| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:07 -0400 (Fri, 24 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" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 230/2359 | 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 | ERROR | skipped | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BiRewire |
| Version: 3.41.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL BiRewire |
| StartedAt: 2025-10-23 20:21:14 -0000 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 20:21:42 -0000 (Thu, 23 Oct 2025) |
| EllapsedTime: 28.5 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL BiRewire
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BiRewire’ ...
** this is package ‘BiRewire’ version ‘3.41.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)