Package: HMMcopy

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HMMcopy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HMMcopy_1.22.0.tar.gz

StartedAt: 2018-10-16 21:59:53 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:01:23 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 90.4 seconds

RetCode: 0

Status:  OK

CheckDir: HMMcopy.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:HMMcopy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HMMcopy_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/HMMcopy.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HMMcopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HMMcopy’ 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 ‘HMMcopy’ 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 ... NOTE
Package in Depends field not imported from: ‘geneplotter’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
correctReadcount: no visible global function definition for ‘loess’
correctReadcount: no visible global function definition for ‘predict’
correctReadcount: no visible global function definition for ‘approxfun’
correctReadcount: no visible global function definition for ‘lowess’
manualSegment: no visible global function definition for ‘dnorm’
plotBias: no visible global function definition for ‘par’
plotBias: no visible global function definition for ‘plot’
plotBias: no visible global function definition for ‘densCols’
plotCorrection: no visible global function definition for ‘par’
plotCorrection: no visible global function definition for ‘plot’
plotParam: no visible global function definition for ‘plot’
plotParam: no visible global function definition for ‘lines’
plotSegments: no visible binding for global variable ‘segments’
plotSegments: no visible global function definition for ‘plot’
plotSegments: no visible global function definition for ‘lines’
rangedDataToSeg: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  approxfun densCols dnorm lines loess lowess par plot predict segments
  write.table
Consider adding
  importFrom("grDevices", "densCols")
  importFrom("graphics", "lines", "par", "plot", "segments")
  importFrom("stats", "approxfun", "dnorm", "loess", "lowess", "predict")
  importFrom("utils", "write.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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* 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-3.7-bioc/meat/HMMcopy.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 HMMcopy
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘HMMcopy’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c forward_backward.c -o forward_backward.o
forward_backward.c:28:13: warning: unused variable 'tmp' [-Wunused-variable]
  int K, T, tmp;
            ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c register.c -o register.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c viterbi.c -o viterbi.o
viterbi.c:21:13: warning: unused variable 'tmp' [-Wunused-variable]
  int K, T, tmp;
            ^
1 warning generated.
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 HMMcopy.so forward_backward.o register.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/HMMcopy/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 (HMMcopy)

name	user	system	elapsed
HMMcopy-input	0.109	0.008	0.118
HMMcopy-output	0.233	0.048	0.288
HMMcopy-package	2.905	0.217	3.147
HMMcopy-visualize	0.839	0.038	0.882
HMMsegment	0.222	0.029	0.252
correctReadcount	0.535	0.013	0.549
wigsToRangedData	0.105	0.004	0.110