ELMER 1.1.1
Lijing Yao
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ELMER | | Last Changed Rev: 107508 / Revision: 107696 | | Last Changed Date: 2015-08-17 11:04:16 -0700 (Mon, 17 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / 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 ELMER_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ELMER.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘1.1.1’
* 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 ‘ELMER’ can be installed ... [33s/35s] OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘ELMER.data’ ‘Homo.sapiens’
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get.feature.probe: no visible binding for global variable
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
motif.enrichment.plot: no visible binding for global variable ‘upperOR’
motif.enrichment.plot: no visible binding for global variable ‘lowerOR’
motif.enrichment.plot: no visible binding for global variable ‘motif’
motif.enrichment.plot: no visible binding for global variable ‘OR’
scatter: no visible binding for global variable ‘value’
TF.rank.plot: no visible binding for global variable ‘pvalue’
TF.rank.plot: no visible binding for global variable ‘label’
txs: no visible binding for global variable ‘Homo.sapiens’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [141s/143s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
get.feature.probe 18.953 2.295 21.978
get.pair 14.459 0.619 15.089
GetNearGenes 10.276 0.770 11.926
schematic.plot 10.383 0.285 10.680
getGeneInfo 7.969 0.429 8.404
fetch.pair 8.057 0.230 8.314
get.permu 6.434 0.477 6.912
getSymbol 5.634 0.305 5.939
scatter.plot 5.735 0.120 5.862
txs 5.530 0.284 5.881
getGeneID 5.358 0.280 5.638
get.enriched.motif 4.770 0.666 5.439
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/ELMER.Rcheck/00check.log’
for details.
* installing *source* package ‘ELMER’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
* DONE (ELMER)