Andrea Gobbi
| Snapshot Date: 2025-10-12 13:45 -0400 (Sun, 12 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BiRewire |
| git_branch: devel |
| git_last_commit: fc05c96 |
| git_last_commit_date: 2025-04-15 10:26:28 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-13 12:03 -0400 (Mon, 13 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
| 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 | ||||
| Package 228/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiRewire 3.41.0 (landing page) Andrea Gobbi
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the BiRewire package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BiRewire |
| Version: 3.41.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BiRewire_3.41.0.tar.gz |
| StartedAt: 2025-10-12 21:35:51 -0400 (Sun, 12 Oct 2025) |
| EndedAt: 2025-10-12 21:39:54 -0400 (Sun, 12 Oct 2025) |
| EllapsedTime: 243.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiRewire.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BiRewire_3.41.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BiRewire.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BiRewire/DESCRIPTION’ ... OK
* this is package ‘BiRewire’ version ‘3.41.0’
* 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:149:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:221:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:229:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:280:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:332:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:339:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:402:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:454:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:461:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:588:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:652:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:737:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:844:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:893:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:962:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:1066:30: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
BiRewire.c:1096:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:1144:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
BiRewire.c:1149:30: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
BiRewire.c:1183:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
interface.c:105:25: warning: too many arguments for format [-Wformat-extra-args]
interface.c:147:25: warning: too many arguments for format [-Wformat-extra-args]
interface.c:252:25: warning: too many arguments for format [-Wformat-extra-args]
interface.c:296:25: warning: too many arguments for format [-Wformat-extra-args]
See ‘/home/biocbuild/bbs-3.22-bioc/meat/BiRewire.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
birewire.analysis.bipartite.Rd: igraph, get.incidence
birewire.analysis.dsg.Rd: igraph
birewire.analysis.undirected.Rd: igraph, get.adjacency
birewire.bipartite.from.incidence.Rd: igraph, graph.incidence
birewire.induced.bipartite.Rd: igraph
birewire.rewire.bipartite.Rd: igraph, get.incidence
birewire.rewire.undirected.Rd: igraph, get.adjacency
birewire.sampler.bipartite.Rd: write_stm_CLUTO, read_stm_CLUTO
birewire.sampler.undirected.Rd: write_stm_CLUTO, read_stm_CLUTO
birewire.slum.to.sparseMatrix.Rd: read_stm_CLUTO, igraph,
graph.adjacency
birewire.visual.monitoring.bipartite.Rd: Rtsne
birewire.visual.monitoring.dsg.Rd: Rtsne
birewire.visual.monitoring.undirected.Rd: Rtsne
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 72.754 0.198 73.613
birewire.visual.monitoring.dsg 19.018 0.120 19.476
birewire.visual.monitoring.undirected 7.352 0.246 7.749
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/BiRewire.Rcheck/00check.log’
for details.
BiRewire.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BiRewire
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BiRewire’ ...
** this is package ‘BiRewire’ version ‘3.41.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c BiRewire.c -o BiRewire.o
BiRewire.c: In function ‘analysis’:
BiRewire.c:149:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
149 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c: In function ‘analysis_ex’:
BiRewire.c:221:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
221 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c:229:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
229 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c: In function ‘rewire_bipartite’:
BiRewire.c:280:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
280 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c: In function ‘rewire_bipartite_ex’:
BiRewire.c:332:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
332 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c:339:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
339 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c: In function ‘rewire_sparse_bipartite’:
BiRewire.c:402:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
402 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c: In function ‘rewire_sparse_bipartite_ex’:
BiRewire.c:454:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
454 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c:461:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
461 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c: In function ‘analysis_undirected’:
BiRewire.c:588:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
588 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c: In function ‘analysis_undirected_ex’:
BiRewire.c:652:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
652 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c:737:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
737 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c: In function ‘rewire’:
BiRewire.c:844:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
844 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c: In function ‘rewire_ex’:
BiRewire.c:893:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
893 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c:962:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
962 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
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:1096:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
1096 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
BiRewire.c: In function ‘rewire_sparse_ex’:
BiRewire.c:1144:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
1144 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
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) )) {
| ~^~~
BiRewire.c:1183:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
1183 | Rprintf("DONE in %d seconds \n",-(tin-tfin));
| ~^ ~~~~~~~~~~~
| | |
| int time_t {aka long int}
| %ld
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c interface.c -o interface.o
interface.c: In function ‘R_rewire_bipartite’:
interface.c:105:25: warning: too many arguments for format [-Wformat-extra-args]
105 | warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
interface.c: In function ‘R_rewire_sparse_bipartite’:
interface.c:147:25: warning: too many arguments for format [-Wformat-extra-args]
147 | warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
interface.c: In function ‘R_rewire’:
interface.c:252:25: warning: too many arguments for format [-Wformat-extra-args]
252 | warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
interface.c: In function ‘R_rewire_sparse’:
interface.c:296:25: warning: too many arguments for format [-Wformat-extra-args]
296 | warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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')
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[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 -- Sun Oct 12 21:38:45 2025
***********************************************
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: `graph.bipartite()` was deprecated in igraph 2.1.0.
ℹ Please use `make_bipartite_graph()` instead.
2: `get.incidence()` was deprecated in igraph 2.0.0.
ℹ Please use `as_biadjacency_matrix()` instead.
3: `is.igraph()` was deprecated in igraph 2.0.0.
ℹ Please use `is_igraph()` instead.
4: `erdos.renyi.game()` was deprecated in igraph 0.8.0.
ℹ Please use `sample_gnp()` instead.
5: `get.adjacency()` was deprecated in igraph 2.0.0.
ℹ Please use `as_adjacency_matrix()` instead.
>
> proc.time()
user system elapsed
12.513 0.460 13.197
BiRewire.Rcheck/BiRewire-Ex.timings
| name | user | system | elapsed | |
| birewire.analysis.bipartite | 0.245 | 0.094 | 0.345 | |
| birewire.analysis.dsg | 0.034 | 0.003 | 0.037 | |
| birewire.analysis.undirected | 72.754 | 0.198 | 73.613 | |
| birewire.bipartite.from.incidence | 0.009 | 0.007 | 0.017 | |
| birewire.build.dsg | 0.013 | 0.002 | 0.016 | |
| birewire.induced.bipartite | 0.003 | 0.000 | 0.003 | |
| birewire.rewire.bipartite | 0.008 | 0.004 | 0.013 | |
| birewire.rewire.bipartite.and.projections | 0.424 | 0.012 | 0.437 | |
| birewire.rewire.dsg | 0.007 | 0.001 | 0.008 | |
| birewire.rewire.undirected | 0.835 | 0.039 | 0.877 | |
| birewire.similarity | 0.028 | 0.000 | 0.048 | |
| birewire.similarity.dsg | 0.052 | 0.001 | 0.057 | |
| birewire.visual.monitoring.bipartite | 1.533 | 0.010 | 1.596 | |
| birewire.visual.monitoring.dsg | 19.018 | 0.120 | 19.476 | |
| birewire.visual.monitoring.undirected | 7.352 | 0.246 | 7.749 | |