T. Cokelaer
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CNORfuzzy |
| Branch: master |
| Last Commit: 03c1b58 |
| Last Changed Date: 2018-10-30 11:54:30 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:05:42 -0400 (Tue, 09 Apr 2019).
| Package 300/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CNORfuzzy 1.25.0 T. Cokelaer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: CNORfuzzy |
| Version: 1.25.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNORfuzzy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNORfuzzy_1.25.0.tar.gz |
| StartedAt: 2019-04-09 00:49:31 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 00:51:51 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 139.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNORfuzzy.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNORfuzzy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNORfuzzy_1.25.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CNORfuzzy.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.25.0’
* 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 ... 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 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
.getk: no visible global function definition for ‘approx’
.std: no visible global function definition for ‘var’
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’
compileMultiRes: no visible global function definition for ‘par’
compileMultiRes: no visible global function definition for ‘plot’
compileMultiRes: no visible global function definition for ‘axis’
compileMultiRes: no visible global function definition for ‘mtext’
compileMultiRes: no visible global function definition for ‘legend’
computeScoreFuzzy: no visible global function definition for
‘indexFinder’
computeScoreFuzzy: no visible global function definition for ‘getFit’
gaDiscreteT1: no visible global function definition for ‘indexFinder’
gaDiscreteT1: no visible global function definition for ‘runif’
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’
shift: no visible global function definition for ‘tail’
shift: no visible global function definition for ‘head’
simulate: no visible global function definition for ‘indexFinder’
writeNetworkW: no visible global function definition for ‘writeDot’
writeNetworkW: no visible global function definition for ‘write.table’
Undefined global functions or variables:
approx axis checkSignals findNONC getFit head indexFinder legend
mtext nloptr par plot plotOptimResultsPan prep4sim preprocessing
runif tail var write.table writeDot
Consider adding
importFrom("graphics", "axis", "legend", "mtext", "par", "plot")
importFrom("stats", "approx", "runif", "var")
importFrom("utils", "head", "tail", "write.table")
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
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
CNORwrapFuzzy 21.9 0.723 22.874
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/CNORfuzzy.Rcheck/00check.log’
for details.
CNORfuzzy.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNORfuzzy
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CNORfuzzy’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c simulatorT1.c -o simulatorT1.o
simulatorT1.c:320:28: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if((track_cond == nCond)) {
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorT1.c:320:28: note: remove extraneous parentheses around the comparison to silence this warning
if((track_cond == nCond)) {
˜ ^ ˜
simulatorT1.c:320:28: note: use '=' to turn this equality comparison into an assignment
if((track_cond == nCond)) {
^˜
=
1 warning generated.
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 CNORfuzzy.so simulatorT1.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-CNORfuzzy/00new/CNORfuzzy/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CNORfuzzy)
CNORfuzzy.Rcheck/tests/runTests.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.
> require("CNORfuzzy") || stop("unable to load CNORfuzzy")
Loading required package: CNORfuzzy
Loading required package: CellNOptR
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: hash
hash-2.2.6.1 provided by Decision Patterns
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
Loading required package: ggplot2
Loading required package: nloptr
[1] TRUE
> BiocGenerics:::testPackage("CNORfuzzy")
[1] "Begining Optimization"
[1] "Discrete GA Finished in: 20.07526 secs"
[1] "Calling interpretDiscreteGA"
[1] "Calling first Refinement"
[1] "...First Refinement Complete 0.3902478 secs"
[1] "Calling second Refinement"
[1] "...Second Refinement Complete 0.3916781 secs"
[1] 0
[1] "Calling reduceFuzzy 1"
[1] "...done 0.02176189 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 1e-04
[1] "Calling reduceFuzzy 2"
[1] "...done 0.01789093 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 5e-04
[1] "Calling reduceFuzzy 3"
[1] "...done 0.01750112 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.001
[1] "Calling reduceFuzzy 4"
[1] "...done 0.02042413 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.003
[1] "Calling reduceFuzzy 5"
[1] "...done 0.02011395 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.005
[1] "Calling reduceFuzzy 6"
[1] "...done 0.01964808 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.01
[1] "Calling reduceFuzzy 7"
[1] "...done 0.01933408 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] "RedRef Finished. Total time RedRef 0.1423728 secs"
[1] "Total Time: 21.13646 secs"
[1] "The following species are measured: Akt, Hsp27, NFkB, Erk, p90RSK, Jnk, cJun"
[1] "The following species are stimulated: EGF, TNFa"
[1] "The following species are inhibited: Raf, PI3K"
[1] "The following species are not observable and/or not controllable: "
[1] "The following species are measured: Akt, Hsp27, NFkB, Erk, p90RSK, Jnk, cJun"
[1] "The following species are stimulated: EGF, TNFa"
[1] "The following species are inhibited: Raf, PI3K"
[1] 0.1316292
RUNIT TEST PROTOCOL -- Tue Apr 9 00:51:43 2019
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
CNORfuzzy RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
24.037 1.179 25.550
CNORfuzzy.Rcheck/CNORfuzzy-Ex.timings
| name | user | system | elapsed | |
| CNORfuzzy-package | 0.030 | 0.005 | 0.035 | |
| CNORwrapFuzzy | 21.900 | 0.723 | 22.874 | |
| compileMultiRes | 0.006 | 0.002 | 0.008 | |
| defaultParametersFuzzy | 0.006 | 0.002 | 0.007 | |
| gaDiscreteT1 | 3.077 | 0.030 | 3.179 | |
| interpretDiscreteGA | 0.006 | 0.001 | 0.010 | |
| plotMeanFuzzyFit | 0.005 | 0.001 | 0.006 | |
| prep4simFuzzy | 0.011 | 0.001 | 0.013 | |
| simFuzzyT1 | 0.015 | 0.002 | 0.017 | |
| writeFuzzyNetwork | 0.006 | 0.002 | 0.009 | |