Package: erma

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:erma.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings erma_1.0.0.tar.gz

StartedAt: 2019-10-16 02:38:54 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:47:03 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 489.4 seconds

RetCode: 0

Status:  OK

CheckDir: erma.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:erma.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings erma_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/erma.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘erma/DESCRIPTION’ ... OK
* this is package ‘erma’ 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 ‘erma’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 199.1Mb
  sub-directories of 1Mb or more:
    bed_tabix  161.3Mb
    data        37.1Mb
* 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 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
geneTxRange: no visible global function definition for ‘select’
genemodelOLD: no visible binding for global variable ‘exonsBy’
stateProfile: no visible binding for global variable ‘states_25’
stateProfile: no visible binding for global variable ‘short_celltype’
stateProfile: no visible binding for global variable ‘name’
statesByRange: no visible binding for global variable ‘mod’
statesByRange: no visible binding for global variable ‘upstream’
statesByRange: no visible binding for global variable ‘downstream’
statesByRange : : no visible binding for global variable
  ‘tss’
statesByRange: no visible binding for global variable ‘states_25’
Undefined global functions or variables:
  downstream exonsBy mod name select short_celltype states_25 tss
  upstream
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
erma-package 14.824  2.703  14.933
stateProfile  7.622  2.628   7.639
* 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-3.9-bioc/meat/erma.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL erma
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘erma’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (erma)

name	user	system	elapsed
ErmaSet-class	0.553	0.012	0.566
erma-package	14.824	2.703	14.933
genemodel	3.051	0.335	3.386
mapmeta	0.313	0.007	0.321
stateProfile	7.622	2.628	7.639
states_25	0.003	0.004	0.006