Valentina Iotchkova
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/garfield |
| git_branch: RELEASE_3_21 |
| git_last_commit: 1fb0803 |
| git_last_commit_date: 2025-04-15 10:58:43 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 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 781/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| garfield 1.36.0 (landing page) Valentina Iotchkova
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the garfield package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/garfield.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: garfield |
| Version: 1.36.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL garfield |
| StartedAt: 2025-10-13 20:12:20 -0000 (Mon, 13 Oct 2025) |
| EndedAt: 2025-10-13 20:12:41 -0000 (Mon, 13 Oct 2025) |
| EllapsedTime: 21.9 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL garfield
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘garfield’ ...
** this is package ‘garfield’ version ‘1.36.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (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/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c garfield_init.c -o garfield_init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c garfield_perm.cpp -o garfield_perm.o
garfield_perm.cpp: In function ‘void batchfeep(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, const std::vector<bin>&, const std::vector<double>&, int, int, bool, int, double, int, std::vector<bool>)’:
garfield_perm.cpp:306:29: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘long int’ [-Wformat=]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ~^ ~~~
| | |
| char* long int
| %ld
garfield_perm.cpp:306:32: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘int’ [-Wformat=]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ~^ ~~~~~~
| | |
| char* int
| %d
garfield_perm.cpp:306:38: warning: format ‘%s’ expects argument of type ‘char*’, but argument 4 has type ‘double’ [-Wformat=]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| char* double
| %f
garfield_perm.cpp:306:41: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ^~
garfield_perm.cpp:306:46: warning: format ‘%s’ expects argument of type ‘char*’, but argument 5 has type ‘int’ [-Wformat=]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ~^ ~~~~~~
| | |
| char* int
| %d
garfield_perm.cpp:306:83: warning: format ‘%s’ expects argument of type ‘char*’, but argument 6 has type ‘double’ [-Wformat=]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| char* double
| %f
garfield_perm.cpp: In function ‘int garfield_perm(char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**)’:
garfield_perm.cpp:356:27: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘int’ [-Wformat=]
356 | Rprintf("%s",nannot);
| ~^ ~~~~~~
| | |
| | int
| char*
| %d
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c garfield_prep.cpp -o garfield_prep.o
garfield_prep.cpp:144:28: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
144 | struct Enumerator : public iterator<input_iterator_tag, typename Iterator::value_type> {
| ^~~~~~~~
In file included from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_algobase.h:65,
from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/algorithm:60,
from garfield_prep.cpp:19:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
garfield_prep.cpp:225:37: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
225 | struct TagsOutputIterator1 : public iterator<output_iterator_tag,void,void,void,void> {
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
garfield_prep.cpp:234:37: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
234 | struct TagsOutputIterator2 : public iterator<output_iterator_tag,void,void,void,void> {
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
garfield_prep.cpp:245:38: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
245 | struct TagRefOutputIterator : public iterator<output_iterator_tag,void,void,void,void> {
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
garfield_prep.cpp:273:37: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
273 | struct PrintOutputIterator : public iterator<output_iterator_tag,void,void,void,void> {
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o garfield.so garfield_init.o garfield_perm.o garfield_prep.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-garfield/00new/garfield/libs
** R
** 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 (garfield)