Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:35:16 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 380/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORfuzzy 1.42.0  (landing page)
T. Cokelaer
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/CNORfuzzy
git_branch: RELEASE_3_17
git_last_commit: cba5030
git_last_commit_date: 2023-04-25 10:23:51 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for CNORfuzzy on nebbiolo1


To the developers/maintainers of the CNORfuzzy package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNORfuzzy.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CNORfuzzy
Version: 1.42.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CNORfuzzy.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CNORfuzzy_1.42.0.tar.gz
StartedAt: 2023-10-15 20:13:18 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 20:14:40 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 82.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CNORfuzzy.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CNORfuzzy.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CNORfuzzy_1.42.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CNORfuzzy.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CNORfuzzy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORfuzzy’ version ‘1.42.0’
* 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
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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
.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 ‘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 plotOptimResultsPan prep4sim preprocessing runif
  tail var write.table writeDot
Consider adding
  importFrom("graphics", "axis", "legend", "mtext", "par")
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
CNORwrapFuzzy 10.818  0.144  10.962
* 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 ...
  ‘CNORfuzzy-vignette.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/CNORfuzzy.Rcheck/00check.log’
for details.



Installation output

CNORfuzzy.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CNORfuzzy
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘CNORfuzzy’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c simulatorT1.c -o simulatorT1.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o CNORfuzzy.so simulatorT1.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-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)

Tests output

CNORfuzzy.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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

Attaching package: 'BiocGenerics'

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, aperm, 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.max, which.min

Loading required package: RCurl
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: rmarkdown
Loading required package: nloptr
[1] TRUE
> BiocGenerics:::testPackage("CNORfuzzy")
[1] "Begining Optimization"
[1] "Discrete GA Finished in: 11.57523 secs"
[1] "Calling interpretDiscreteGA"
[1] "Calling first Refinement"
[1] "...First Refinement Complete 0.1360359 secs"
[1] "Calling second Refinement"
[1] "...Second Refinement Complete 0.1674099 secs"
[1] 0
[1] "Calling reduceFuzzy 1"
[1] "...done 0.0113287 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 1e-04
[1] "Calling reduceFuzzy 2"
[1] "...done 0.009079695 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 5e-04
[1] "Calling reduceFuzzy 3"
[1] "...done 0.008941889 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.001
[1] "Calling reduceFuzzy 4"
[1] "...done 0.008780241 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.003
[1] "Calling reduceFuzzy 5"
[1] "...done 0.008549213 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.005
[1] "Calling reduceFuzzy 6"
[1] "...done 0.008345604 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.01
[1] "Calling reduceFuzzy 7"
[1] "...done 0.008479834 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] "RedRef Finished.  Total time RedRef  0.06659794 secs"
[1] "Total Time:  11.99297 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 -- Sun Oct 15 20:14:20 2023 
*********************************************** 
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 
 13.959   0.280  14.228 

Example timings

CNORfuzzy.Rcheck/CNORfuzzy-Ex.timings

nameusersystemelapsed
CNORfuzzy-package0.0150.0040.019
CNORwrapFuzzy10.818 0.14410.962
compileMultiRes0.0040.0000.003
defaultParametersFuzzy0.0030.0000.003
gaDiscreteT13.0530.0283.081
interpretDiscreteGA0.0020.0020.004
plotMeanFuzzyFit0.0020.0010.004
prep4simFuzzy0.0060.0000.006
simFuzzyT10.0070.0000.007
writeFuzzyNetwork0.0000.0030.003