Package: exomeCopy

Version: 1.29.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:exomeCopy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings exomeCopy_1.29.0.tar.gz

StartedAt: 2019-04-09 00:48:44 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:50:46 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 122.1 seconds

RetCode: 0

Status:  OK

CheckDir: exomeCopy.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:exomeCopy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings exomeCopy_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/exomeCopy.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘exomeCopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomeCopy’ version ‘1.29.0’
* 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 ‘exomeCopy’ 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.ExomeCopy
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
emFn : <anonymous>: no visible global function definition for ‘dnbinom’
exomeCopy: no visible global function definition for ‘lm’
exomeCopy: no visible global function definition for ‘optim’
exomeCopy: no visible global function definition for ‘new’
exomeCopy: no visible global function definition for ‘Rle’
getGCcontent: no visible global function definition for
  ‘letterFrequency’
plot.ExomeCopy: no visible global function definition for ‘segments’
plot.ExomeCopy: no visible global function definition for ‘legend’
plotCompiledCNV: no visible global function definition for ‘axis’
plotCompiledCNV: no visible global function definition for ‘segments’
plot,ExomeCopy-missing: no visible global function definition for
  ‘segments’
plot,ExomeCopy-missing: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  Rle axis dnbinom legend letterFrequency lm new optim segments
Consider adding
  importFrom("graphics", "axis", "legend", "segments")
  importFrom("methods", "new")
  importFrom("stats", "dnbinom", "lm", "optim")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘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-3.9-bioc/meat/exomeCopy.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 exomeCopy
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘exomeCopy’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c exomeCopy.c -o exomeCopy.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 exomeCopy.so exomeCopy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/exomeCopy/libs
** 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
* DONE (exomeCopy)

name	user	system	elapsed
ExomeCopy-class	0.002	0.001	0.002
compileCopyCountSegments	3.439	0.196	3.654
copyCountSegments	3.460	0.168	3.658
countBamInGRanges	0.407	0.011	0.421
exomeCopy	3.366	0.182	3.575
generateBackground	0.261	0.002	0.264
getGCcontent	0.018	0.001	0.019
negLogLike	0.009	0.001	0.011
plot.exomeCopyObject	3.377	0.161	3.564
plotCompiledCNV	3.438	0.156	3.614
subdivideGRanges	0.095	0.001	0.096