Closed nunotexbsd closed 10 months ago
Enchufa2
commented
11 months ago No clue as to what could be failing, because we are OK on CRAN.
nunotexbsd
commented
11 months ago Hashicorp/Atlas® Vagrant™:
Instances can be deployed using the vagrant utility:
% vagrant init freebsd/FreeBSD-13.2-RELEASE
% vagrant upFrom testthat.Rout.fail:
== Failed tests ================================================================
-- Failure ('test_math.R:60:3'): we can take logarithms units ------------------
units(log1p(ux)) (`actual`) not equal to units(as_units("ln(re 1 m)", force_single_symbol = TRUE)) (`expected`).
`actual$numerator`: "1 ln(re 1 m)"
`expected$numerator`: "ln(re 1 m)"
-- Failure ('test_math.R:63:3'): we can take logarithms units ------------------
units(log(ux)) (`actual`) not equal to units(as_units("ln(re 1 m)", force_single_symbol = TRUE)) (`expected`).
`actual$numerator`: "1 ln(re 1 m)"
`expected$numerator`: "ln(re 1 m)"
[ FAIL 2 | WARN 0 | SKIP 11 | PASS 439 ]Could you please run the following and report the output?
#include <stdio.h>
#include <math.h>
#include <udunits2/udunits2.h>
int main() {
ut_set_error_message_handler((ut_error_message_handler) ut_ignore);
ut_system *sys = ut_read_xml(NULL);
ut_encoding enc = UT_UTF8;
ut_set_error_message_handler((ut_error_message_handler) vprintf);
ut_unit *meter = ut_parse(sys, "1 m", enc);
ut_unit *logmeter = ut_log(exp(1), meter);
char out[128];
ut_format(logmeter, out, sizeof(out), enc);
printf("%s\n", out);
ut_free(meter);
ut_free(logmeter);
ut_free_system(sys);
return 0;
}Save this as test.c and then
$ gcc test.c -l udunits2 && ./a.out
ln(re 1 m)(...)
Forgot to add -l udunits2
@Enchufa2
Changed #include <udunits2/udunits2.h> to #include <udunits2.h>
It compiles without any warning and ./a.out gives result: ln(re 1 m)
nunotexbsd
commented
10 months ago @Enchufa2
It fails with clang with a core dump:
clang test.c -shared -L/usr/local/lib/R/lib -Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -B/usr/local/bin -L/usr/local/lib -I/usr/local/include -ludunits2
./a.out: Segmentation fault (core dumped)
Maybe the problem is from clang?
I'm a little bit confused but it seems that FreeBSD ports framework uses clang + gcc fortran for compiling for what I see in package build log:
using C++ compiler: 'FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152)'
gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R-cran-units/work/units/src'
c++ -std=gnu++17 -I"/usr/local/lib/R/include" -DNDEBUG -DUDUNITS2_DIR=0 -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I'/usr/local/lib/R/library/Rcpp/include' -DLIBICONV_PLUG -I/usr/local/in
clude -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include -c RcppExports.cpp -o
RcppExports.o
c++ -std=gnu++17 -I"/usr/local/lib/R/include" -DNDEBUG -DUDUNITS2_DIR=0 -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I'/usr/local/lib/R/library/Rcpp/include' -DLIBICONV_PLUG -I/usr/local/in
clude -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include -c udunits.cpp -o udu
nits.o
c++ -std=gnu++17 -shared -L/usr/local/lib/R/lib -Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -B/usr/local/bin -L/usr/local/lib -fstack-protector-strong -o units.so RcppExports.o udunits.o -lexpat -lexpa
t -ludunits2 -L/usr/local/lib/R/lib -lR
gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R-cran-units/work/units/src'
installing to /wrkdirs/usr/ports/math/R-cran-units/work/stage/usr/local/lib/R/library/00LOCK-units/00new/units/libsWe are compiling a program in my example above, not a shared library, so -shared shouldn't be added. With clang, try
$ clang test.c -ludunits2 -lm && ./a.out
ln(re 1 m)I spinned a FreeBSD 14 virtual machine using the official qcow2 image, and I see:
$ clang test.c -ludunits2 -lm -I/usr/local/include -L/usr/local/lib && ./a.out
1 ln(re 1 m)So this may be an upstream bug in udunits2, because in all the other platforms (and other bases within the same platform) do not show that leading 1. I suggest to submit this upstream, and we can close this.
units works just fine, with or without that 1. And as said, all checks are ok on CRAN. So meanwhile you can safely skip those two tests in FreeBSD.
Enchufa2
commented
10 months ago In fact,
$ gcc12 test.c -ludunits2 -lm -I/usr/local/include -L/usr/local/lib && ./a.out
ln(re 1 m)produces the correct output in FreeBSD, and clang-16 does too on Linux. So... it may be some issue with FreeBSD's clang... I don't know, but units seems to be ok.
Tests failure on FreeBSD14/R4.3.1 Port: https://www.freshports.org/math/R-cran-units/
Any clues? Thanks