Hi,

The testsuite is nearly perfect except one below:

Bernoulli distribution: ... PASS. Bernoulli distribution: ...... PASS. Beta distribution: ... PASS. Beta distribution: gsl: simplex.c:265: ERROR: non-finite function value encountered Default GSL error handler invoked.

gsl version: 1.16

Hello!

I'm working on a package for macports but the testing suite fails on 'sort_example' with El Capitan 10.11.3:

../build-aux/test-driver: line 107: 78802 Segmentation fault: 11  "$@" > $log_file 2>&1
FAIL: sort_example

Looks to be line 117 of the 'tests/sort_example' shell script,

117       exec "$progdir/$program" ${1+"$@"}

Which when run directly confirms the symptom:

tests$ pwd
[...]/ports/math/apophenia/work/apophenia-1.0/tests
tests$ ./sort_example
Segmentation fault: 11

I know this is a wrapped call to the binary, but without the shell script's env attached the error from the standalone call isn't really much to go on. I'm also not sure how to load this all together into LLDB. Any tips?

.libs$ pwd
[...]/ports/math/apophenia/work/apophenia-1.0/tests/.libs
.libs$ ./sort_example
dyld: Library not loaded: /opt/local/lib/libapophenia.2.dylib
  Referenced from: /opt/local/var/macports/build/[...]/ports_math_apophenia/apophenia/work/apophenia-1.0/tests/.libs/./sort_example
  Reason: image not found
Trace/BPT trap: 5

I've currently got the macport pulling the release tarball "v1.0.tar.gz" dated 2015-11-30. Some observations:

1. I'm unable to reproduce the symptom in Ubuntu 14.04.4 "trusty".
2. I re-installed Xcode and the command-line tools just for grins but no luck.
3. I went back to release tag 0.999a dated 2014-08-04 and all tests PASSED. Looks like there was a commit on sort_example.c that day.
4. I also noticed there are more tests in 0.999a, 35 total as opposed to 30 in v1.0.
5. Release 0.999b doesn't build and never reaches 'make check' on my system.
6. Every once in awhile the 'test_apop' test also fails with "Aborted" but it's intermittent, and I've found that if I uninstall gsl and sqlite3, then re-build, that issue goes away. I see Issue #10 from Aug. 2014 was similar.

So I'm not sure where to go from here to troubleshoot further. I'd be happy to try and debug it but I would need some guidance in that area. Given that some tests have been removed since 2014, how important is this sort_example test?

Thanks for your help. Rob

This has no formula available so Mac OSX users cannot brew install apophenia

I created a pull request https://github.com/Homebrew/homebrew-core/pull/331 (now closed, see below) against the homebrew-core project to build apophenia from scratch.

But really, that should be part of this project, not something written and maintained by outsiders.

I do observe that there's a macports portfile as well, apparently maintained outside this project, also.

On a Debian Wheezy desktop, I cloned the git repository for Apophenia, checked out the "pkg" branch, and ran ./configure successfully. However, when I run "make all" I get

CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/rsmith/warez/Apophenia/missing aclocal-1.13 -I m4 /home/rsmith/warez/Apophenia/missing: line 81: aclocal-1.13: command not found WARNING: 'aclocal-1.13' is missing on your system. You should only need it if you modified 'acinclude.m4' or 'configure.ac' or m4 files included by 'configure.ac'. The 'aclocal' program is part of the GNU Automake package: http://www.gnu.org/software/automake It also requires GNU Autoconf, GNU m4 and Perl in order to run: http://www.gnu.org/software/autoconf http://www.gnu.org/software/m4/ http://www.perl.org/ make: *** [aclocal.m4] Error 127

I have automake 1.11 installed, and both "aclocal" and "aclocal-1.11" are installed in /usr/bin/. I did not modify any files, so I was hoping automake 1.11 in Wheezy would work. Any suggestions?

Hi,

I'm going to package it into Fedora, I need a versioned tarball.

I can handle the version by gittags, so please tag the releases from now on.

Thanks.

Whenever I try to install the latest, I get:

In file included from apop_db.c:21:0:
apop_db_mysql.c:6:23: fatal error: my_global.h: No such file or directory
compilation terminated.

To get around this, I comment out lines 12427-12434 in config, which I assume prevents me from interfacing with mysql.

#if test "x$ac_cv_lib_mysqlclient_mysql_query" = xyes; then :
#  cat >>confdefs.h <<_ACEOF
#define HAVE_LIBMYSQLCLIENT 1
#_ACEOF

#  LIBS="-lmysqlclient $LIBS"

#fi

Hi,

Some functions/macros are not working. I noticed there are no prototype declaration in the apop.h file. Can you please resolve this.

Thank you.

For example apop_matrix_to_data or apop_vector_to_data.

/usr/bin/ld: error: undefined symbol: apop_matrix_to_data

Hi,

I am getting the following errors when trying to compile:

../../apophenia-pkg/model/apop_histogram.c:116:21: error: expected expression OMP_for_reduce(+:ll, int i=0; i< datasize; i++){ ^ ../../apophenia-pkg/apop_internal.h:65:33: note: expanded from macro 'OMP_for_reduce'

define OMP_for_reduce(...) for(VA_ARGS)

                            ^

../../apophenia-pkg/model/apop_histogram.c:116:38: error: use of undeclared identifier 'i' OMP_for_reduce(+:ll, int i=0; i< datasize; i++){ ^ ../../apophenia-pkg/apop_internal.h:65:33: note: expanded from macro 'OMP_for_reduce'

define OMP_for_reduce(...) for(VA_ARGS)

                            ^

../../apophenia-pkg/model/apop_histogram.c:116:51: error: use of undeclared identifier 'i' OMP_for_reduce(+:ll, int i=0; i< datasize; i++){

I am able to compile fine on Linux. Is this a clang issue? I am using clang-602.0.49, Apple LLVM version 6.1.0.

Thanks, Neil

This line will prevent errors such as the following on Mac OS X: automake: warning: source file '$(top_builddir)/eg/apop_map_row.c' is in a subdirectory, automake: but option 'subdir-objects' is disabled

Hello,

I'm very interested in Apophenia but I'm working mostly with very sparse data and wasn't able to find any mention about sparse data support on http://apophenia.info/ , in 21st Century C and Modeling With Data.

The sparsity comes often from one-hot encoding of categorical variables with high cardinality (50-100.000) and I want to apply logistic regression type models to this data. I plan to write a specialised solver myself but I'm wondering if you could recommend a sparse matrix library (such as CSPARSE) that would work well with Apophenia or if I missed already included support for sparse matrices.

best, Immanuel

This is minor issue I get when using the latest git version. In the tests/utilities_test script, in the function fixed_read(), the line

if Diff $($SQLITE3 td.db "select col_2 from td where rowid=4") 2.71828

compares the output of a sqlite3 query to 2.71828. However, this doesn't work with my current $HOME/.sqliterc which includes "headers=on" because then the column name is compared instead of its contents. Using the command line option "-noheader" fixes this, but I don't know if there are side effects from using other nodefaults in a sqliterc file. The version of sqlite3 I'm using does not seem to have an option for ignoring the sqliterc.

Two object files build with no symbols on macOS 10.6.8:

/opt/local/bin/ranlib: file: .libs/libapophenia.a(asprintf.o) has no symbols
/opt/local/bin/ranlib: file: .libs/libapophenia.a(libapopmodel_la-apop_wishart.o) has no symbols
ranlib: file: .libs/libapophenia.a(asprintf.o) has no symbols
ranlib: file: .libs/libapophenia.a(libapopmodel_la-apop_wishart.o) has no symbols

Then, three tests fail:

../../../build-aux/test-driver: line 112: 25908 Bus error               "$@" >> "$log_file" 2>&1
FAIL: test_apop
../../../build-aux/test-driver: line 112: 26497 Abort trap              "$@" >> "$log_file" 2>&1
FAIL: distribution_tests
FAIL: ../eg/test_updating

Complete output:

make  check-TESTS
PASS: utilities_test
PASS: db_tests
PASS: error_test
PASS: factors
PASS: nist_tests
PASS: sort_example
../../../build-aux/test-driver: line 112: 25908 Bus error               "$@" >> "$log_file" 2>&1
FAIL: test_apop
PASS: ../eg/apop_map_row
PASS: ../eg/binning
PASS: ../eg/boot_clt
PASS: ../eg/data_fill
PASS: ../eg/draw_to_db
PASS: ../eg/db_fns
PASS: ../eg/dot_products
PASS: ../eg/entropy_vector
PASS: ../eg/iv
PASS: ../eg/ks_tests
PASS: ../eg/logit
PASS: ../eg/fake_logit
PASS: ../eg/normalization_demo
PASS: ../eg/ols
PASS: ../eg/ols_oneliner
PASS: ../eg/parameterization
PASS: ../eg/simple_subsets
PASS: ../eg/t_test_by_rows
PASS: ../eg/test_distances
PASS: ../eg/test_fisher
PASS: ../eg/test_harmonic
PASS: ../eg/test_pruning
PASS: ../eg/test_regex
../../../build-aux/test-driver: line 112: 26497 Abort trap              "$@" >> "$log_file" 2>&1
FAIL: distribution_tests
PASS: lognormal_test
PASS: rake_test
PASS: test_kernel_ll
PASS: update_via_rng
PASS: ../eg/cross_models
PASS: ../eg/dconstrain
PASS: ../eg/entropy_model
PASS: ../eg/faithful
PASS: ../eg/f_test
PASS: ../eg/fix_params
PASS: ../eg/hills2
PASS: ../eg/jack
PASS: ../eg/jacobian
PASS: ../eg/ml_imputation
PASS: ../eg/pmf_test
PASS: ../eg/some_cdfs
PASS: ../eg/test_kl_divergence
PASS: ../eg/test_ranks
FAIL: ../eg/test_updating
PASS: ../eg/transform
============================================================================
Testsuite summary for apophenia 1.0
============================================================================
# TOTAL: 51
# PASS:  48
# SKIP:  0
# XFAIL: 0
# FAIL:  3
# XPASS: 0
# ERROR: 0
============================================================================
See tests/test-suite.log
Please report to [email protected]
============================================================================
make[4]: *** [test-suite.log] Error 1
make[3]: *** [check-TESTS] Error 2
make[2]: *** [check-am] Error 2
make[1]: *** [check-recursive] Error 1
make: *** [distcheck] Error 1

I am trying to build apophenia from the latest commit, and configure (autoconf, in effect) ignores arguments passed:

1. --build= is ignored, and configure forced cpu_arch instead of build_arch.
2. --with-mysql=no is ignored, and the build eventually fails on:

  CCLD     libapopkernel.la
  CCLD     libapophenia.la
**ld: library not found for -lmysqlclient**
collect2: ld returned 1 exit status
make[3]: *** [libapophenia.la] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [distcheck] Error 1

3. --disable-silent-rules is ignored, no verbose output.

I am trying to build the latest commit from here on 10.6 for PPC, and get the following error:

Undefined symbols:
  "_gomp_thread_attr", referenced from:
      _gomp_run_sched_chunk in libgomp.a(env.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[3]: *** [test_apop] Error 1
make[2]: *** [check-am] Error 2
make[1]: *** [check-recursive] Error 1
make: *** [distcheck] Error 1

---------------------

OK, built. From the apophenia-1.0 directory, you can run: make && sudo make install
--->  Building apophenia
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_math_apophenia/apophenia/work/apophenia-113671c16afa1724f9f225acdc88e838770071ce" && /usr/bin/make -j4 -w all 
make: Entering directory `/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_math_apophenia/apophenia/work/b-k-apophenia-113671c'
make: *** No rule to make target `all'.  Stop.

Any idea how to fix this?

Hello,

I've just installed apophenia on my system running Ubuntu 20.04 (libgsl23).

The first example, census.c from the page http://apophenia.info/gentle.html, compiles well:

$ make census cc -Wall -Wextra -g census.c -lapophenia -lgsl -lgslcblas -lsqlite3 -o census census.c: In function ‘main’: census.c:7:5: warning: missing initializer for field ‘output_pipe’ of ‘variadic_type_apop_model_print’ {aka ‘struct ’} [-Wmissing-field-initializers] 7 | apop_model_print(est); | ^~~~~~~~~~~~~~~~ In file included from census.c:1: /usr/local/include/apop.h:452:2: note: ‘output_pipe’ declared here 452 | apop_varad_declare(void, apop_model_print, apop_model * model; FILE *output_pipe); | ^~~~~~~~~~~~~~~~~~

But I get an error when running it:

$ ./census gsl: ../gsl/gsl_vector_double.h:180: ERROR: index out of range Default GSL error handler invoked.

which I tracked, with gdb, to:

apop_ols.c:166 ll += logl(gsl_ran_gaussian_pdf(gsl_vector_get(errors, i), sigma)* weight * x_prob);

Hi,

I recently upgraded all the packages in my OS , and unfortunately, can't get apophenia to run:

ld-elf.so.1: Shared object "libmysqlclient.so.18" not found, required by "libapophenia.so.2"

Is there a way to get rid of this dependence. I use sqlite- not mysql.

Thank you.

Hi,

Just wanted to clarify.

The plot function may also have been deprecated- many of the examples from the book don't work. Can you please provide list of errata or something equivalent, and perhaps some alternatives, so that for those us following your (MWD) book can get all the examples/macros to work. Thank you. Appreciate it.

/usr/bin/ld: error: undefined symbol: apop_plot_histogram

referenced by cltdemo.c:23 /tmp/cltdemo-a5e244.o:(main)

ated. /usr/bin/ld: error: undefined symbol: apop_plot_histogram

referenced by cltdemo.c:23 /tmp/cltdemo-a5e244.o:(main)