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 |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings cgdv17_0.3.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-data-experiment/meat/cgdv17.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cgdv17’ can be installed ... [43s/46s] 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
* 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 ... [21s/21s] 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
‘/home/biocbuild/bbs-3.0-data-experiment/meat/cgdv17.Rcheck/00check.log’
for details.
* 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%
* DONE (cgdv17)