r-quantities/units

0.8-3: Tests fail

nunotexbsd opened this issue · 8 comments

nunotexbsd commented

Tests failure on FreeBSD14/R4.3.1
Port: https://www.freshports.org/math/R-cran-units/

CRAN_DEPENDS=   R-cran-Rcpp>=0.12.10:devel/R-cran-Rcpp
BUILD_DEPENDS=  ${CRAN_DEPENDS}
LIB_DEPENDS=    libudunits2.so:science/udunits
RUN_DEPENDS=    ${CRAN_DEPENDS}
TEST_DEPENDS=   R-cran-testthat>0:devel/R-cran-testthat

* using log directory '/wrkdirs/usr/ports/math/R-cran-units/work/units.Rcheck'
* using R version 4.3.1 (2023-06-16)
* using platform: amd64-portbld-freebsd14.0 (64-bit)
* R was compiled by
    FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152)
    GNU Fortran (FreeBSD Ports Collection) 12.2.0
* running under: FreeBSD 14amd64-main 14.0-ALPHA1 FreeBSD 14.0-ALPHA1 1400094 amd64
* using session charset: ASCII
* using options '--no-manual --no-build-vignettes'
* checking for file 'units/DESCRIPTION' ... OK
* this is package 'units' version '0.8-3'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking:
  'NISTunits', 'measurements', 'xml2', 'dplyr', 'ggplot2', 'vdiffr',
  'rmarkdown'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'units' can be installed ... OK
* used C++ compiler: 'FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152)'
* 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 R 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 startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'ggplot2'
* 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  * plot/ggplot2-nolab.svg
  * plot/ggplot2-transformed.svg
  * plot/plot-boxplot.svg
  * plot/plot-default.svg
  * plot/plot-degree-c.svg
  * plot/plot-division.svg
  * plot/plot-hist.svg
  * plot/plot-inverse.svg
  * plot/plot-lab.svg
  * plot/plot-line.svg
  * plot/plot-nothing.svg
  * plot/plot-npower.svg
  * plot/plot-parentheses.svg
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... NONE
  'measurement_units_in_R.Rmd' using 'UTF-8'... OK
  'units.Rmd' using 'UTF-8'... OK
* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 1 ERROR, 3 NOTEs

Any clues?
Thanks

Enchufa2 commented

No clue as to what could be failing, because we are OK on CRAN.

  • Was the previous version ok?
  • Could you please provide the full logs from the check?
  • Or is there any link to see them online?
  • Or could you please provide a vagrant file to reproduce this?
nunotexbsd commented
  • Was the previous version ok?
    No
  • Could you please provide the full logs from the check?
    yes
  • Or is there any link to see them online?
    https://people.freebsd.org/~eduardo/logs/units.Rcheck/
  • Or could you please provide a vagrant file to reproduce this?
    I'm new to vagrant but FreeBSD supports it:
    Hashicorp/Atlas® Vagrant™:
    Instances can be deployed using the vagrant utility:

      % vagrant init freebsd/FreeBSD-13.2-RELEASE
      % vagrant up

From 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 ]
Enchufa2 commented

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)
nunotexbsd commented

(...)
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

@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/libs
Enchufa2 commented

We 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)
Enchufa2 commented

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

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.

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