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BioC experimental data: CHECK report for cgdv17 on moscato1

This page was generated on 2015-04-08 17:41:06 -0700 (Wed, 08 Apr 2015).

Package 34/219HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cgdv17 0.3.2
VJ Carey
Snapshot Date: 2015-04-08 06:15:26 -0700 (Wed, 08 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_0/experiment/pkgs/cgdv17
Last Changed Rev: 3075 / Revision: 3266
Last Changed Date: 2014-10-13 14:52:40 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: cgdv17
Version: 0.3.2
Command: rm -rf cgdv17.buildbin-libdir cgdv17.Rcheck && mkdir cgdv17.buildbin-libdir cgdv17.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cgdv17.buildbin-libdir cgdv17_0.3.2.tar.gz >cgdv17.Rcheck\00install.out 2>&1 && cp cgdv17.Rcheck\00install.out cgdv17-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=cgdv17.buildbin-libdir --install="check:cgdv17-install.out" --force-multiarch --no-vignettes --timings cgdv17_0.3.2.tar.gz
StartedAt: 2015-04-08 09:23:38 -0700 (Wed, 08 Apr 2015)
EndedAt: 2015-04-08 09:39:04 -0700 (Wed, 08 Apr 2015)
EllapsedTime: 925.8 seconds
RetCode: 0
Status:  OK  
CheckDir: cgdv17.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cgdv17.buildbin-libdir cgdv17.Rcheck && mkdir cgdv17.buildbin-libdir cgdv17.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cgdv17.buildbin-libdir cgdv17_0.3.2.tar.gz >cgdv17.Rcheck\00install.out 2>&1 && cp cgdv17.Rcheck\00install.out cgdv17-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=cgdv17.buildbin-libdir --install="check:cgdv17-install.out" --force-multiarch --no-vignettes --timings cgdv17_0.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-data-experiment/meat/cgdv17.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cgdv17/DESCRIPTION' ... OK
* this is package 'cgdv17' version '0.3.2'
* 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 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 'build' directory ... 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'GGtools' 'TxDb.Hsapiens.UCSC.hg19.knownGene' 'VariantAnnotation'
  'methods' 'org.Hs.eg.db' 'parallel'
  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("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'
.variantGRanges : <anonymous>: no visible global function definition
  for 'ranges'
.variantGRanges : <anonymous>: no visible global function definition
  for 'elementMetadata'
padToReference : fixup: no visible global function definition for
  'overlapsAny'
padToReference: no visible global function definition for
  'elementMetadata'
padToReference : DS: no visible global function definition for
  'overlapsAny'
padToReference : DS: no visible global function definition for
  'DNAStringSet'
padToReference: no visible global function definition for
  'elementLengths'
padToReference: no visible global function definition for
  'DNAStringSet'
upstreamToEntrez: no visible binding for global variable
  'org.Hs.egCHRLOC'
upstreamToEntrez: no visible global function definition for 'GRanges'
upstreamToEntrez: no visible global function definition for 'IRanges'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [20s] OK
** running examples for arch 'x64' ... [23s] 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

NOTE: There were 5 notes.
See
  'D:/biocbld/bbs-3.0-data-experiment/meat/cgdv17.Rcheck/00check.log'
for details.

cgdv17.Rcheck/00install.out:


install for i386

* installing *source* package 'cgdv17' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: %in%
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: %in%

install for x64

* installing *source* package 'cgdv17' ...
** testing if installed package can be loaded
No methods found in "IRanges" for requests: %in%
* MD5 sums
packaged installation of 'cgdv17' as cgdv17_0.3.2.zip
* DONE (cgdv17)

cgdv17.Rcheck/examples_i386/cgdv17-Ex.timings:

nameusersystemelapsed
raggedVariantSet-class000

cgdv17.Rcheck/examples_x64/cgdv17-Ex.timings:

nameusersystemelapsed
raggedVariantSet-class000