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This page was generated on 2024-12-24 11:39 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 220/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.39.0  (landing page)
Andrea Gobbi
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/BiRewire
git_branch: devel
git_last_commit: 8cf10d9
git_last_commit_date: 2024-10-29 09:48:11 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for BiRewire on nebbiolo1

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.

raw results


Summary

Package: BiRewire
Version: 3.39.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BiRewire_3.39.0.tar.gz
StartedAt: 2024-12-23 20:11:51 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 20:15:00 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 189.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BiRewire.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BiRewire_3.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BiRewire.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BiRewire/DESCRIPTION’ ... OK
* this is package ‘BiRewire’ version ‘3.39.0’
* 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-3.21-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          61.190  0.124  61.319
birewire.visual.monitoring.dsg        15.864  0.054  15.918
birewire.visual.monitoring.undirected  6.241  0.112   6.352
* 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-3.21-bioc/meat/BiRewire.Rcheck/00check.log’
for details.


Installation output

BiRewire.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BiRewire
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘BiRewire’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -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 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -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 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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)

Tests output

BiRewire.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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] "You are using a matrix with NA. 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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[1] "K= 1"
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RUNIT TEST PROTOCOL -- Mon Dec 23 20:14:12 2024 
*********************************************** 
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 
 11.600   1.728  13.314 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.2090.2540.463
birewire.analysis.dsg0.0270.0010.028
birewire.analysis.undirected61.190 0.12461.319
birewire.bipartite.from.incidence0.0130.0260.039
birewire.build.dsg0.0100.0030.012
birewire.induced.bipartite0.0030.0000.003
birewire.rewire.bipartite0.0130.0190.032
birewire.rewire.bipartite.and.projections0.3630.0110.374
birewire.rewire.dsg0.0080.0000.008
birewire.rewire.undirected0.7140.0580.772
birewire.similarity0.0240.0000.024
birewire.similarity.dsg0.0420.0020.044
birewire.visual.monitoring.bipartite1.2890.0051.294
birewire.visual.monitoring.dsg15.864 0.05415.918
birewire.visual.monitoring.undirected6.2410.1126.352