Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 382/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CNORfuzzy 1.47.0 (landing page) T. Cokelaer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
Package: CNORfuzzy |
Version: 1.47.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNORfuzzy.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CNORfuzzy_1.47.0.tar.gz |
StartedAt: 2024-06-10 01:05:50 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 01:07:45 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 115.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNORfuzzy.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNORfuzzy.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CNORfuzzy_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CNORfuzzy.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'CNORfuzzy/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CNORfuzzy' version '1.47.0' * 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 * used C compiler: 'gcc.exe (GCC) 13.2.0' * 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 code 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 '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 ... NOTE Argument items with no description in Rd file 'CNORwrapFuzzy.Rd': 'verbose' * 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 x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/CNORfuzzy/libs/x64/CNORfuzzy.dll': Found '_exit', possibly from '_exit' (C) 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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed CNORwrapFuzzy 15.08 0.7 15.89 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/CNORfuzzy.Rcheck/00check.log' for details.
CNORfuzzy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CNORfuzzy ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'CNORfuzzy' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c simulatorT1.c -o simulatorT1.o gcc -shared -s -static-libgcc -o CNORfuzzy.dll tmp.def simulatorT1.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-CNORfuzzy/00new/CNORfuzzy/libs/x64 ** 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 ** 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 version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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, 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: 10.69864 secs" [1] "Calling interpretDiscreteGA" [1] "Calling first Refinement" [1] "...First Refinement Complete 0.3659821 secs" [1] "Calling second Refinement" [1] "...Second Refinement Complete 0.3002541 secs" [1] 0 [1] "Calling reduceFuzzy 1" [1] "...done 0.01478195 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 1e-04 [1] "Calling reduceFuzzy 2" [1] "...done 0.01347184 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 5e-04 [1] "Calling reduceFuzzy 3" [1] "...done 0.01317501 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 0.001 [1] "Calling reduceFuzzy 4" [1] "...done 0.01244307 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 0.003 [1] "Calling reduceFuzzy 5" [1] "...done 0.01248813 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 0.005 [1] "Calling reduceFuzzy 6" [1] "...done 0.01259995 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 0.01 [1] "Calling reduceFuzzy 7" [1] "...done 0.01395798 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] "RedRef Finished. Total time RedRef 0.09677911 secs" [1] "Total Time: 11.49361 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 -- Mon Jun 10 01:07:33 2024 *********************************************** 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 13.31 2.12 15.34
CNORfuzzy.Rcheck/CNORfuzzy-Ex.timings
name | user | system | elapsed | |
CNORfuzzy-package | 0.00 | 0.00 | 0.03 | |
CNORwrapFuzzy | 15.08 | 0.70 | 15.89 | |
compileMultiRes | 0 | 0 | 0 | |
defaultParametersFuzzy | 0.01 | 0.00 | 0.02 | |
gaDiscreteT1 | 2.89 | 0.14 | 3.06 | |
interpretDiscreteGA | 0 | 0 | 0 | |
plotMeanFuzzyFit | 0.02 | 0.00 | 0.02 | |
prep4simFuzzy | 0.00 | 0.01 | 0.01 | |
simFuzzyT1 | 0.01 | 0.00 | 0.02 | |
writeFuzzyNetwork | 0 | 0 | 0 | |