Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:58:08 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE BiRewire PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 187/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
BiRewire 3.20.0 Andrea Gobbi
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK |
Package: BiRewire |
Version: 3.20.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiRewire_3.20.0.tar.gz |
StartedAt: 2020-10-16 23:09:47 -0400 (Fri, 16 Oct 2020) |
EndedAt: 2020-10-16 23:14:28 -0400 (Fri, 16 Oct 2020) |
EllapsedTime: 281.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiRewire.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiRewire_3.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiRewire.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiRewire/DESCRIPTION’ ... OK * this is package ‘BiRewire’ version ‘3.20.0’ * 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 ‘BiRewire’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE birewire.analysis.bipartite: no visible binding for global variable ‘sd’ birewire.analysis.bipartite: no visible global function definition for ‘qt’ birewire.analysis.bipartite: no visible global function definition for ‘par’ birewire.analysis.bipartite: no visible global function definition for ‘polygon’ birewire.analysis.bipartite: no visible global function definition for ‘lines’ birewire.analysis.bipartite: no visible global function definition for ‘abline’ birewire.analysis.bipartite: no visible global function definition for ‘legend’ birewire.analysis.dsg: no visible global function definition for ‘dev.off’ birewire.analysis.dsg: no visible binding for global variable ‘sd’ birewire.analysis.dsg: no visible global function definition for ‘qt’ birewire.analysis.dsg: no visible global function definition for ‘polygon’ birewire.analysis.dsg: no visible global function definition for ‘lines’ birewire.analysis.dsg: no visible global function definition for ‘abline’ birewire.analysis.dsg: no visible global function definition for ‘legend’ birewire.analysis.undirected: no visible binding for global variable ‘sd’ birewire.analysis.undirected: no visible global function definition for ‘qt’ birewire.analysis.undirected: no visible global function definition for ‘par’ birewire.analysis.undirected: no visible global function definition for ‘polygon’ birewire.analysis.undirected: no visible global function definition for ‘lines’ birewire.analysis.undirected: no visible global function definition for ‘abline’ birewire.analysis.undirected: no visible global function definition for ‘legend’ birewire.load.dsg: no visible global function definition for ‘read.table’ birewire.sampler.bipartite: no visible global function definition for ‘write.table’ birewire.sampler.undirected: no visible global function definition for ‘write.table’ birewire.save.dsg: no visible global function definition for ‘write.table’ birewire.visual.monitoring.bipartite: no visible global function definition for ‘par’ birewire.visual.monitoring.bipartite: no visible global function definition for ‘colorRampPalette’ birewire.visual.monitoring.bipartite: no visible global function definition for ‘text’ birewire.visual.monitoring.dsg: no visible global function definition for ‘par’ birewire.visual.monitoring.dsg: no visible global function definition for ‘colorRampPalette’ birewire.visual.monitoring.dsg: no visible global function definition for ‘text’ birewire.visual.monitoring.undirected: no visible global function definition for ‘par’ birewire.visual.monitoring.undirected: no visible global function definition for ‘colorRampPalette’ birewire.visual.monitoring.undirected: no visible global function definition for ‘text’ Undefined global functions or variables: abline colorRampPalette dev.off legend lines par polygon qt read.table sd text write.table Consider adding importFrom("grDevices", "colorRampPalette", "dev.off") importFrom("graphics", "abline", "legend", "lines", "par", "polygon", "text") importFrom("stats", "qt", "sd") importFrom("utils", "read.table", "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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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 birewire.analysis.undirected 73.347 0.223 73.671 birewire.visual.monitoring.dsg 67.831 0.390 68.297 birewire.visual.monitoring.undirected 18.283 0.424 18.734 birewire.visual.monitoring.bipartite 10.589 0.094 10.691 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiRewire.Rcheck/00check.log’ for details.
BiRewire.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiRewire ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘BiRewire’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c BiRewire.c -o BiRewire.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c interface.c -o interface.o clang -mmacosx-version-min=10.13 -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 BiRewire.so BiRewire.o interface.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-BiRewire/00new/BiRewire/libs ** R ** data ** 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 (BiRewire)
BiRewire.Rcheck/tests/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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(BiRewire) || stop("unable to load MyPackage") Loading required package: BiRewire Loading required package: igraph Attaching package: 'igraph' The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Loading required package: slam Loading required package: tsne Loading required package: Matrix [1] TRUE > BiocGenerics:::testPackage('BiRewire') 0% [ ] 1% [ ] 2% [= ] 3% [= ] 4% [== ] 5% [== ] 6% [=== ] 7% [=== ] 8% [==== ] 9% [==== ] 10% [===== ] 11% [===== ] 12% [====== ] 13% [====== ] 14% [======= ] 15% [======= ] 16% [======== ] 17% [======== ] 18% [========= ] 19% [========= ] 20% [========== ] 21% [========== ] 22% [=========== ] 23% [=========== ] 24% [============ ] 25% [============ ] 26% [============= ] 27% [============= ] 28% [============== ] 29% [============== ] 30% [=============== ] 31% [=============== ] 32% [================ ] 33% [================ ] 34% 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It is strongly suggested to use MAXITER_MUL=100 and exact=TRUE because the number of configuration with the NA constrain can terribly decrease, the routine will use these." 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|Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 12.3491057240232 Epoch: Iteration #200 error is: 0.639900337491756 Epoch: Iteration #300 error is: 0.361443326977947 Epoch: Iteration #400 error is: 0.298555313856849 Epoch: Iteration #500 error is: 0.272856832222482 Epoch: Iteration #600 error is: 0.263232992163215 Epoch: Iteration #700 error is: 0.258223627302762 Epoch: Iteration #800 error is: 0.254482179933518 Epoch: Iteration #900 error is: 0.25260621507154 Epoch: Iteration #1000 error is: 0.25206646333342 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 12.8211594189852 Epoch: Iteration #200 error is: 0.336595577181804 Epoch: Iteration #300 error is: 0.267112597708876 Epoch: Iteration #400 error is: 0.253401557781613 Epoch: Iteration #500 error is: 0.252047194651973 Epoch: Iteration #600 error is: 0.251973488609767 Epoch: Iteration #700 error is: 0.251942668315491 Epoch: Iteration #800 error is: 0.251937627309287 Epoch: Iteration #900 error is: 0.251937317396788 Epoch: Iteration #1000 error is: 0.25193730939791 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 12.7593452856214 Epoch: Iteration #200 error is: 0.629790039069155 Epoch: Iteration #300 error is: 0.304323916533342 Epoch: Iteration #400 error is: 0.265579966129857 Epoch: Iteration #500 error is: 0.254850730047046 Epoch: Iteration #600 error is: 0.252372888364364 Epoch: Iteration #700 error is: 0.251877493935712 Epoch: Iteration #800 error is: 0.251361115739329 Epoch: Iteration #900 error is: 0.250983242318094 Epoch: Iteration #1000 error is: 0.250853637699107 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 10.4721970936506 Epoch: Iteration #200 error is: 0.278574830615449 Epoch: Iteration #300 error is: 0.252331099716998 Epoch: Iteration #400 error is: 0.251939500480088 Epoch: Iteration #500 error is: 0.251936449007082 Epoch: Iteration #600 error is: 0.251936155948569 Epoch: Iteration #700 error is: 0.251936150209381 Epoch: Iteration #800 error is: 0.251936150077151 Epoch: Iteration #900 error is: 0.251936149917479 Epoch: Iteration #1000 error is: 0.251936149705086 [1] "K= 1" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 9.07031973471647 Epoch: Iteration #200 error is: 0.324977563699156 Epoch: Iteration #300 error is: 0.2699264271005 Epoch: Iteration #400 error is: 0.264548666451 Epoch: Iteration #500 error is: 0.255675054770505 Epoch: Iteration #600 error is: 0.252784639747329 Epoch: Iteration #700 error is: 0.250913777507382 Epoch: Iteration #800 error is: 0.250833477641645 Epoch: Iteration #900 error is: 0.250833243559848 Epoch: Iteration #1000 error is: 0.250833242567488 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 11.0114334295223 Epoch: Iteration #200 error is: 0.307028816456408 Epoch: Iteration #300 error is: 0.266727854408426 Epoch: Iteration #400 error is: 0.256110910485888 Epoch: Iteration #500 error is: 0.253208073932948 Epoch: Iteration #600 error is: 0.251579976547978 Epoch: Iteration #700 error is: 0.250882878159705 Epoch: Iteration #800 error is: 0.250832686042422 Epoch: Iteration #900 error is: 0.250831631621647 Epoch: Iteration #1000 error is: 0.250831537681968 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 8.1686130005559 Epoch: Iteration #200 error is: 0.261214560036443 Epoch: Iteration #300 error is: 0.251936060313636 Epoch: Iteration #400 error is: 0.251935522414503 Epoch: Iteration #500 error is: 0.25193551872248 Epoch: Iteration #600 error is: 0.251935518210455 Epoch: Iteration #700 error is: 0.251935517982958 Epoch: Iteration #800 error is: 0.251935517648555 Epoch: Iteration #900 error is: 0.251935517201058 Epoch: Iteration #1000 error is: 0.251935516642956 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 8.88870415458443 Epoch: Iteration #200 error is: 0.252481635553544 Epoch: Iteration #300 error is: 0.250820733973808 Epoch: Iteration #400 error is: 0.250820687577118 Epoch: Iteration #500 error is: 0.250820622524679 Epoch: Iteration #600 error is: 0.250820551961659 Epoch: Iteration #700 error is: 0.250820501445466 Epoch: Iteration #800 error is: 0.250820470879214 Epoch: Iteration #900 error is: 0.250820450272716 Epoch: Iteration #1000 error is: 0.250820431022302 RUNIT TEST PROTOCOL -- Fri Oct 16 23:14:19 2020 *********************************************** Number of test functions: 8 Number of errors: 0 Number of failures: 0 1 Test Suite : BiRewire RUnit Tests - 8 test functions, 0 errors, 0 failures Number of test functions: 8 Number of errors: 0 Number of failures: 0 Warning messages: 1: In if (class(X) == "dist") { : the condition has length > 1 and only the first element will be used 2: In if (class(X) == "dist") { : the condition has length > 1 and only the first element will be used 3: In if (class(X) == "dist") { : the condition has length > 1 and only the first element will be used 4: In if (class(X) == "dist") { : the condition has length > 1 and only the first element will be used 5: In if (class(X) == "dist") { : the condition has length > 1 and only the first element will be used 6: In if (class(X) == "dist") { : the condition has length > 1 and only the first element will be used 7: In if (class(X) == "dist") { : the condition has length > 1 and only the first element will be used 8: In if (class(X) == "dist") { : the condition has length > 1 and only the first element will be used > > proc.time() user system elapsed 29.904 2.588 32.600
BiRewire.Rcheck/BiRewire-Ex.timings
name | user | system | elapsed | |
birewire.analysis.bipartite | 0.161 | 0.472 | 0.641 | |
birewire.analysis.dsg | 0.061 | 0.014 | 0.075 | |
birewire.analysis.undirected | 73.347 | 0.223 | 73.671 | |
birewire.bipartite.from.incidence | 0.014 | 0.047 | 0.060 | |
birewire.build.dsg | 0.014 | 0.002 | 0.016 | |
birewire.induced.bipartite | 0.005 | 0.002 | 0.007 | |
birewire.rewire.bipartite | 0.007 | 0.024 | 0.031 | |
birewire.rewire.bipartite.and.projections | 0.138 | 0.019 | 0.157 | |
birewire.rewire.dsg | 0.006 | 0.003 | 0.009 | |
birewire.rewire.undirected | 0.977 | 0.078 | 1.055 | |
birewire.similarity | 0.008 | 0.001 | 0.009 | |
birewire.similarity.dsg | 0.186 | 0.012 | 0.197 | |
birewire.visual.monitoring.bipartite | 10.589 | 0.094 | 10.691 | |
birewire.visual.monitoring.dsg | 67.831 | 0.390 | 68.297 | |
birewire.visual.monitoring.undirected | 18.283 | 0.424 | 18.734 | |