BioC 3.3: CHECK report for COSNet on linux2.bioconductor.org
This page was generated on 2015-10-27 12:12:47 -0400 (Tue, 27 Oct 2015).
COSNet 1.5.0 Marco Frasca
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COSNet | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
Summary
Package: COSNet |
Version: 1.5.0 |
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings COSNet_1.5.0.tar.gz |
StartedAt: 2015-10-27 03:00:05 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 03:00:45 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 40.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: COSNet.Rcheck |
Warnings: 0 |
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings COSNet_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/COSNet.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.0’
* 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 ... [1s/1s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/26s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
cosnet.cross.validation 23.366 0.211 23.587
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [1s/1s]
[1s/1s] 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
‘/home/biocbuild/bbs-3.3-bioc/meat/COSNet.Rcheck/00check.log’
for details.
COSNet.Rcheck/00install.out:
* installing *source* package ‘COSNet’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c COSNet.c -o COSNet.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o COSNet.so COSNet.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/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)
COSNet.Rcheck/COSNet-Ex.timings:
name | user | system | elapsed
|
COSNet | 0.624 | 0.012 | 0.637 |
|
cosnet.cross.validation | 23.366 | 0.211 | 23.587 |
|
find.division.not.strat | 0.002 | 0.000 | 0.001 |
|
find.division.strat | 0.002 | 0.000 | 0.001 |
|
generate_labels | 0.002 | 0.000 | 0.001 |
|
generate_points | 0.002 | 0.000 | 0.003 |
|
optimize_pos_above | 0.384 | 0.036 | 0.421 |
|
optimizep | 0.354 | 0.020 | 0.375 |
|
reg_data | 0.525 | 0.052 | 0.576 |
|
runSubnet | 0.500 | 0.020 | 0.521 |
|