BioC 3.6: CHECK report for CODEX on malbec1

Package: CODEX

Version: 1.9.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CODEX_1.9.0.tar.gz

StartedAt: 2017-08-15 22:09:23 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:13:12 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 228.6 seconds

RetCode: 0

Status:  OK

CheckDir: CODEX.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CODEX_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CODEX.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.9.0’
* 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   26.120  0.016  26.551
normalize2  20.264  0.008  20.378
getcoverage  9.040  0.208  11.088
* 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-3.6-bioc/meat/CODEX.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
bambedObjDemo	0.000	0.000	0.001
choiceofK	0.020	0.004	0.021
coverageObjDemo	0	0	0
gcDemo	0.000	0.000	0.001
getbambed	0.020	0.000	0.103
getcoverage	9.040	0.208	11.088
getgc	0.844	0.032	1.460
getmapp	0.068	0.008	0.075
mappDemo	0.000	0.000	0.001
mapp_ref	0.028	0.000	0.031
mappability	0.000	0.000	0.001
normObjDemo	0	0	0
normalize	26.120	0.016	26.551
normalize2	20.264	0.008	20.378
qc	0.020	0.008	0.028
qcObjDemo	0.000	0.000	0.001
segment	0.120	0.012	0.131