BioC 3.4: CHECK report for RCAS on zin1

Package: RCAS

Version: 0.99.4

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RCAS_0.99.4.tar.gz

StartedAt: 2016-09-20 11:17:47 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:25:22 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 455.4 seconds

RetCode: 0

Status:  OK

CheckDir: RCAS.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RCAS_0.99.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RCAS.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCAS’ version ‘0.99.4’
* 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 ‘RCAS’ can be installed ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
runTopGO: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
runMotifRG                           31.584  1.652  19.509
getMotifSummaryTable                 30.076  1.456  19.390
calculateCoverageProfileList          9.912  0.152  10.066
calculateCoverageProfile              9.112  0.152   9.266
calculateCoverageProfileListFromTxdb  8.716  0.136   8.849
getTargetedGenesTable                 7.116  0.140   7.256
summarizeQueryRegions                 6.916  0.156   7.071
getTxdbFeaturesFromGff                6.560  0.120   6.682
getTxdbFeatures                       5.664  0.076   5.743
retrieveOrthologs                     0.112  0.004  12.762
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/RCAS.Rcheck/00check.log’
for details.

* installing *source* package ‘RCAS’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (RCAS)

name	user	system	elapsed
calculateCoverageProfile	9.112	0.152	9.266
calculateCoverageProfileFromTxdb	4.640	0.120	4.762
calculateCoverageProfileList	9.912	0.152	10.066
calculateCoverageProfileListFromTxdb	8.716	0.136	8.849
createControlRegions	0.256	0.000	0.258
createOrthologousMsigdbDataset	0	0	0
extractSequences	0.992	0.024	1.022
getFeatureBoundaryCoverage	4.228	0.084	4.323
getFeatureBoundaryCoverageBin	4.776	0.088	4.872
getMotifSummaryTable	30.076	1.456	19.390
getTargetedGenesTable	7.116	0.140	7.256
getTxdbFeatures	5.664	0.076	5.743
getTxdbFeaturesFromGff	6.560	0.120	6.682
importBed	0.216	0.004	0.221
importGtf	0.000	0.000	0.001
parseMsigdb	0.004	0.000	0.002
printMsigdbDataset	0.16	0.02	0.18
queryGff	0.988	0.056	1.044
retrieveOrthologs	0.112	0.004	12.762
runMSIGDB	2.476	0.072	2.549
runMotifRG	31.584	1.652	19.509
runReport	0.004	0.000	0.002
runTopGO	0.000	0.000	0.001
summarizeQueryRegions	6.916	0.156	7.071