ggtut 0.7.0
VJ Carey
| Snapshot Date: 2015-06-27 06:15:26 -0700 (Sat, 27 Jun 2015) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ggtut | | Last Changed Rev: 3281 / Revision: 3341 | | Last Changed Date: 2015-04-16 13:20:43 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggtut_0.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/ggtut.Rcheck’
* using R version 3.2.1 (2015-06-18)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggtut/DESCRIPTION’ ... OK
* this is package ‘ggtut’ version ‘0.7.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘GGtools’ ‘ff’ ‘GenomicRanges’ ‘snpStats’ ‘GGdata’ ‘GenomicFeatures’
‘ChIPpeakAnno’ ‘Rsamtools’ ‘cheung2010’
‘SNPlocs.Hsapiens.dbSNP.20120608’ ‘hmyriB36’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘ggtut’ can be installed ... [47s/51s] OK
* checking installed package size ... NOTE
installed size is 189.3Mb
sub-directories of 1Mb or more:
bam 15.1Mb
data 22.3Mb
ffarchives 136.9Mb
ffobjects 1.6Mb
images 12.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘GenomicFeatures’ ‘ChIPpeakAnno’
A package should be listed in only one of these fields.
* 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 ‘TxDb.Hsapiens.UCSC.hg18.knownGene’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘cheung2010’ ‘ChIPpeakAnno’ ‘ff’ ‘GenomicFeatures’ ‘GenomicRanges’
‘GGdata’ ‘GGtools’ ‘hmyriB36’ ‘Rsamtools’
‘SNPlocs.Hsapiens.dbSNP.20120608’ ‘snpStats’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getFixedBFL: no visible global function definition for ‘BamFileList’
getFixedBFL: no visible global function definition for ‘path’
hg18tx: no visible binding for global variable
‘TxDb.Hsapiens.UCSC.hg18.knownGene’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/33s] OK
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.2-data-experiment/meat/ggtut.Rcheck/00check.log’
for details.
* installing *source* package ‘ggtut’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘stats::IQR’ when loading ‘GGBase’
No methods found in "IRanges" for requests: aggregate
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘stats::IQR’ when loading ‘GGBase’
No methods found in "IRanges" for requests: aggregate
* DONE (ggtut)