Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:25:29 -0400 (Wed, 17 Oct 2018).
Package 153/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
BiRewire 3.12.0 Andrea Gobbi
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: BiRewire |
Version: 3.12.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BiRewire_3.12.0.tar.gz |
StartedAt: 2018-10-15 22:50:48 -0400 (Mon, 15 Oct 2018) |
EndedAt: 2018-10-15 22:53:35 -0400 (Mon, 15 Oct 2018) |
EllapsedTime: 167.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BiRewire.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BiRewire_3.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/BiRewire.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘3.12.0’ * 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-3.7-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 ‘plot’ 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 ‘plot’ 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 ‘plot’ 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 ‘plot’ 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 ‘plot’ 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 ‘plot’ 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 plot polygon qt read.table sd text write.table Consider adding importFrom("grDevices", "colorRampPalette", "dev.off") importFrom("graphics", "abline", "legend", "lines", "par", "plot", "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 or elapsed time > 5s user system elapsed birewire.analysis.undirected 63.392 0.024 63.464 birewire.visual.monitoring.dsg 30.280 0.020 30.324 birewire.visual.monitoring.undirected 10.076 0.052 10.136 * 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-3.7-bioc/meat/BiRewire.Rcheck/00check.log’ for details.
BiRewire.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL BiRewire ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘BiRewire’ ... ** libs gcc -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c interface.c -o interface.o gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/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 * DONE (BiRewire)
BiRewire.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 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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[================================================= ] 99% [================================================= ] 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: 9.59120615102367 Epoch: Iteration #200 error is: 0.270048609713418 Epoch: Iteration #300 error is: 0.252320604961527 Epoch: Iteration #400 error is: 0.250899706854962 Epoch: Iteration #500 error is: 0.250827466968141 Epoch: Iteration #600 error is: 0.250827208585288 Epoch: Iteration #700 error is: 0.250826828554401 Epoch: Iteration #800 error is: 0.250826389372716 Epoch: Iteration #900 error is: 0.250825989768167 Epoch: Iteration #1000 error is: 0.250825701157596 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 9.52326259894762 Epoch: Iteration #200 error is: 0.293336072135115 Epoch: Iteration #300 error is: 0.257231990489985 Epoch: Iteration #400 error is: 0.251069213631521 Epoch: Iteration #500 error is: 0.250845521183961 Epoch: Iteration #600 error is: 0.250830445721032 Epoch: Iteration #700 error is: 0.250830216180935 Epoch: Iteration #800 error is: 0.250830055524207 Epoch: Iteration #900 error is: 0.25082983298304 Epoch: Iteration #1000 error is: 0.250829555213072 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 11.881737282577 Epoch: Iteration #200 error is: 0.708219259199639 Epoch: Iteration #300 error is: 0.337321652404132 Epoch: Iteration #400 error is: 0.281967936699871 Epoch: Iteration #500 error is: 0.273537540884971 Epoch: Iteration #600 error is: 0.267543398290758 Epoch: Iteration #700 error is: 0.2605456000924 Epoch: Iteration #800 error is: 0.254056027163181 Epoch: Iteration #900 error is: 0.252711905384342 Epoch: Iteration #1000 error is: 0.252563035047791 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 16.3339456060415 Epoch: Iteration #200 error is: 1.24002950796814 Epoch: Iteration #300 error is: 0.693850856906718 Epoch: Iteration #400 error is: 0.378887995477417 Epoch: Iteration #500 error is: 0.334667505853834 Epoch: Iteration #600 error is: 0.323934491165954 Epoch: Iteration #700 error is: 0.302306507603828 Epoch: Iteration #800 error is: 0.280391801434911 Epoch: Iteration #900 error is: 0.266773772990888 Epoch: Iteration #1000 error is: 0.259458388679545 [1] "K= 1" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 30.4265224858559 Epoch: Iteration #200 error is: 0.467479126923667 Epoch: Iteration #300 error is: 0.356498122326203 Epoch: Iteration #400 error is: 0.298196618964196 Epoch: Iteration #500 error is: 0.270867229887853 Epoch: Iteration #600 error is: 0.253144349823939 Epoch: Iteration #700 error is: 0.251613451568877 Epoch: Iteration #800 error is: 0.251305111192794 Epoch: Iteration #900 error is: 0.251028128353868 Epoch: Iteration #1000 error is: 0.250880886537123 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 16.698504060577 Epoch: Iteration #200 error is: 0.496612910107163 Epoch: Iteration #300 error is: 0.302179768267932 Epoch: Iteration #400 error is: 0.261181431260651 Epoch: Iteration #500 error is: 0.25346706878614 Epoch: Iteration #600 error is: 0.252618957742884 Epoch: Iteration #700 error is: 0.252399441401195 Epoch: Iteration #800 error is: 0.252243217895929 Epoch: Iteration #900 error is: 0.252093412719985 Epoch: Iteration #1000 error is: 0.25198534937889 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 29.7044858667424 Epoch: Iteration #200 error is: 0.674978889809518 Epoch: Iteration #300 error is: 0.41228780709279 Epoch: Iteration #400 error is: 0.316034208148203 Epoch: Iteration #500 error is: 0.294928973077181 Epoch: Iteration #600 error is: 0.276544138443948 Epoch: Iteration #700 error is: 0.259245053827381 Epoch: Iteration #800 error is: 0.254076710506813 Epoch: Iteration #900 error is: 0.252960048968193 Epoch: Iteration #1000 error is: 0.252492304347459 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 15.3095676418787 Epoch: Iteration #200 error is: 0.257690172550201 Epoch: Iteration #300 error is: 0.252602310092186 Epoch: Iteration #400 error is: 0.252262897050957 Epoch: Iteration #500 error is: 0.251942928438166 Epoch: Iteration #600 error is: 0.251935693730175 Epoch: Iteration #700 error is: 0.251935690508255 Epoch: Iteration #800 error is: 0.251935690282713 Epoch: Iteration #900 error is: 0.25193568995652 Epoch: Iteration #1000 error is: 0.251935689534162 RUNIT TEST PROTOCOL -- Mon Oct 15 22:53:32 2018 *********************************************** 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 > > proc.time() user system elapsed 17.348 0.540 17.937
BiRewire.Rcheck/BiRewire-Ex.timings
name | user | system | elapsed | |
birewire.analysis.bipartite | 0.060 | 0.072 | 0.134 | |
birewire.analysis.dsg | 0.056 | 0.008 | 0.063 | |
birewire.analysis.undirected | 63.392 | 0.024 | 63.464 | |
birewire.bipartite.from.incidence | 0.004 | 0.008 | 0.012 | |
birewire.build.dsg | 0.008 | 0.000 | 0.008 | |
birewire.induced.bipartite | 0.004 | 0.000 | 0.003 | |
birewire.rewire.bipartite | 0.004 | 0.008 | 0.011 | |
birewire.rewire.bipartite.and.projections | 0.100 | 0.000 | 0.098 | |
birewire.rewire.dsg | 0.004 | 0.000 | 0.004 | |
birewire.rewire.undirected | 0.624 | 0.016 | 0.639 | |
birewire.similarity | 0.008 | 0.000 | 0.008 | |
birewire.similarity.dsg | 0.020 | 0.004 | 0.023 | |
birewire.visual.monitoring.bipartite | 4.696 | 0.008 | 4.706 | |
birewire.visual.monitoring.dsg | 30.280 | 0.020 | 30.324 | |
birewire.visual.monitoring.undirected | 10.076 | 0.052 | 10.136 | |