Package: exomeCopy

Version: 1.28.0

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_1.28.0.tar.gz

StartedAt: 2019-04-15 23:51:48 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:53:48 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 120.8 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_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/exomeCopy.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.28.0’
* 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 ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-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/3.5/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/3.5/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	0.001	0.000	0.002
compileCopyCountSegments	3.771	0.190	4.016
copyCountSegments	3.987	0.180	4.205
countBamInGRanges	0.448	0.008	0.460
exomeCopy	3.709	0.180	3.926
generateBackground	0.304	0.007	0.312
getGCcontent	0.031	0.001	0.034
negLogLike	0.012	0.000	0.014
plot.exomeCopyObject	3.913	0.174	4.122
plotCompiledCNV	3.985	0.173	4.201
subdivideGRanges	0.089	0.001	0.092