BioC 3.3: CHECK report for coMET on linux2.bioconductor.org

Package: coMET

Version: 1.3.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.3.0.tar.gz

StartedAt: 2015-10-20 02:52:11 -0400 (Tue, 20 Oct 2015)

EndedAt: 2015-10-20 02:59:31 -0400 (Tue, 20 Oct 2015)

EllapsedTime: 439.4 seconds

RetCode: 0

Status:  OK

CheckDir: coMET.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/coMET.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.3.0’
* 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 ‘coMET’ can be installed ... [19s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* 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 ... [52s/202s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
comet.web     14.213  0.082 144.327
coMET-package  4.251  0.041  24.371
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/11s]
 [11s/11s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/coMET.Rcheck/00check.log’
for details.

* installing *source* package ‘coMET’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (coMET)

name	user	system	elapsed
COSMICTrack	0.605	0.004	0.611
ClinVarCnvTrack	0.505	0.004	0.510
ClinVarMainTrack	0.520	0.000	0.521
CoreillCNVTrack	0.384	0.000	0.384
DNAseUCSC	0.353	0.000	0.354
GADTrack	0.475	0.000	0.475
GWASTrack	0.087	0.000	0.086
GeneReviewsTrack	0.439	0.000	0.439
HistoneAll	4.537	0.000	4.540
HistoneOne	0.395	0.004	0.399
ISCATrack	0.528	0.000	0.529
RepeatMaskerTrack	0.760	0.004	0.763
chrUCSC2ENSEMBL	0.000	0.000	0.001
chromatinHMMAll	3.604	0.004	3.608
chromatinHMMOne	0.329	0.000	0.329
coMET-package	4.251	0.041	24.371
comet	3.513	0.008	3.523
comet.list	1.349	0.004	1.353
comet.web	14.213	0.082	144.327
cpgIslandsUCSC	0.424	0.000	0.425
gcContent	0.277	0.000	0.278
genesENSEMBL	0.943	0.000	0.943
genesNameENSEMBL	0.005	0.000	0.005
knownGenesUCSC	1.132	0.000	1.133
regulationBiomart	0.233	0.000	0.234
snpBiomart	0.346	0.000	0.346
snpLocationsUCSC	0.919	0.000	0.918
structureBiomart	0.321	0.000	0.322
transcriptENSEMBL	0.519	0.000	0.518
xenorefGenesUCSC	0.686	0.000	0.686