpMatrix’
Missing object imported by a ':::' call: ‘IRanges:::newCompressedList’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getRVS: warning in dir(system.file("rowranges", package = packname),
  full = TRUE): partial argument match of 'full' to 'full.names'
padToReference: warning in matrix("0/0", nr = length(allv), nc =
  length(lens)): partial argument match of 'nr' to 'nrow'
padToReference: warning in matrix("0/0", nr = length(allv), nc =
  length(lens)): partial argument match of 'nc' to 'ncol'
padToReference : DS: no visible global function definition for
  ‘DNAStringSet’
padToReference: no visible global function definition for
  ‘DNAStringSet’
upstreamToEntrez: no visible binding for global variable
  ‘org.Hs.egCHRLOC’
Undefined global functions or variables:
  DNAStringSet org.Hs.egCHRLOC
* checking Rd files ... NOTE
prepare_Rd: cgdv17-package.Rd:51-52: Dropping empty section \references
prepare_Rd: cgdv17-package.Rd:54-55: Dropping empty section \seealso
prepare_Rd: cgdv17-package.Rd:56-57: Dropping empty section \examples
prepare_Rd: countVariants.Rd:53-54: Dropping empty section \examples
prepare_Rd: getRVS.Rd:34-40: Dropping empty section \value
prepare_Rd: getRVS.Rd:47-49: Dropping empty section \note
prepare_Rd: getRVS.Rd:41-43: Dropping empty section \references
prepare_Rd: getRVS.Rd:53-55: Dropping empty section \seealso
prepare_Rd: getRVS.Rd:56-57: Dropping empty section \examples
prepare_Rd: padToReference.Rd:32-34: Dropping empty section \details
prepare_Rd: padToReference.Rd:35-41: Dropping empty section \value
prepare_Rd: padToReference.Rd:48-50: Dropping empty section \note
prepare_Rd: padToReference.Rd:42-44: Dropping empty section \references
prepare_Rd: padToReference.Rd:54-56: Dropping empty section \seealso
prepare_Rd: padToReference.Rd:57-58: Dropping empty section \examples
prepare_Rd: raggedVariantSet-class.Rd:40-42: Dropping empty section \note
prepare_Rd: raggedVariantSet-class.Rd:34-36: Dropping empty section \references
prepare_Rd: raggedVariantSet-class.Rd:46-49: Dropping empty section \seealso
prepare_Rd: variantGRanges.Rd:31-33: Dropping empty section \details
prepare_Rd: variantGRanges.Rd:34-40: Dropping empty section \value
prepare_Rd: variantGRanges.Rd:47-49: Dropping empty section \note
prepare_Rd: variantGRanges.Rd:41-43: Dropping empty section \references
prepare_Rd: variantGRanges.Rd:53-55: Dropping empty section \seealso
prepare_Rd: variantGRanges.Rd:56-57: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'raggedVariantSet,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
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 ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] 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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/cgdv17.Rcheck/00check.log’
for details.

* installing *source* package ‘cgdv17’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cgdv17)

name	user	system	elapsed
raggedVariantSet-class	0.002	0.000	0.001