Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:54:28 -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: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BiRewire_3.20.0.tar.gz |
StartedAt: 2020-10-16 23:21:10 -0400 (Fri, 16 Oct 2020) |
EndedAt: 2020-10-16 23:25:04 -0400 (Fri, 16 Oct 2020) |
EllapsedTime: 234.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BiRewire.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BiRewire_3.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/BiRewire.Rcheck’ * using R version 4.0.3 (2020-10-10) * 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 ‘3.20.0’ * 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 ... 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-3.11-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 80.376 0.028 80.406 birewire.visual.monitoring.dsg 43.824 0.004 43.827 birewire.visual.monitoring.undirected 15.034 0.039 15.076 birewire.visual.monitoring.bipartite 6.632 0.016 6.648 * 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-3.11-bioc/meat/BiRewire.Rcheck/00check.log’ for details.
BiRewire.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL BiRewire ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘BiRewire’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.11-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] 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] if( a!=c && b!=d & a!=d && c!=b && (( ad==1 && cb==1 )|| (ac==1 && bd==1) )) { ~^~~ gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c interface.c -o interface.o gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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: 10.297257298482 Epoch: Iteration #200 error is: 0.374450350210195 Epoch: Iteration #300 error is: 0.278468482966166 Epoch: Iteration #400 error is: 0.266420399430777 Epoch: Iteration #500 error is: 0.252643447403927 Epoch: Iteration #600 error is: 0.251566612575161 Epoch: Iteration #700 error is: 0.250963677054184 Epoch: Iteration #800 error is: 0.250842391777024 Epoch: Iteration #900 error is: 0.250831768991318 Epoch: Iteration #1000 error is: 0.250831046392554 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 9.89543776128833 Epoch: Iteration #200 error is: 0.273292242381988 Epoch: Iteration #300 error is: 0.251391195822766 Epoch: Iteration #400 error is: 0.250827549314677 Epoch: Iteration #500 error is: 0.250827480355224 Epoch: Iteration #600 error is: 0.25082729830997 Epoch: Iteration #700 error is: 0.250826872980356 Epoch: Iteration #800 error is: 0.250825958533727 Epoch: Iteration #900 error is: 0.250824505406633 Epoch: Iteration #1000 error is: 0.250823283621274 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 10.3722100832017 Epoch: Iteration #200 error is: 0.450211217447663 Epoch: Iteration #300 error is: 0.264672252295313 Epoch: Iteration #400 error is: 0.255030996712804 Epoch: Iteration #500 error is: 0.252634087390626 Epoch: Iteration #600 error is: 0.252308729400936 Epoch: Iteration #700 error is: 0.251963846940812 Epoch: Iteration #800 error is: 0.251442019292435 Epoch: Iteration #900 error is: 0.250993032451922 Epoch: Iteration #1000 error is: 0.25085359825547 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 10.1229131937439 Epoch: Iteration #200 error is: 0.251236921064527 Epoch: Iteration #300 error is: 0.250818683302575 Epoch: Iteration #400 error is: 0.250818409297528 Epoch: Iteration #500 error is: 0.250818122809486 Epoch: Iteration #600 error is: 0.25081795674974 Epoch: Iteration #700 error is: 0.250817882235004 Epoch: Iteration #800 error is: 0.250817839641132 Epoch: Iteration #900 error is: 0.250817798780495 Epoch: Iteration #1000 error is: 0.250817750220799 [1] "K= 1" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 11.4287793108568 Epoch: Iteration #200 error is: 0.531194988449514 Epoch: Iteration #300 error is: 0.272927249709536 Epoch: Iteration #400 error is: 0.255274080207419 Epoch: Iteration #500 error is: 0.252952892689482 Epoch: Iteration #600 error is: 0.252646517889564 Epoch: Iteration #700 error is: 0.252559837016582 Epoch: Iteration #800 error is: 0.252430858840979 Epoch: Iteration #900 error is: 0.252113604269028 Epoch: Iteration #1000 error is: 0.251437416900669 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 9.21158572407318 Epoch: Iteration #200 error is: 0.255425995524771 Epoch: Iteration #300 error is: 0.251244200963563 Epoch: Iteration #400 error is: 0.250829195707363 Epoch: Iteration #500 error is: 0.250829035911936 Epoch: Iteration #600 error is: 0.250828709203023 Epoch: Iteration #700 error is: 0.250828131586157 Epoch: Iteration #800 error is: 0.250827257153669 Epoch: Iteration #900 error is: 0.250826241844081 Epoch: Iteration #1000 error is: 0.250825438543912 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 11.2234505814837 Epoch: Iteration #200 error is: 0.340916351791435 Epoch: Iteration #300 error is: 0.265111312576241 Epoch: Iteration #400 error is: 0.253602284751736 Epoch: Iteration #500 error is: 0.252585302225842 Epoch: Iteration #600 error is: 0.252313084639458 Epoch: Iteration #700 error is: 0.251776266120371 Epoch: Iteration #800 error is: 0.251080390337909 Epoch: Iteration #900 error is: 0.250850269580762 Epoch: Iteration #1000 error is: 0.25083419433195 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 12.7217952393004 Epoch: Iteration #200 error is: 0.520530690896532 Epoch: Iteration #300 error is: 0.31373052442552 Epoch: Iteration #400 error is: 0.266254717394669 Epoch: Iteration #500 error is: 0.254412604672389 Epoch: Iteration #600 error is: 0.25276483529858 Epoch: Iteration #700 error is: 0.252237679689605 Epoch: Iteration #800 error is: 0.251975964139674 Epoch: Iteration #900 error is: 0.251940089712316 Epoch: Iteration #1000 error is: 0.251938134505641 RUNIT TEST PROTOCOL -- Fri Oct 16 23:25:00 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 24.142 0.632 24.767
BiRewire.Rcheck/BiRewire-Ex.timings
name | user | system | elapsed | |
birewire.analysis.bipartite | 0.123 | 0.083 | 0.207 | |
birewire.analysis.dsg | 0.053 | 0.007 | 0.061 | |
birewire.analysis.undirected | 80.376 | 0.028 | 80.406 | |
birewire.bipartite.from.incidence | 0.010 | 0.008 | 0.018 | |
birewire.build.dsg | 0.011 | 0.000 | 0.012 | |
birewire.induced.bipartite | 0.005 | 0.000 | 0.005 | |
birewire.rewire.bipartite | 0.007 | 0.007 | 0.015 | |
birewire.rewire.bipartite.and.projections | 0.129 | 0.004 | 0.133 | |
birewire.rewire.dsg | 0.006 | 0.001 | 0.006 | |
birewire.rewire.undirected | 0.785 | 0.016 | 0.801 | |
birewire.similarity | 0.151 | 0.003 | 0.155 | |
birewire.similarity.dsg | 0.027 | 0.000 | 0.027 | |
birewire.visual.monitoring.bipartite | 6.632 | 0.016 | 6.648 | |
birewire.visual.monitoring.dsg | 43.824 | 0.004 | 43.827 | |
birewire.visual.monitoring.undirected | 15.034 | 0.039 | 15.076 | |