Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 380/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CNORfuzzy 1.42.0 (landing page) T. Cokelaer
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the CNORfuzzy package: - 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: 1.42.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNORfuzzy.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNORfuzzy_1.42.0.tar.gz |
StartedAt: 2023-10-17 10:38:45 -0400 (Tue, 17 Oct 2023) |
EndedAt: 2023-10-17 10:40:46 -0400 (Tue, 17 Oct 2023) |
EllapsedTime: 121.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNORfuzzy.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNORfuzzy.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNORfuzzy_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CNORfuzzy.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CNORfuzzy/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CNORfuzzy’ version ‘1.42.0’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ‘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 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 12.39 0.197 19.252 * 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-3.17-bioc-mac-arm64/meat/CNORfuzzy.Rcheck/00check.log’ for details.
CNORfuzzy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNORfuzzy ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘CNORfuzzy’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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 -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CNORfuzzy.so simulatorT1.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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 version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (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: 17.03214 secs" [1] "Calling interpretDiscreteGA" [1] "Calling first Refinement" [1] "...First Refinement Complete 0.3468451 secs" [1] "Calling second Refinement" [1] "...Second Refinement Complete 0.297219 secs" [1] 0 [1] "Calling reduceFuzzy 1" [1] "...done 0.01636887 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 1e-04 [1] "Calling reduceFuzzy 2" [1] "...done 0.01472902 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 5e-04 [1] "Calling reduceFuzzy 3" [1] "...done 0.01042509 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 0.001 [1] "Calling reduceFuzzy 4" [1] "...done 0.01568604 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 0.003 [1] "Calling reduceFuzzy 5" [1] "...done 0.014364 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 0.005 [1] "Calling reduceFuzzy 6" [1] "...done 0.03907394 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] 0.01 [1] "Calling reduceFuzzy 7" [1] "...done 0.01441383 secs" [1] "Reduction did not change Model. Copying previous refinement" [1] "RedRef Finished. Total time RedRef 0.1299491 secs" [1] "Total Time: 17.86794 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 Oct 17 10:40:31 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 15.170 0.401 22.147
CNORfuzzy.Rcheck/CNORfuzzy-Ex.timings
name | user | system | elapsed | |
CNORfuzzy-package | 0.006 | 0.003 | 0.021 | |
CNORwrapFuzzy | 12.390 | 0.197 | 19.252 | |
compileMultiRes | 0.003 | 0.001 | 0.005 | |
defaultParametersFuzzy | 0.003 | 0.001 | 0.005 | |
gaDiscreteT1 | 2.185 | 0.028 | 3.120 | |
interpretDiscreteGA | 0.003 | 0.002 | 0.007 | |
plotMeanFuzzyFit | 0.003 | 0.001 | 0.005 | |
prep4simFuzzy | 0.005 | 0.001 | 0.010 | |
simFuzzyT1 | 0.007 | 0.001 | 0.013 | |
writeFuzzyNetwork | 0.003 | 0.001 | 0.006 | |