BioC 3.2: CHECK report for COSNet on perceval

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings COSNet_1.3.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/COSNet.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.3.3’
* 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 ... [2s/2s] 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'.
* 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 ... [55s/55s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
cosnet.cross.validation 46.917  3.483  50.605
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/2s]
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  COSNet RUnit Tests - 9 test functions, 0 errors, 1 failure
  FAILURE in test_cosnet.cross.validation: Error in checkEquals(min(res$predictions), 1) : 
    Mean relative difference: 2
  
  Test files with failing tests
  
     test_cosnet.cross.validation.R 
       test_cosnet.cross.validation 
  
  
  Error in BiocGenerics:::testPackage("COSNet") : 
    unit tests failed for package COSNet
  Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/COSNet.Rcheck/00check.log’
for details.


R version 3.2.2 Patched (2015-08-14 r69078) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("COSNet")
COSNet: Cost-Sensitive algorithm for binary classification in graphs.
Timing stopped at: 0.22 0.013 0.233 
Error in checkEquals(min(res$predictions), 1) : 
  Mean relative difference: 2
0.526 


RUNIT TEST PROTOCOL -- Sun Aug 23 23:44:29 2015 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
COSNet RUnit Tests - 9 test functions, 0 errors, 1 failure
FAILURE in test_cosnet.cross.validation: Error in checkEquals(min(res$predictions), 1) : 
  Mean relative difference: 2

Test files with failing tests

   test_cosnet.cross.validation.R 
     test_cosnet.cross.validation 


Error in BiocGenerics:::testPackage("COSNet") : 
  unit tests failed for package COSNet
Execution halted

* installing *source* package ‘COSNet’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c COSNet.c -o COSNet.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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-3.2-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	0.797	0.070	0.914
cosnet.cross.validation	46.917	3.483	50.605
find.division.not.strat	0.002	0.001	0.002
find.division.strat	0.002	0.000	0.002
generate_labels	0.001	0.000	0.002
generate_points	0.003	0.000	0.003
optimize_pos_above	0.624	0.104	0.729
optimizep	0.454	0.063	0.517
reg_data	0.716	0.086	0.804
runSubnet	0.623	0.090	0.712

BioC 3.2: CHECK report for COSNet on perceval

Summary

Command output