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BioC 3.5: CHECK report for CODEX on malbec2

This page was generated on 2017-10-18 14:16:30 -0400 (Wed, 18 Oct 2017).

Package 258/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CODEX 1.8.0
Yuchao Jiang
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/CODEX
Branch: RELEASE_3_5
Last Commit: cb12205
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CODEX
Version: 1.8.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CODEX_1.8.0.tar.gz
StartedAt: 2017-10-17 22:12:10 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:15:59 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 229.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CODEX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CODEX_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/CODEX.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Rsamtools’ ‘GenomeInfoDb’ ‘BSgenome.Hsapiens.UCSC.hg19’ ‘IRanges’
  ‘Biostrings’ ‘S4Vectors’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... 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
choiceofK: no visible global function definition for ‘pdf’
choiceofK: no visible global function definition for ‘par’
choiceofK: no visible global function definition for ‘plot’
choiceofK: no visible global function definition for ‘dev.off’
getbambed: no visible global function definition for ‘read.table’
normalize : <anonymous>: no visible global function definition for
  ‘smooth.spline’
normalize : <anonymous>: no visible global function definition for
  ‘predict’
normalize: no visible global function definition for ‘glm’
normalize: no visible binding for global variable ‘poisson’
normalize: no visible global function definition for ‘lm’
normalize2 : <anonymous>: no visible global function definition for
  ‘smooth.spline’
normalize2 : <anonymous>: no visible global function definition for
  ‘predict’
normalize2: no visible global function definition for ‘glm’
normalize2: no visible binding for global variable ‘poisson’
normalize2: no visible global function definition for ‘lm’
Undefined global functions or variables:
  dev.off glm lm par pdf plot poisson predict read.table smooth.spline
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "glm", "lm", "poisson", "predict", "smooth.spline")
  importFrom("utils", "read.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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
normalize   26.172  0.036  26.634
normalize2  21.388  0.028  21.495
getcoverage  9.724  0.288  10.747
* 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-3.5-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
bambedObjDemo0.0000.0000.002
choiceofK0.0320.0000.034
coverageObjDemo0.0040.0000.001
gcDemo0.0000.0000.002
getbambed0.0280.0000.050
getcoverage 9.724 0.28810.747
getgc1.0160.0561.347
getmapp0.0720.0000.070
mappDemo0.0000.0000.001
mapp_ref0.0600.0000.061
mappability0.0000.0000.001
normObjDemo0.0040.0000.001
normalize26.172 0.03626.634
normalize221.388 0.02821.495
qc0.0360.0000.035
qcObjDemo000
segment0.1200.0160.138