Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:03 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
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 195/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiRewire 3.27.2 (landing page) Andrea Gobbi
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: BiRewire |
Version: 3.27.2 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiRewire.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BiRewire_3.27.2.tar.gz |
StartedAt: 2022-03-17 18:34:55 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 18:37:25 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 150.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BiRewire.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiRewire.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BiRewire_3.27.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BiRewire.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'BiRewire/DESCRIPTION' ... OK * this is package 'BiRewire' version '3.27.2' * 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 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 'D:/biocbuild/bbs-3.15-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 for x64 is not available File 'D:/biocbuild/bbs-3.15-bioc/R/library/BiRewire/libs/x64/BiRewire.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed birewire.analysis.undirected 42.81 0.19 43.00 birewire.visual.monitoring.dsg 25.04 0.04 25.14 birewire.visual.monitoring.undirected 7.77 1.99 9.75 * 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 'D:/biocbuild/bbs-3.15-bioc/meat/BiRewire.Rcheck/00check.log' for details.
BiRewire.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BiRewire ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'BiRewire' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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) )) { ~^~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c interface.c -o interface.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o BiRewire.dll tmp.def BiRewire.o interface.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BiRewire/00new/BiRewire/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'BiRewire' finding HTML links ... done BRCA_binary_matrix html BiRewire-package html birewire.analysis.bipartite html finding level-2 HTML links ... done birewire.analysis.dsg html birewire.analysis.undirected html birewire.bipartite.from.incidence html birewire.build.dsg html birewire.induced.bipartite html birewire.load.dsg html birewire.rewire.bipartite html birewire.rewire.bipartite.and.projections html birewire.rewire.dsg html birewire.rewire.undirected html birewire.sampler.bipartite html birewire.sampler.dsg html birewire.sampler.undirected html birewire.similarity html birewire.similarity.dsg html birewire.slum.to.sparseMatrix html birewire.visual.monitoring.bipartite html birewire.visual.monitoring.dsg html birewire.visual.monitoring.undirected html test_dsg html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiRewire) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'cytolib' is missing or broken Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'rhdf5filters' is missing or broken done
BiRewire.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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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[================================================ ] 98% [================================================= ] 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: 11.0505127882334 Epoch: Iteration #200 error is: 0.772652264055672 Epoch: Iteration #300 error is: 0.397487247953898 Epoch: Iteration #400 error is: 0.280760345769107 Epoch: Iteration #500 error is: 0.259091623646084 Epoch: Iteration #600 error is: 0.254997790936026 Epoch: Iteration #700 error is: 0.253167143389094 Epoch: Iteration #800 error is: 0.252545970492054 Epoch: Iteration #900 error is: 0.252157341073522 Epoch: Iteration #1000 error is: 0.251981431214053 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 19.8107387746929 Epoch: Iteration #200 error is: 0.308407231559607 Epoch: Iteration #300 error is: 0.257881707485068 Epoch: Iteration #400 error is: 0.252926304728919 Epoch: Iteration #500 error is: 0.25226916924391 Epoch: Iteration #600 error is: 0.251287370407972 Epoch: Iteration #700 error is: 0.250843812856562 Epoch: Iteration #800 error is: 0.250829997841219 Epoch: Iteration #900 error is: 0.250829724989187 Epoch: Iteration #1000 error is: 0.250829585210705 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 10.690594800702 Epoch: Iteration #200 error is: 0.450081080239838 Epoch: Iteration #300 error is: 0.284280964131654 Epoch: Iteration #400 error is: 0.265323055181785 Epoch: Iteration #500 error is: 0.255368724115304 Epoch: Iteration #600 error is: 0.253678523220985 Epoch: Iteration #700 error is: 0.253222443526643 Epoch: Iteration #800 error is: 0.252359399872392 Epoch: Iteration #900 error is: 0.251956795911389 Epoch: Iteration #1000 error is: 0.251937944281105 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 11.2607544777803 Epoch: Iteration #200 error is: 0.311824962975579 Epoch: Iteration #300 error is: 0.254284383181705 Epoch: Iteration #400 error is: 0.251424922319902 Epoch: Iteration #500 error is: 0.250833073073481 Epoch: Iteration #600 error is: 0.250831699736812 Epoch: Iteration #700 error is: 0.250831673463463 Epoch: Iteration #800 error is: 0.250831625485188 Epoch: Iteration #900 error is: 0.250831542704449 Epoch: Iteration #1000 error is: 0.250831403883177 [1] "K= 1" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 8.47530794551176 Epoch: Iteration #200 error is: 0.26522652111404 Epoch: Iteration #300 error is: 0.251982840550093 Epoch: Iteration #400 error is: 0.251941200370265 Epoch: Iteration #500 error is: 0.251936250373598 Epoch: Iteration #600 error is: 0.251936178234775 Epoch: Iteration #700 error is: 0.251936178008099 Epoch: Iteration #800 error is: 0.251936177879283 Epoch: Iteration #900 error is: 0.251936177699712 Epoch: Iteration #1000 error is: 0.251936177471678 [1] "K= 5" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 18.1722699500644 Epoch: Iteration #200 error is: 0.991868683523669 Epoch: Iteration #300 error is: 0.412626081911966 Epoch: Iteration #400 error is: 0.283774845201664 Epoch: Iteration #500 error is: 0.25635851510182 Epoch: Iteration #600 error is: 0.254220954165704 Epoch: Iteration #700 error is: 0.253856556870977 Epoch: Iteration #800 error is: 0.253763458918559 Epoch: Iteration #900 error is: 0.253628520645228 Epoch: Iteration #1000 error is: 0.25324992657136 [1] "K= 100" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 11.717682078604 Epoch: Iteration #200 error is: 0.435327377959452 Epoch: Iteration #300 error is: 0.28326060047567 Epoch: Iteration #400 error is: 0.261674417990308 Epoch: Iteration #500 error is: 0.253032653634919 Epoch: Iteration #600 error is: 0.252608691386586 Epoch: Iteration #700 error is: 0.252452092440929 Epoch: Iteration #800 error is: 0.252298566456367 Epoch: Iteration #900 error is: 0.252124834878059 Epoch: Iteration #1000 error is: 0.251994305916417 [1] "K= n" sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 | Epoch: Iteration #100 error is: 11.5654784816942 Epoch: Iteration #200 error is: 0.719705782729881 Epoch: Iteration #300 error is: 0.337708895065834 Epoch: Iteration #400 error is: 0.27415637252822 Epoch: Iteration #500 error is: 0.261308936388417 Epoch: Iteration #600 error is: 0.254900503956985 Epoch: Iteration #700 error is: 0.252463591197737 Epoch: Iteration #800 error is: 0.25221287183619 Epoch: Iteration #900 error is: 0.252140451415117 Epoch: Iteration #1000 error is: 0.252073976778923 RUNIT TEST PROTOCOL -- Thu Mar 17 18:37:15 2022 *********************************************** 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 15.00 0.90 15.95
BiRewire.Rcheck/BiRewire-Ex.timings
name | user | system | elapsed | |
birewire.analysis.bipartite | 0.06 | 0.09 | 0.16 | |
birewire.analysis.dsg | 0.05 | 0.02 | 0.06 | |
birewire.analysis.undirected | 42.81 | 0.19 | 43.00 | |
birewire.bipartite.from.incidence | 0 | 0 | 0 | |
birewire.build.dsg | 0.01 | 0.00 | 0.02 | |
birewire.induced.bipartite | 0 | 0 | 0 | |
birewire.rewire.bipartite | 0.02 | 0.00 | 0.01 | |
birewire.rewire.bipartite.and.projections | 0.08 | 0.00 | 0.08 | |
birewire.rewire.dsg | 0 | 0 | 0 | |
birewire.rewire.undirected | 0.44 | 0.07 | 0.50 | |
birewire.similarity | 0.01 | 0.00 | 0.02 | |
birewire.similarity.dsg | 0.02 | 0.00 | 0.01 | |
birewire.visual.monitoring.bipartite | 3.53 | 0.03 | 3.56 | |
birewire.visual.monitoring.dsg | 25.04 | 0.04 | 25.14 | |
birewire.visual.monitoring.undirected | 7.77 | 1.99 | 9.75 | |