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cgdv17 0.0.17
VJ Carey
Snapshot Date: 2012-06-21 11:15:08 -0700 (Thu, 21 Jun 2012)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/cgdv17
Last Changed Rev: 2043 / Revision: 2088
Last Changed Date: 2012-04-14 07:53:59 -0700 (Sat, 14 Apr 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  ERROR  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: cgdv17
Version: 0.0.17
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cgdv17_0.0.17.tar.gz
StartedAt: 2012-06-21 14:05:18 -0700 (Thu, 21 Jun 2012)
EndedAt: 2012-06-21 14:17:03 -0700 (Thu, 21 Jun 2012)
EllapsedTime: 705.5 seconds
RetCode: 0
Status:  OK 
CheckDir: cgdv17.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/cgdv17.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'cgdv17/DESCRIPTION' ... OK
* this is package 'cgdv17' version '0.0.17'
* 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 whether package 'cgdv17' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 240.1Mb
  sub-directories of 1Mb or more:
    data       5.6Mb
    rowdata  224.9Mb
    vcf        9.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* checking top-level 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 for unstated 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
getRVS: warning in dir(system.file("rowdata", 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'
* 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 ... OK
* 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 examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  '/Users/biocbuild/bbs-2.11-data-experiment/meat/cgdv17.Rcheck/00check.log'
for details.

cgdv17.Rcheck/00install.out:

* installing *source* package 'cgdv17' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'cgdv.Rnw' 
** testing if installed package can be loaded
Creating a generic function for 'ls' from package 'base' in package 'AnnotationDbi'
Creating a generic function for 'eapply' from package 'base' in package 'AnnotationDbi'
Creating a generic function for 'exists' from package 'base' in package 'AnnotationDbi'
Creating a generic function for 'sample' from package 'base' in package 'AnnotationDbi'
Warning in namespaceImportMethods(ns, loadNamespace(imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "AnnotationDbi" (malformed exports?)
Warning in namespaceImportMethods(ns, loadNamespace(imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "AnnotationDbi" (malformed exports?)

* DONE (cgdv17)

cgdv17.Rcheck/cgdv17-Ex.timings:

nameusersystemelapsed
raggedVariantSet-class0.0020.0010.002