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

This page was generated on 2015-10-27 17:26:56 -0400 (Tue, 27 Oct 2015).

Package 212/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.2.0
Tiphaine Martin
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/coMET
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


coMET.Rcheck/00install.out:

* 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)

coMET.Rcheck/coMET-Ex.timings:

nameusersystemelapsed
COSMICTrack0.5750.0040.580
ClinVarCnvTrack0.2890.0000.289
ClinVarMainTrack0.330.000.33
CoreillCNVTrack0.2820.0000.283
DNAseUCSC0.3490.0000.349
GADTrack0.2740.0040.280
GWASTrack0.0540.0000.055
GeneReviewsTrack0.2720.0000.272
HistoneAll2.9060.0002.909
HistoneOne0.3650.0000.366
ISCATrack0.4820.0040.488
RepeatMaskerTrack0.8140.0040.819
chrUCSC2ENSEMBL0.0000.0000.002
chromatinHMMAll4.0510.0244.081
chromatinHMMOne0.5350.0000.536
coMET-package 3.841 0.01736.050
comet3.1590.0043.163
comet.list1.3560.0041.364
comet.web 15.415 0.126150.054
cpgIslandsUCSC0.2340.0000.234
gcContent0.1690.0000.168
genesENSEMBL0.5770.0000.577
genesNameENSEMBL0.0030.0000.003
knownGenesUCSC0.9200.0000.919
regulationBiomart0.3890.0000.389
snpBiomart0.5520.0000.553
snpLocationsUCSC1.5470.0001.548
structureBiomart0.5100.0000.515
transcriptENSEMBL0.8430.0000.845
xenorefGenesUCSC0.7000.0000.704