Package: ASEB

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ASEB_1.22.0.tar.gz

StartedAt: 2018-04-12 00:33:05 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:33:32 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 27.5 seconds

RetCode: 0

Status:  OK

CheckDir: ASEB.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 ASEB_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ASEB.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASEB/DESCRIPTION’ ... OK
* this is package ‘ASEB’ version ‘1.22.0’
* 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 ‘ASEB’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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
SequenceInfo: no visible global function definition for ‘new’
drawEScurve,data.frame: no visible global function definition for ‘pdf’
drawEScurve,data.frame: no visible global function definition for
  ‘jpeg’
drawEScurve,data.frame: no visible global function definition for
  ‘lines’
drawEScurve,data.frame: no visible global function definition for ‘rgb’
drawEScurve,data.frame: no visible global function definition for
  ‘dev.off’
drawStat,data.frame: no visible global function definition for ‘pdf’
drawStat,data.frame: no visible global function definition for ‘jpeg’
drawStat,data.frame: no visible global function definition for ‘lines’
drawStat,data.frame: no visible global function definition for
  ‘dev.off’
ids,SequenceInfo: no visible global function definition for ‘slot’
ids<-,SequenceInfo-character: no visible global function definition for
  ‘slot<-’
sequences,SequenceInfo: no visible global function definition for
  ‘slot’
sequences<-,SequenceInfo-character: no visible global function
  definition for ‘slot<-’
show,SequenceInfo: no visible global function definition for ‘show’
Undefined global functions or variables:
  dev.off jpeg lines new pdf rgb show slot slot<-
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "pdf", "rgb")
  importFrom("graphics", "lines")
  importFrom("methods", "new", "show", "slot", "slot<-")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘ASEB/libs/ASEB.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘asebC.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘asebC.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/ASEB.Rcheck/00check.log’
for details.

* installing *source* package ‘ASEB’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c asebC.cpp -o asebC.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ASEB.so asebC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/ASEB.Rcheck/ASEB/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ASEB)

name	user	system	elapsed
SequenceInfo	0.002	0.001	0.002
asebProteins	1.405	0.019	1.434
asebSites	0.965	0.015	0.995
drawEScurve	0.992	0.013	1.022
drawStat	1.306	0.013	1.353
readSequence	0.690	0.002	0.700