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BioC 3.2: CHECK report for CNORfuzzy on zin1

This page was generated on 2016-04-23 10:12:37 -0700 (Sat, 23 Apr 2016).

Package 196/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORfuzzy 1.12.0
T. Cokelaer
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CNORfuzzy
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNORfuzzy
Version: 1.12.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CNORfuzzy_1.12.0.tar.gz
StartedAt: 2016-04-22 23:20:17 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:21:33 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 76.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CNORfuzzy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CNORfuzzy_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/CNORfuzzy.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNORfuzzy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORfuzzy’ version ‘1.12.0’
* 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 ‘CNORfuzzy’ can be installed ... [4s/4s] 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 ... NOTE
Packages in Depends field not imported from:
  ‘CellNOptR’ ‘nloptr’
  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
CNORwrapFuzzy: no visible global function definition for ‘checkSignals’
CNORwrapFuzzy: no visible global function definition for
  ‘preprocessing’
CNORwrapFuzzy: no visible global function definition for ‘getFit’
CNORwrapFuzzy: no visible global function definition for ‘indexFinder’
cSimulator: no visible global function definition for ‘indexFinder’
computeScoreFuzzy: no visible global function definition for
  ‘indexFinder’
computeScoreFuzzy: no visible global function definition for ‘getFit’
gaDiscreteT1: no visible global function definition for ‘indexFinder’
getEC50: no visible global function definition for ‘nloptr’
getMeanFuzzy: no visible global function definition for ‘indexFinder’
getMeanModel: no visible global function definition for ‘indexFinder’
getNetworkInfoFuzzy: no visible global function definition for
  ‘indexFinder’
getNetworkInfoFuzzy: no visible global function definition for
  ‘findNONC’
getRefinedModel: no visible global function definition for
  ‘indexFinder’
getRefinedModel : objFunParams: no visible global function definition
  for ‘getFit’
getRefinedModel: no visible global function definition for ‘nloptr’
plotMeanFuzzyFit: no visible global function definition for
  ‘indexFinder’
plotMeanFuzzyFit: no visible global function definition for
  ‘plotOptimResultsPan’
prep4simFuzzy: no visible global function definition for ‘prep4sim’
prep4simFuzzy: no visible global function definition for ‘indexFinder’
rSimFuzzyT1: no visible global function definition for ‘indexFinder’
rSimulator: no visible global function definition for ‘indexFinder’
reduceFuzzy: no visible global function definition for ‘indexFinder’
reduceFuzzy: no visible global function definition for ‘getFit’
simulate: no visible global function definition for ‘indexFinder’
writeNetworkW: no visible global function definition for ‘writeDot’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
CNORwrapFuzzy 20.121  0.016   20.15
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [18s/18s]
 [18s/18s] 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-3.2-bioc/meat/CNORfuzzy.Rcheck/00check.log’
for details.


CNORfuzzy.Rcheck/00install.out:

* installing *source* package ‘CNORfuzzy’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c simulatorT1.c -o simulatorT1.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o CNORfuzzy.so simulatorT1.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/CNORfuzzy.Rcheck/CNORfuzzy/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNORfuzzy)

CNORfuzzy.Rcheck/CNORfuzzy-Ex.timings:

nameusersystemelapsed
CNORfuzzy-package0.0090.0000.015
CNORwrapFuzzy20.121 0.01620.150
compileMultiRes0.0040.0000.003
defaultParametersFuzzy0.0030.0000.004
gaDiscreteT13.0990.0043.105
interpretDiscreteGA0.0040.0000.004
plotMeanFuzzyFit0.0040.0000.003
prep4simFuzzy0.0060.0000.006
simFuzzyT10.0080.0000.008
writeFuzzyNetwork0.0040.0000.004