Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:21 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 203/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiRewire 3.31.0 (landing page) Andrea Gobbi
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
Package: BiRewire |
Version: 3.31.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiRewire.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BiRewire_3.31.0.tar.gz |
StartedAt: 2022-12-28 22:03:22 -0500 (Wed, 28 Dec 2022) |
EndedAt: 2022-12-28 22:05:48 -0500 (Wed, 28 Dec 2022) |
EllapsedTime: 145.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BiRewire.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiRewire.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BiRewire_3.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/BiRewire.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'BiRewire/DESCRIPTION' ... OK * this is package 'BiRewire' version '3.31.0' * 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 whether package 'BiRewire' can be installed ... WARNING Found the following significant warnings: BiRewire.c:1066:30: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] BiRewire.c:1149:30: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/BiRewire.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 12.2.0' * 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 'F:/biocbuild/bbs-3.17-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 nor [v]sprintf. 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 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 56.89 0.06 56.96 birewire.visual.monitoring.dsg 10.60 0.19 10.78 birewire.visual.monitoring.undirected 5.07 0.99 6.06 * 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 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/BiRewire.Rcheck/00check.log' for details.
BiRewire.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL BiRewire ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'BiRewire' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BiRewire.c -o BiRewire.o BiRewire.c: In function 'rewire_sparse': BiRewire.c:1066:30: 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:1149:30: 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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interface.c -o interface.o gcc -shared -s -static-libgcc -o BiRewire.dll tmp.def BiRewire.o interface.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BiRewire/00new/BiRewire/libs/x64 ** 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 ** 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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 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: Rtsne 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" [1] "K= 5" [1] "K= 100" [1] "K= n" [1] "K= 1" [1] "K= 5" [1] "K= 100" [1] "K= n" RUNIT TEST PROTOCOL -- Wed Dec 28 22:05:38 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 > > proc.time() user system elapsed 6.03 1.18 7.25
BiRewire.Rcheck/BiRewire-Ex.timings
name | user | system | elapsed | |
birewire.analysis.bipartite | 0.05 | 0.17 | 0.22 | |
birewire.analysis.dsg | 0.06 | 0.02 | 0.09 | |
birewire.analysis.undirected | 56.89 | 0.06 | 56.96 | |
birewire.bipartite.from.incidence | 0.00 | 0.02 | 0.01 | |
birewire.build.dsg | 0 | 0 | 0 | |
birewire.induced.bipartite | 0.00 | 0.02 | 0.01 | |
birewire.rewire.bipartite | 0.00 | 0.01 | 0.02 | |
birewire.rewire.bipartite.and.projections | 0.05 | 0.03 | 0.08 | |
birewire.rewire.dsg | 0 | 0 | 0 | |
birewire.rewire.undirected | 0.75 | 0.05 | 0.79 | |
birewire.similarity | 0.00 | 0.02 | 0.02 | |
birewire.similarity.dsg | 0.01 | 0.00 | 0.02 | |
birewire.visual.monitoring.bipartite | 0.44 | 0.04 | 0.48 | |
birewire.visual.monitoring.dsg | 10.60 | 0.19 | 10.78 | |
birewire.visual.monitoring.undirected | 5.07 | 0.99 | 6.06 | |