BioC 3.3: CHECK report for coMET on morelia

Package: coMET

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coMET_1.3.0.tar.gz

StartedAt: 2016-04-21 00:48:42 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 01:01:50 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 788.2 seconds

RetCode: 0

Status:  OK

CheckDir: coMET.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coMET_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/coMET.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [33s/39s] 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 ... NOTE
create.color.bar: no visible global function definition for
  'read.table'
read.config: no visible global function definition for 'read.table'
read.file.cormatrix: no visible global function definition for
  'read.delim'
read.file.mydata: no visible global function definition for
  'read.delim'
read.file.mydata.large: no visible global function definition for
  'read.delim'
write.comet.list: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  read.delim read.table write.table
Consider adding
  importFrom("utils", "read.delim", "read.table", "write.table")
to your NAMESPACE file.
* 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 ... [69s/412s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
comet.web     17.679  0.413 337.908
coMET-package  6.134  0.110  26.316
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [17s/19s]
 [17s/19s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/coMET.Rcheck/00check.log’
for details.

* installing *source* package ‘coMET’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
* DONE (coMET)

name	user	system	elapsed
COSMICTrack	1.518	0.012	1.554
ClinVarCnvTrack	0.559	0.045	0.606
ClinVarMainTrack	0.480	0.003	0.485
CoreillCNVTrack	0.493	0.003	0.495
DNAseUCSC	0.548	0.003	0.551
GADTrack	0.546	0.003	0.553
GWASTrack	0.114	0.002	0.155
GeneReviewsTrack	0.448	0.002	0.451
HistoneAll	4.460	0.011	4.577
HistoneOne	0.378	0.002	0.401
ISCATrack	0.470	0.003	0.509
RepeatMaskerTrack	0.604	0.003	0.607
chrUCSC2ENSEMBL	0.001	0.000	0.001
chromatinHMMAll	4.176	0.011	4.221
chromatinHMMOne	0.507	0.002	0.514
coMET-package	6.134	0.110	26.316
comet	4.101	0.027	4.149
comet.list	1.519	0.018	1.540
comet.web	17.679	0.413	337.908
cpgIslandsUCSC	0.379	0.002	0.439
gcContent	0.269	0.006	0.282
genesENSEMBL	1.000	0.004	1.011
genesNameENSEMBL	0.006	0.002	0.722
knownGenesUCSC	1.349	0.005	1.835
regulationBiomart	0.478	0.003	0.511
snpBiomart	0.593	0.003	0.602
snpLocationsUCSC	1.432	0.004	1.446
structureBiomart	0.538	0.004	0.545
transcriptENSEMBL	0.812	0.003	0.821
xenorefGenesUCSC	0.819	0.003	0.833