Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:36 -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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiRewire_3.24.0.tar.gz |
StartedAt: 2021-10-14 09:03:54 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:06:46 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 172.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BiRewire.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiRewire_3.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BiRewire.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘BiRewire’ can be installed ... WARNING Found the following significant warnings: BiRewire.c:1066:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] BiRewire.c:1149:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] See ‘/home/biocbuild/bbs-3.13-bioc/meat/BiRewire.Rcheck/00install.out’ for details. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed birewire.analysis.undirected 64.929 0.167 65.102 birewire.visual.monitoring.dsg 27.683 0.056 27.740 birewire.visual.monitoring.undirected 9.558 0.040 9.611 * 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: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/BiRewire.Rcheck/00check.log’ for details.
BiRewire.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BiRewire ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘BiRewire’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BiRewire.c -o BiRewire.o BiRewire.c: In function ‘rewire_sparse’: BiRewire.c:1066:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] 1066 | if( a!=c && b!=d & a!=d && c!=b && (( ad==1 && cb==1 )|| (ac==1 && bd==1) )) { | ~^~~ BiRewire.c: In function ‘rewire_sparse_ex’: BiRewire.c:1149:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] 1149 | if( a!=c && b!=d & a!=d && c!=b && (( ad==1 && cb==1 )|| (ac==1 && bd==1) )) { | ~^~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c interface.c -o interface.o gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/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-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(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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[================================================= ] DONE in 0 seconds [1] "K= 1" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 17.8463574158693 Epoch: Iteration #200 error is: 1.00528483904162 Epoch: Iteration #300 error is: 0.403417266061403 Epoch: Iteration #400 error is: 0.292698712910508 Epoch: Iteration #500 error is: 0.271271449864765 Epoch: Iteration #600 error is: 0.263481596137533 Epoch: Iteration #700 error is: 0.26037936251555 Epoch: Iteration #800 error is: 0.258292620710633 Epoch: Iteration #900 error is: 0.256452945366032 Epoch: Iteration #1000 error is: 0.254863949543748 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 14.3925713447589 Epoch: Iteration #200 error is: 0.923846194908076 Epoch: Iteration #300 error is: 0.444817629264364 Epoch: Iteration #400 error is: 0.287825555917287 Epoch: Iteration #500 error is: 0.273145471751798 Epoch: Iteration #600 error is: 0.267147131297912 Epoch: Iteration #700 error is: 0.262041987413647 Epoch: Iteration #800 error is: 0.256701007204662 Epoch: Iteration #900 error is: 0.254176486547829 Epoch: Iteration #1000 error is: 0.253843424923458 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 14.2968810111358 Epoch: Iteration #200 error is: 0.921215982534477 Epoch: Iteration #300 error is: 0.561529478734318 Epoch: Iteration #400 error is: 0.36855033147769 Epoch: Iteration #500 error is: 0.279396345537993 Epoch: Iteration #600 error is: 0.264033470929194 Epoch: Iteration #700 error is: 0.258391862825996 Epoch: Iteration #800 error is: 0.255093428422358 Epoch: Iteration #900 error is: 0.253738683129278 Epoch: Iteration #1000 error is: 0.25310880055536 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 13.044864296125 Epoch: Iteration #200 error is: 0.453968088780104 Epoch: Iteration #300 error is: 0.276146799973358 Epoch: Iteration #400 error is: 0.255485558124513 Epoch: Iteration #500 error is: 0.251685477884547 Epoch: Iteration #600 error is: 0.251092358669204 Epoch: Iteration #700 error is: 0.250866338739603 Epoch: Iteration #800 error is: 0.250834159298613 Epoch: Iteration #900 error is: 0.250831529133131 Epoch: Iteration #1000 error is: 0.25083130752673 [1] "K= 1" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 25.3199820937147 Epoch: Iteration #200 error is: 0.286599312158033 Epoch: Iteration #300 error is: 0.253700494870565 Epoch: Iteration #400 error is: 0.252392033519545 Epoch: Iteration #500 error is: 0.251938276620834 Epoch: Iteration #600 error is: 0.251936938900726 Epoch: Iteration #700 error is: 0.251936693929833 Epoch: Iteration #800 error is: 0.251936684836777 Epoch: Iteration #900 error is: 0.251936684707904 Epoch: Iteration #1000 error is: 0.251936684647443 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 13.3096202521307 Epoch: Iteration #200 error is: 0.546907657972712 Epoch: Iteration #300 error is: 0.306569917156515 Epoch: Iteration #400 error is: 0.268001381090087 Epoch: Iteration #500 error is: 0.25870341496316 Epoch: Iteration #600 error is: 0.254833555144435 Epoch: Iteration #700 error is: 0.253926549618181 Epoch: Iteration #800 error is: 0.253830310677659 Epoch: Iteration #900 error is: 0.253815462254545 Epoch: Iteration #1000 error is: 0.253808317266062 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 18.9026439379208 Epoch: Iteration #200 error is: 0.26931107780931 Epoch: Iteration #300 error is: 0.252984577484852 Epoch: Iteration #400 error is: 0.251958575217056 Epoch: Iteration #500 error is: 0.251935162699281 Epoch: Iteration #600 error is: 0.251935029648532 Epoch: Iteration #700 error is: 0.251935029304857 Epoch: Iteration #800 error is: 0.251935028805651 Epoch: Iteration #900 error is: 0.25193502811215 Epoch: Iteration #1000 error is: 0.251935027229526 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 24.5715496744224 Epoch: Iteration #200 error is: 0.370946711265956 Epoch: Iteration #300 error is: 0.270977923212868 Epoch: Iteration #400 error is: 0.254349739803354 Epoch: Iteration #500 error is: 0.252753624914369 Epoch: Iteration #600 error is: 0.251382603414836 Epoch: Iteration #700 error is: 0.25089215952148 Epoch: Iteration #800 error is: 0.250834302188001 Epoch: Iteration #900 error is: 0.250830240474623 Epoch: Iteration #1000 error is: 0.250829994849339 RUNIT TEST PROTOCOL -- Thu Oct 14 09:06:43 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 16.826 2.144 18.960
BiRewire.Rcheck/BiRewire-Ex.timings
name | user | system | elapsed | |
birewire.analysis.bipartite | 0.070 | 0.267 | 0.337 | |
birewire.analysis.dsg | 0.019 | 0.016 | 0.036 | |
birewire.analysis.undirected | 64.929 | 0.167 | 65.102 | |
birewire.bipartite.from.incidence | 0.004 | 0.028 | 0.032 | |
birewire.build.dsg | 0.008 | 0.000 | 0.008 | |
birewire.induced.bipartite | 0.002 | 0.000 | 0.002 | |
birewire.rewire.bipartite | 0.001 | 0.031 | 0.031 | |
birewire.rewire.bipartite.and.projections | 0.063 | 0.012 | 0.076 | |
birewire.rewire.dsg | 0.004 | 0.000 | 0.004 | |
birewire.rewire.undirected | 0.492 | 0.056 | 0.549 | |
birewire.similarity | 0.008 | 0.000 | 0.008 | |
birewire.similarity.dsg | 0.015 | 0.004 | 0.018 | |
birewire.visual.monitoring.bipartite | 4.473 | 0.024 | 4.497 | |
birewire.visual.monitoring.dsg | 27.683 | 0.056 | 27.740 | |
birewire.visual.monitoring.undirected | 9.558 | 0.040 | 9.611 | |