gwascat 1.10.0
VJ Carey
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/gwascat | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | 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 gwascat_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/gwascat.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 ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘1.10.0’
* 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 ‘gwascat’ can be installed ... [24s/25s] OK
* checking installed package size ... NOTE
installed size is 30.6Mb
sub-directories of 1Mb or more:
data 25.0Mb
obo 1.3Mb
olddata 2.2Mb
tab 1.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘Gviz’ ‘SNPlocs.Hsapiens.dbSNP.20120608’ ‘ggbio’ ‘graph’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bindcadd_snv: no visible global function definition for ‘findOverlaps’
chklocs: no visible binding for global variable ‘gwrngs19’
chklocs: no visible global function definition for ‘getSNPlocs’
descendants: no visible global function definition for ‘adj’
gwcex2gviz: no visible global function definition for ‘exons’
gwcex2gviz: no visible global function definition for ‘GeneRegionTrack’
gwcex2gviz: no visible global function definition for ‘DataTrack’
gwcex2gviz: no visible global function definition for ‘displayPars’
gwcex2gviz: no visible global function definition for ‘displayPars<-’
gwcex2gviz: no visible global function definition for ‘plotTracks’
gwcex2gviz: no visible global function definition for ‘GenomeAxisTrack’
makeCurrentGwascat: no visible binding for global variable ‘si.hs.38’
obo2graphNEL: no visible global function definition for
‘nodeDataDefaults<-’
obo2graphNEL: no visible global function definition for ‘nodeData<-’
obo2graphNEL: no visible global function definition for ‘nodes’
parentingDF: no visible global function definition for ‘subGraph’
parentingDF: no visible global function definition for ‘nodeData’
parentingDF: no visible global function definition for ‘extractFromTo’
snpGenos: no visible global function definition for ‘getSNPlocs’
traitsManh: no visible global function definition for ‘autoplot’
traitsManh: no visible global function definition for ‘aes’
traitsManh: no visible binding for global variable ‘Pvalue_mlog’
variantProps: no visible binding for global variable ‘gwrngs’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [35s/38s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
gwcex2gviz 9.397 0.252 10.360
riskyAlleleCount 8.760 0.088 8.889
* 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 3 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/gwascat.Rcheck/00check.log’
for details.