gwascat 1.12.0
VJ Carey
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/gwascat | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | 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-3.1-bioc/R/bin/R CMD check --no-vignettes --timings gwascat_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/gwascat.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘1.12.0’
* 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 ... [20s/29s] OK
* checking installed package size ... NOTE
installed size is 30.7Mb
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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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:
‘SNPlocs.Hsapiens.dbSNP.20120608’ ‘ggbio’ ‘graph’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘VariantAnnotation’
All declared Imports should be used.
':::' call which should be '::': ‘gQTLstats:::queryVCF’
See the note in ?`:::` about the use of this operator.
* 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’
ldtagr: no visible global function definition for ‘rowRanges’
ldtagr: no visible global function definition for ‘col.summary’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/34s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
riskyAlleleCount 6.359 0.030 8.108
gwcex2gviz 3.683 0.086 5.234
* 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
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.1-bioc/meat/gwascat.Rcheck/00check.log’
for details.
* installing *source* package ‘gwascat’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (gwascat)