BioC 3.2: CHECK report for coMET on linux1.bioconductor.org

Package: coMET

Version: 1.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.2.0.tar.gz

StartedAt: 2015-10-27 02:24:25 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:32:40 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 494.9 seconds

RetCode: 0

Status:  OK

CheckDir: coMET.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/coMET.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 ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.2.0’
* 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 ... [25s/25s] 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 ... [54s/220s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
comet.web     15.415  0.126 150.054
coMET-package  3.841  0.017  36.050
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [13s/13s]
 [13s/13s] 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-3.2-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	0.575	0.004	0.580
ClinVarCnvTrack	0.289	0.000	0.289
ClinVarMainTrack	0.33	0.00	0.33
CoreillCNVTrack	0.282	0.000	0.283
DNAseUCSC	0.349	0.000	0.349
GADTrack	0.274	0.004	0.280
GWASTrack	0.054	0.000	0.055
GeneReviewsTrack	0.272	0.000	0.272
HistoneAll	2.906	0.000	2.909
HistoneOne	0.365	0.000	0.366
ISCATrack	0.482	0.004	0.488
RepeatMaskerTrack	0.814	0.004	0.819
chrUCSC2ENSEMBL	0.000	0.000	0.002
chromatinHMMAll	4.051	0.024	4.081
chromatinHMMOne	0.535	0.000	0.536
coMET-package	3.841	0.017	36.050
comet	3.159	0.004	3.163
comet.list	1.356	0.004	1.364
comet.web	15.415	0.126	150.054
cpgIslandsUCSC	0.234	0.000	0.234
gcContent	0.169	0.000	0.168
genesENSEMBL	0.577	0.000	0.577
genesNameENSEMBL	0.003	0.000	0.003
knownGenesUCSC	0.920	0.000	0.919
regulationBiomart	0.389	0.000	0.389
snpBiomart	0.552	0.000	0.553
snpLocationsUCSC	1.547	0.000	1.548
structureBiomart	0.510	0.000	0.515
transcriptENSEMBL	0.843	0.000	0.845
xenorefGenesUCSC	0.700	0.000	0.704