BioC 3.3: CHECK report for COSNet on oaxaca

Package: COSNet

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings COSNet_1.6.0.tar.gz

StartedAt: 2016-10-13 00:37:28 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:38:12 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 43.9 seconds

RetCode: 0

Status:  OK

CheckDir: COSNet.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings COSNet_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/COSNet.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COSNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COSNet’ version ‘1.6.0’
* 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 ‘COSNet’ 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 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
File ‘COSNet/R/COSNet.R’:
  .onAttach calls:
    cat("COSNet: Cost-Sensitive algorithm for binary classification in graphs.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

generate_labels: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘COSNet/libs/COSNet.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘COSNet.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘COSNet.o’

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

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
Examples with CPU or elapsed time > 5s
                          user system elapsed
cosnet.cross.validation 20.125  1.563   21.85
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.3-bioc/meat/COSNet.Rcheck/00check.log’
for details.

* installing *source* package ‘COSNet’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c COSNet.c -o COSNet.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 COSNet.so COSNet.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/COSNet.Rcheck/COSNet/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
COSNet: Cost-Sensitive algorithm for binary classification in graphs.
* DONE (COSNet)

name	user	system	elapsed
COSNet	0.523	0.039	0.740
cosnet.cross.validation	20.125	1.563	21.850
find.division.not.strat	0.002	0.000	0.002
find.division.strat	0.003	0.000	0.003
generate_labels	0.001	0.000	0.002
generate_points	0.003	0.000	0.003
optimize_pos_above	0.442	0.063	0.506
optimizep	0.354	0.027	0.381
reg_data	0.424	0.042	0.466
runSubnet	0.414	0.041	0.456