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BioC 3.2: CHECK report for CODEX on perceval

This page was generated on 2015-11-10 14:49:26 -0800 (Tue, 10 Nov 2015).

Package 207/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CODEX 1.2.0
Yuchao Jiang
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CODEX
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  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: CODEX
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CODEX_1.2.0.tar.gz
StartedAt: 2015-11-10 03:33:16 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 03:38:13 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 297.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CODEX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CODEX_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CODEX.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CODEX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CODEX’ 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 ‘CODEX’ can be installed ... [20s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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
getbambed: no visible global function definition for ‘IRanges’
getcoverage: no visible global function definition for ‘RangesList’
getcoverage: no visible global function definition for ‘IRanges’
getcoverage: no visible global function definition for ‘countOverlaps’
getgc: no visible global function definition for ‘unmasked’
getgc: no visible global function definition for ‘Views’
getgc: no visible global function definition for ‘alphabetFrequency’
getmapp: no visible global function definition for ‘countOverlaps’
* 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 ... [86s/90s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
normalize   36.011  0.807  36.820
normalize2  28.135  0.430  28.566
getcoverage  8.908  0.567  13.201
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/CODEX.Rcheck/00check.log’
for details.


CODEX.Rcheck/00install.out:

* installing *source* package ‘CODEX’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CODEX)

CODEX.Rcheck/CODEX-Ex.timings:

nameusersystemelapsed
bambedObjDemo0.0010.0020.003
choiceofK0.0120.0010.012
coverageObjDemo0.0010.0000.001
gcDemo0.0020.0000.001
getbambed0.0590.0020.119
getcoverage 8.908 0.56713.201
getgc1.1090.0951.310
getmapp0.0600.0060.065
mappDemo0.0010.0000.001
mapp_ref0.0070.0010.007
mappability0.0010.0000.001
normObjDemo0.0010.0000.001
normalize36.011 0.80736.820
normalize228.135 0.43028.566
qc0.0320.0000.033
qcObjDemo0.0010.0010.001
segment0.2390.0390.278