Package: SMAP

Version: 1.47.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SMAP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SMAP_1.47.0.tar.gz

StartedAt: 2019-04-09 03:50:18 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:50:55 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 36.6 seconds

RetCode: 0

Status:  OK

CheckDir: SMAP.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:SMAP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SMAP_1.47.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SMAP.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 ‘SMAP/DESCRIPTION’ ... OK
* this is package ‘SMAP’ version ‘1.47.0’
* 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 ‘SMAP’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘SMAP/R/AllClasses.R’:
  .onLoad calls:
    require("methods", quietly = TRUE)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

.draw.dist,gaussparam: no visible global function definition for
  ‘abline’
plot,SMAPObservations-missing: no visible global function definition
  for ‘par’
plot,SMAPObservations-missing: no visible global function definition
  for ‘points’
plot,SMAPObservations-missing: no visible global function definition
  for ‘abline’
plot,SMAPObservations-missing: no visible global function definition
  for ‘box’
plot,SMAPObservations-missing: no visible global function definition
  for ‘axis’
profilePlot,SMAPProfile: no visible global function definition for
  ‘par’
profilePlot,SMAPProfile: no visible global function definition for
  ‘points’
profilePlot,SMAPProfile: no visible global function definition for
  ‘abline’
profilePlot,SMAPProfile: no visible global function definition for
  ‘box’
profilePlot,SMAPProfile: no visible global function definition for
  ‘axis’
profilePlot,SMAPProfiles: no visible global function definition for
  ‘par’
profilePlot,SMAPProfiles: no visible global function definition for
  ‘abline’
profilePlot,SMAPProfiles: no visible global function definition for
  ‘box’
profilePlot,SMAPProfiles: no visible global function definition for
  ‘axis’
Undefined global functions or variables:
  abline axis box par points
Consider adding
  importFrom("graphics", "abline", "axis", "box", "par", "points")
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 ... 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
Examples with CPU or elapsed time > 5s
     user system elapsed
smap 5.55  0.065   5.674
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/SMAP.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 SMAP
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SMAP’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gradient.c -o gradient.o
gradient.c:247:10: warning: unused variable 'tmp' [-Wunused-variable]
                double tmp;
                       ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c overlap.c -o overlap.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c prob.c -o prob.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c viterbi.c -o viterbi.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 SMAP.so gradient.o init.o overlap.o prob.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/SMAP/libs
** R
** data
** 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 (SMAP)

name	user	system	elapsed
GBM	0.404	0.030	0.439
SMAPObservations	0.646	0.042	0.702
smap	5.550	0.065	5.674