Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:29 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the BiRewire package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiRewire.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 194/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiRewire 3.24.0 (landing page) Andrea Gobbi
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 3.24.0 |
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_3.24.0.tar.gz |
StartedAt: 2021-10-14 16:51:44 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 16:55:55 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 251.3 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_3.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/BiRewire.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘3.24.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 71.328 0.197 71.613 birewire.visual.monitoring.dsg 57.689 0.368 58.093 birewire.visual.monitoring.undirected 16.446 0.345 16.802 birewire.visual.monitoring.bipartite 8.981 0.095 9.088 * 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-3.13-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/4.1/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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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: 19.612639371649 Epoch: Iteration #200 error is: 0.857030717052881 Epoch: Iteration #300 error is: 0.522687185144837 Epoch: Iteration #400 error is: 0.33011123047053 Epoch: Iteration #500 error is: 0.282823579409205 Epoch: Iteration #600 error is: 0.26540228793868 Epoch: Iteration #700 error is: 0.258853848473128 Epoch: Iteration #800 error is: 0.255134423941981 Epoch: Iteration #900 error is: 0.253302996667505 Epoch: Iteration #1000 error is: 0.252610790853235 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 9.99086239878309 Epoch: Iteration #200 error is: 0.339845691325571 Epoch: Iteration #300 error is: 0.257378700006327 Epoch: Iteration #400 error is: 0.254405738240569 Epoch: Iteration #500 error is: 0.253581229023367 Epoch: Iteration #600 error is: 0.252531486757702 Epoch: Iteration #700 error is: 0.251342977983352 Epoch: Iteration #800 error is: 0.250862029779055 Epoch: Iteration #900 error is: 0.250833565802055 Epoch: Iteration #1000 error is: 0.250832895307298 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 9.23767000150073 Epoch: Iteration #200 error is: 0.312219039805867 Epoch: Iteration #300 error is: 0.254314437000334 Epoch: Iteration #400 error is: 0.252212707385588 Epoch: Iteration #500 error is: 0.251019291751366 Epoch: Iteration #600 error is: 0.250834672214303 Epoch: Iteration #700 error is: 0.250830610316087 Epoch: Iteration #800 error is: 0.25083045755699 Epoch: Iteration #900 error is: 0.250830316658847 Epoch: Iteration #1000 error is: 0.250830136312183 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 10.0078414989719 Epoch: Iteration #200 error is: 0.280964587060796 Epoch: Iteration #300 error is: 0.252887095546938 Epoch: Iteration #400 error is: 0.251836270101522 Epoch: Iteration #500 error is: 0.250832859128257 Epoch: Iteration #600 error is: 0.250828123995319 Epoch: Iteration #700 error is: 0.250827881275946 Epoch: Iteration #800 error is: 0.25082754019314 Epoch: Iteration #900 error is: 0.250827156575003 Epoch: Iteration #1000 error is: 0.250826799176581 [1] "K= 1" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 9.91196347240898 Epoch: Iteration #200 error is: 0.257079442295357 Epoch: Iteration #300 error is: 0.253458868601962 Epoch: Iteration #400 error is: 0.250819359522329 Epoch: Iteration #500 error is: 0.250818978952155 Epoch: Iteration #600 error is: 0.250818504465716 Epoch: Iteration #700 error is: 0.250818194372099 Epoch: Iteration #800 error is: 0.250818069137601 Epoch: Iteration #900 error is: 0.250818018988622 Epoch: Iteration #1000 error is: 0.250817983327716 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 16.9181840525269 Epoch: Iteration #200 error is: 0.60626389315974 Epoch: Iteration #300 error is: 0.349173041021035 Epoch: Iteration #400 error is: 0.299026178924191 Epoch: Iteration #500 error is: 0.278791419318705 Epoch: Iteration #600 error is: 0.270584608783478 Epoch: Iteration #700 error is: 0.26515039861481 Epoch: Iteration #800 error is: 0.255650807002343 Epoch: Iteration #900 error is: 0.252404532836066 Epoch: Iteration #1000 error is: 0.251860673726831 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 8.55801959703656 Epoch: Iteration #200 error is: 0.263889378798895 Epoch: Iteration #300 error is: 0.252463666364801 Epoch: Iteration #400 error is: 0.250914682756689 Epoch: Iteration #500 error is: 0.250827244925779 Epoch: Iteration #600 error is: 0.250827085083931 Epoch: Iteration #700 error is: 0.250826873074398 Epoch: Iteration #800 error is: 0.250826638656496 Epoch: Iteration #900 error is: 0.250826428547183 Epoch: Iteration #1000 error is: 0.250826270783998 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 9.71823613049876 Epoch: Iteration #200 error is: 0.507525668853669 Epoch: Iteration #300 error is: 0.281271530017402 Epoch: Iteration #400 error is: 0.270168944176129 Epoch: Iteration #500 error is: 0.265339441191442 Epoch: Iteration #600 error is: 0.25438917410257 Epoch: Iteration #700 error is: 0.252368939463213 Epoch: Iteration #800 error is: 0.252234294741005 Epoch: Iteration #900 error is: 0.252104030206734 Epoch: Iteration #1000 error is: 0.252000150503251 RUNIT TEST PROTOCOL -- Thu Oct 14 16:55:46 2021 *********************************************** 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 26.656 2.476 29.292
BiRewire.Rcheck/BiRewire-Ex.timings
name | user | system | elapsed | |
birewire.analysis.bipartite | 0.130 | 0.346 | 0.477 | |
birewire.analysis.dsg | 0.046 | 0.011 | 0.059 | |
birewire.analysis.undirected | 71.328 | 0.197 | 71.613 | |
birewire.bipartite.from.incidence | 0.011 | 0.038 | 0.049 | |
birewire.build.dsg | 0.010 | 0.002 | 0.011 | |
birewire.induced.bipartite | 0.005 | 0.002 | 0.006 | |
birewire.rewire.bipartite | 0.009 | 0.034 | 0.043 | |
birewire.rewire.bipartite.and.projections | 0.095 | 0.010 | 0.106 | |
birewire.rewire.dsg | 0.006 | 0.002 | 0.008 | |
birewire.rewire.undirected | 0.910 | 0.063 | 0.975 | |
birewire.similarity | 0.008 | 0.000 | 0.009 | |
birewire.similarity.dsg | 0.033 | 0.002 | 0.035 | |
birewire.visual.monitoring.bipartite | 8.981 | 0.095 | 9.088 | |
birewire.visual.monitoring.dsg | 57.689 | 0.368 | 58.093 | |
birewire.visual.monitoring.undirected | 16.446 | 0.345 | 16.802 | |