Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.1: CHECK report for coMET on petty

This page was generated on 2015-10-09 09:37:12 -0700 (Fri, 09 Oct 2015).

Package 202/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.0.0
Tiphaine Martin
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/coMET
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: coMET
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coMET_1.0.0.tar.gz
StartedAt: 2015-10-08 22:15:52 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:28:46 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 773.2 seconds
RetCode: 0
Status:  OK 
CheckDir: coMET.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coMET_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/coMET.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.0.0’
* 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 ... [47s/47s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [128s/251s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
comet.web       36.555  2.155 151.497
coMET-package   10.453  1.111  22.513
comet            8.027  0.878   8.731
HistoneAll       7.950  0.588   8.426
chromatinHMMAll  7.907  0.610   8.409
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [23s/24s]
 [24s/24s] 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/coMET.Rcheck/00check.log’
for details.


coMET.Rcheck/00install.out:

* installing *source* package ‘coMET’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (coMET)

coMET.Rcheck/coMET-Ex.timings:

nameusersystemelapsed
COSMICTrack1.6360.1151.735
ClinVarCnvTrack0.9210.0660.976
ClinVarMainTrack0.9520.0691.010
CoreillCNVTrack0.9180.0620.969
DNAseUCSC1.0510.0791.116
GADTrack0.9010.0690.957
GWASTrack0.1560.0120.166
GeneReviewsTrack0.8850.0600.936
HistoneAll7.9500.5888.426
HistoneOne0.7460.0540.788
ISCATrack0.9380.0680.995
RepeatMaskerTrack1.3460.1001.424
chrUCSC2ENSEMBL0.0010.0000.002
chromatinHMMAll7.9070.6108.409
chromatinHMMOne1.0280.0811.094
coMET-package10.453 1.11122.513
comet8.0270.8788.731
comet.list2.4800.5132.867
comet.web 36.555 2.155151.497
cpgIslandsUCSC0.7840.0530.828
gcContent0.4430.0280.466
genesENSEMBL1.8250.1271.929
genesNameENSEMBL0.0080.0010.009
knownGenesUCSC2.3550.1652.489
regulationBiomart0.7230.0470.761
snpBiomart1.0450.0761.107
snpLocationsUCSC2.7030.2032.863
structureBiomart0.9770.0671.033
transcriptENSEMBL1.4910.1071.577
xenorefGenesUCSC1.2780.0901.351