T. Cokelaer
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CNORfuzzy |
| Branch: RELEASE_3_9 |
| Last Commit: fd462ad |
| Last Changed Date: 2019-05-02 11:53:38 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:26:51 -0400 (Wed, 16 Oct 2019).
| Package 305/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CNORfuzzy 1.26.0 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 | |
| Package: CNORfuzzy |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNORfuzzy.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CNORfuzzy_1.26.0.tar.gz |
| StartedAt: 2019-10-16 02:46:36 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:49:18 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 161.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNORfuzzy.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNORfuzzy.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CNORfuzzy_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNORfuzzy.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNORfuzzy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORfuzzy' version '1.26.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/CNORfuzzy/libs/i386/CNORfuzzy.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/CNORfuzzy/libs/x64/CNORfuzzy.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CNORwrapFuzzy 16.33 0.12 16.51
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CNORwrapFuzzy 17.39 0.02 18.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNORfuzzy.Rcheck/00check.log'
for details.
CNORfuzzy.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CNORfuzzy_1.26.0.tar.gz && rm -rf CNORfuzzy.buildbin-libdir && mkdir CNORfuzzy.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNORfuzzy.buildbin-libdir CNORfuzzy_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CNORfuzzy_1.26.0.zip && rm CNORfuzzy_1.26.0.tar.gz CNORfuzzy_1.26.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 404k 100 404k 0 0 8492k 0 --:--:-- --:--:-- --:--:-- 9631k
install for i386
* installing *source* package 'CNORfuzzy' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c simulatorT1.c -o simulatorT1.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o CNORfuzzy.dll tmp.def simulatorT1.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CNORfuzzy.buildbin-libdir/00LOCK-CNORfuzzy/00new/CNORfuzzy/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CNORfuzzy'
finding HTML links ... done
CNORfuzzy-package html
finding level-2 HTML links ... done
CNORwrapFuzzy html
compileMultiRes html
computeScoreFuzzy html
defaultParametersFuzzy html
gaDiscreteT1 html
getRefinedModel html
interpretDiscreteGA html
plotMeanFuzzyFit html
prep4simFuzzy html
reduceFuzzy html
simFuzzyT1 html
writeFuzzyNetwork html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CNORfuzzy' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c simulatorT1.c -o simulatorT1.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o CNORfuzzy.dll tmp.def simulatorT1.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CNORfuzzy.buildbin-libdir/CNORfuzzy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNORfuzzy' as CNORfuzzy_1.26.0.zip
* DONE (CNORfuzzy)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CNORfuzzy' successfully unpacked and MD5 sums checked
|
CNORfuzzy.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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, 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: 20.09388 secs"
[1] "Calling interpretDiscreteGA"
[1] "Calling first Refinement"
[1] "...First Refinement Complete 0.1875 secs"
[1] "Calling second Refinement"
[1] "...Second Refinement Complete 0.15625 secs"
[1] 0
[1] "Calling reduceFuzzy 1"
[1] "...done 0.01562619 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 1e-04
[1] "Calling reduceFuzzy 2"
[1] "...done 0.01562595 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 5e-04
[1] "Calling reduceFuzzy 3"
[1] "...done 0.015625 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.001
[1] "Calling reduceFuzzy 4"
[1] "...done 0.01563001 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.003
[1] "Calling reduceFuzzy 5"
[1] "...done 0.01561999 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.005
[1] "Calling reduceFuzzy 6"
[1] "...done 0.015625 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.01
[1] "Calling reduceFuzzy 7"
[1] "...done 0 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] "RedRef Finished. Total time RedRef 0.09375215 secs"
[1] "Total Time: 20.60951 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 -- Wed Oct 16 02:48:50 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
23.07 0.35 23.65
|
CNORfuzzy.Rcheck/tests_x64/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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, 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: 16.78136 secs"
[1] "Calling interpretDiscreteGA"
[1] "Calling first Refinement"
[1] "...First Refinement Complete 0.2812521 secs"
[1] "Calling second Refinement"
[1] "...Second Refinement Complete 0.250035 secs"
[1] 0
[1] "Calling reduceFuzzy 1"
[1] "...done 0.01562095 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 1e-04
[1] "Calling reduceFuzzy 2"
[1] "...done 0 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 5e-04
[1] "Calling reduceFuzzy 3"
[1] "...done 0.01559806 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.001
[1] "Calling reduceFuzzy 4"
[1] "...done 0.015625 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.003
[1] "Calling reduceFuzzy 5"
[1] "...done 0.01565385 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.005
[1] "Calling reduceFuzzy 6"
[1] "...done 0.01562715 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] 0.01
[1] "Calling reduceFuzzy 7"
[1] "...done 0.01563096 secs"
[1] "Reduction did not change Model. Copying previous refinement"
[1] "RedRef Finished. Total time RedRef 0.09375596 secs"
[1] "Total Time: 17.4689 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 -- Wed Oct 16 02:49:11 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
20.46 0.18 20.64
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CNORfuzzy.Rcheck/examples_i386/CNORfuzzy-Ex.timings
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CNORfuzzy.Rcheck/examples_x64/CNORfuzzy-Ex.timings
|