BioC 3.5: CHECK report for CODEX on oaxaca

Package: CODEX

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CODEX_1.7.0.tar.gz

StartedAt: 2017-03-04 00:58:55 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 01:03:46 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 291.0 seconds

RetCode: 0

Status:  OK

CheckDir: CODEX.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CODEX_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CODEX.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.7.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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   36.795  0.625  41.313
normalize2  26.521  0.303  26.838
getcoverage  7.673  0.483  11.921
* 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-3.5-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	0.001	0.001	0.002
choiceofK	0.085	0.003	0.143
coverageObjDemo	0.001	0.000	0.001
gcDemo	0.001	0.001	0.001
getbambed	0.027	0.002	0.159
getcoverage	7.673	0.483	11.921
getgc	1.286	0.067	1.642
getmapp	0.095	0.005	0.098
mappDemo	0	0	0
mapp_ref	0.042	0.001	0.042
mappability	0.001	0.000	0.001
normObjDemo	0.000	0.000	0.002
normalize	36.795	0.625	41.313
normalize2	26.521	0.303	26.838
qc	0.042	0.000	0.042
qcObjDemo	0.001	0.000	0.001
segment	0.169	0.042	0.211