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gap_packages badly broken #20525

Closed videlec closed 8 years ago

videlec commented 8 years ago

With Sage 7.2.beta6 with gap_packages installed, within a sage --gap session:

gap> LoadPackage("HAPcryst");
#I  polymake command not found. Please set POLYMAKE_COMMAND by hand
----------------------------------------------------------------
Loading  polymaking 0.8.1
(A package for using polymake in GAP)
by Marc Roeder
----------------------------------------------------------------
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Loading  Cryst 4.1.12 (Computing with crystallographic groups)
by Bettina Eick (http://www.icm.tu-bs.de/~beick/),
   Franz Gähler (http://www.math.uni-bielefeld.de/~gaehler/), and
   Werner Nickel (http://www.mathematik.tu-darmstadt.de/~nickel/).
Homepage: http://www.math.uni-bielefeld.de/~gaehler/gap45/packages.php
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Loading  CrystCat 1.1.6 (The crystallographic groups catalog)
by Volkmar Felsch (http://www.math.rwth-aachen.de/~Volkmar.Felsch/) and
   Franz Gähler (http://www.math.uni-bielefeld.de/~gaehler/).
Homepage: http://www.math.uni-bielefeld.de/~gaehler/gap45/packages.php
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Loading  AClib 1.2 (Almost Crystallographic Groups - A Library and Algorithms)
by Karel Dekimpe (http://www.kulak.ac.be/~dekimpe) and
   Bettina Eick (http://www.icm.tu-bs.de/~beick).
Homepage: http://www.icm.tu-bs.de/~beick/so.html
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#I  HAP warning: Set POLYMAKE_PATH manually if needed. 
#I  HAP warning: Set NEATO_PATH manually if needed.
#I  HAP warning: Set DISPLAY_PATH manually if needed.
Error, <opr> is not an operation called from
<compiled or corrupted statement>  called from
<function "local function">( <arguments> )
 called from read-eval loop at line 162 of /usr/local/src/sage-git/local/gap/latest/pkg/Hap1.11/lib/HapCocyclic/gap/ccgroup.gi
you can 'quit;' to quit to outer loop, or
you can 'return;' to continue

A second issue is a mis-installation of guava:

gap> DirectoriesPackagePrograms("guava")[1];
dir("/usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13/bin/x86_64-unknown-linux-gnu-gcc-default64/")

but this directory does not exist, bin is missing below:

$ ls -l /usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13
total 168
-rw-r--r-- 1 jdemeyer jdemeyer 11775 Mar 19 23:17 CHANGES.guava
-rwxr-xr-x 1 jdemeyer jdemeyer  1918 Mar 19 23:17 configure
-rw-r--r-- 1 jdemeyer jdemeyer 51189 Mar 19 23:17 COPYING.guava
drwxr-xr-x 2 jdemeyer jdemeyer  4096 Mar 30 00:32 doc
-rw-r--r-- 1 jdemeyer jdemeyer   368 Mar 19 23:17 gapdoc.g
-rw-r--r-- 1 jdemeyer jdemeyer  2059 Mar 19 23:17 HISTORY.guava
-rw-r--r-- 1 jdemeyer jdemeyer  1364 Mar 19 23:17 init.g
drwxr-xr-x 2 jdemeyer jdemeyer  4096 Mar 30 00:32 lib
-rw-r--r-- 1 jdemeyer jdemeyer 35120 Mar 19 23:17 LICENSE
-rw-r--r-- 1 jdemeyer jdemeyer  2858 Mar 19 23:17 Makefile.in
-rw-r--r-- 1 jdemeyer jdemeyer 11638 Mar 19 23:17 PackageInfo.g
-rw-r--r-- 1 jdemeyer jdemeyer  1420 Mar 19 23:17 read.g
-rw-r--r-- 1 jdemeyer jdemeyer  4882 Mar 19 23:17 README.guava
-rw-r--r-- 1 jdemeyer jdemeyer    98 Mar 19 23:17 README.md
drwxr-xr-x 4 jdemeyer jdemeyer  4096 Mar 30 00:32 src
drwxr-xr-x 2 jdemeyer jdemeyer  4096 Mar 30 00:32 tbl
drwxr-xr-x 2 jdemeyer jdemeyer  4096 Mar 30 00:32 tst

This causes doctest failures:

sage -t --long src/sage/tests/gap_packages.py
**********************************************************************
File "src/sage/tests/gap_packages.py", line 8, in sage.tests.gap_packages
Failed example:
    test_packages(pkgs, only_failures=True)    # optional - gap_packages
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.tests.gap_packages[2]>", line 1, in <module>
        test_packages(pkgs, only_failures=True)    # optional - gap_packages
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 77, in test_packages
        output = libgap.eval('LoadPackage("{0}")'.format(pkg))
      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
        return make_any_gap_element(self, gap_eval(gap_command))
      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
        raise ValueError('libGAP: '+str(msg).strip())
    ValueError: libGAP: Error, <opr> is not an operation
**********************************************************************
File "src/sage/tests/gap_packages.py", line 47, in sage.tests.gap_packages.test_packages
Failed example:
    test_packages(['GAPDoc'])
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.tests.gap_packages.test_packages[1]>", line 1, in <module>
        test_packages(['GAPDoc'])
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 77, in test_packages
        output = libgap.eval('LoadPackage("{0}")'.format(pkg))
      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
        return make_any_gap_element(self, gap_eval(gap_command))
      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
        raise ValueError('libGAP: '+str(msg).strip())
    ValueError: libGAP: 
**********************************************************************
File "src/sage/tests/gap_packages.py", line 54, in sage.tests.gap_packages.test_packages
Failed example:
    pkgs = all_installed_packages()
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.tests.gap_packages.test_packages[2]>", line 1, in <module>
        pkgs = all_installed_packages()
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 109, in all_installed_packages
        for path in libgap.eval('GAP_ROOT_PATHS').sage():
      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
        return make_any_gap_element(self, gap_eval(gap_command))
      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
        raise ValueError('libGAP: '+str(msg).strip())
    ValueError: libGAP: 
**********************************************************************
File "src/sage/tests/gap_packages.py", line 55, in sage.tests.gap_packages.test_packages
Failed example:
    test_packages(pkgs)    # random output
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.tests.gap_packages.test_packages[3]>", line 1, in <module>
        test_packages(pkgs)    # random output
    NameError: name 'pkgs' is not defined
**********************************************************************
File "src/sage/tests/gap_packages.py", line 105, in sage.tests.gap_packages.all_installed_packages
Failed example:
    all_installed_packages()
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.tests.gap_packages.all_installed_packages[1]>", line 1, in <module>
        all_installed_packages()
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 109, in all_installed_packages
        for path in libgap.eval('GAP_ROOT_PATHS').sage():
      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
        return make_any_gap_element(self, gap_eval(gap_command))
      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
        raise ValueError('libGAP: '+str(msg).strip())
    ValueError: libGAP: 
**********************************************************************
3 items had failures:
   1 of   4 in sage.tests.gap_packages
   1 of   3 in sage.tests.gap_packages.all_installed_packages
   3 of   5 in sage.tests.gap_packages.test_packages
    [9 tests, 5 failures, 4.49 s]
sage -t --long src/sage/coding/linear_code.py
**********************************************************************
File "src/sage/coding/linear_code.py", line 3284, in sage.coding.linear_code.AbstractLinearCode.spectrum
Failed example:
    C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[8]>", line 1, in <module>
        C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
        process = Popen(stdout=PIPE, *popenargs, **kwargs)
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
        errread, errwrite)
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
        raise child_exception
    OSError: [Errno 2] No such file or directory
**********************************************************************
File "src/sage/coding/linear_code.py", line 3292, in sage.coding.linear_code.AbstractLinearCode.spectrum
Failed example:
    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[12]>", line 1, in <module>
        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
        process = Popen(stdout=PIPE, *popenargs, **kwargs)
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
        errread, errwrite)
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
        raise child_exception
    OSError: [Errno 2] No such file or directory
**********************************************************************
File "src/sage/coding/linear_code.py", line 3296, in sage.coding.linear_code.AbstractLinearCode.spectrum
Failed example:
    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[14]>", line 1, in <module>
        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
        process = Popen(stdout=PIPE, *popenargs, **kwargs)
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
        errread, errwrite)
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
        raise child_exception
    OSError: [Errno 2] No such file or directory
**********************************************************************
File "src/sage/coding/linear_code.py", line 3300, in sage.coding.linear_code.AbstractLinearCode.spectrum
Failed example:
    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[16]>", line 1, in <module>
        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
        process = Popen(stdout=PIPE, *popenargs, **kwargs)
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
        errread, errwrite)
      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
        raise child_exception
    OSError: [Errno 2] No such file or directory
**********************************************************************
1 item had failures:
   4 of  18 in sage.coding.linear_code.AbstractLinearCode.spectrum
    [634 tests, 4 failures, 26.04 s]
----------------------------------------------------------------------
sage -t --long src/sage/tests/gap_packages.py  # 5 doctests failed
sage -t --long src/sage/coding/linear_code.py  # 4 doctests failed
----------------------------------------------------------------------

CC: @vbraun @dimpase

Component: packages: optional

Author: Dima Pasechnik

Branch/Commit: 9afe2c3

Reviewer: Jeroen Demeyer

Issue created by migration from https://trac.sagemath.org/ticket/20525

videlec commented 8 years ago
comment:1

Attachment: failing_doctests-librae.log

videlec commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,4 +1,4 @@
 Since #20182 there are some failing doctests related to optional packages

-- `coding/linear_code.py`: related to Guava (gap package)
-- `tests/gap_packages.py`: related to gap packages
+- `coding/linear_code.py`: related to Guava (gap package) (see [failing_doctests-librae.log](https://github.com/sagemath/sage-prod/files/10658881/failing_doctests-librae.log))
+- `tests/gap_packages.py`: related to gap packages (see [failing_doctests-librae.log](https://github.com/sagemath/sage-prod/files/10658881/failing_doctests-librae.log))
jdemeyer commented 8 years ago
comment:2

Are you sure that #20182 has anything to do with this? It seems to me that something broke gap_packages.

videlec commented 8 years ago
comment:3

Reformulation: this was not visible before #20182.

jdemeyer commented 8 years ago
comment:4

First of all, what is the exact command that you ran to get those doctest failures?

Replying to @videlec:

this was not visible before #20182.

Did you actually check this or are you just guessing? I.e. by applying #20182 on top of 7.2.beta5 or reverting #20182 from 7.2.beta6?

jdemeyer commented 8 years ago
comment:5

Replying to @jdemeyer:

First of all, what is the exact command that you ran to get those doctest failures?

And did you verify that the same exact command on Sage 7.2.beta5 did not give failures?

videlec commented 8 years ago
comment:6

The exact command I ran was

for pkg in A_LOT_OF_THINGS
do
    sage -p $pkg
done

sage -patchbot

Note that the failing doctests are optional (precisely # optional - gap_packages). The patchbot did not ran those before #20182.

jdemeyer commented 8 years ago
comment:7

First of all, using ./sage -p $pkg to install packages is not at all recommended (use ./sage -i $pkg instead). Second, not running make before starting the patchbot is really wrong.

jdemeyer commented 8 years ago
comment:8

Do you know the answer to [comment:5]?

jdemeyer commented 8 years ago
comment:9

For the record, I can reproduce the problem. I'm just not convinced that #20182 is to blame.

jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,4 +1,193 @@
 Since #20182 there are some failing doctests related to optional packages

-- `coding/linear_code.py`: related to Guava (gap package) (see [failing_doctests-librae.log](https://github.com/sagemath/sage-prod/files/10658881/failing_doctests-librae.log))
-- `tests/gap_packages.py`: related to gap packages (see [failing_doctests-librae.log](https://github.com/sagemath/sage-prod/files/10658881/failing_doctests-librae.log))
+```
+sage -t --long src/sage/tests/gap_packages.py
+**********************************************************************
+File "src/sage/tests/gap_packages.py", line 8, in sage.tests.gap_packages
+Failed example:
+    test_packages(pkgs, only_failures=True)    # optional - gap_packages
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.tests.gap_packages[2]>", line 1, in <module>
+        test_packages(pkgs, only_failures=True)    # optional - gap_packages
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 77, in test_packages
+        output = libgap.eval('LoadPackage("{0}")'.format(pkg))
+      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
+        return make_any_gap_element(self, gap_eval(gap_command))
+      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
+        raise ValueError('libGAP: '+str(msg).strip())
+    ValueError: libGAP: Error, <opr> is not an operation
+**********************************************************************
+File "src/sage/tests/gap_packages.py", line 47, in sage.tests.gap_packages.test_packages
+Failed example:
+    test_packages(['GAPDoc'])
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.tests.gap_packages.test_packages[1]>", line 1, in <module>
+        test_packages(['GAPDoc'])
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 77, in test_packages
+        output = libgap.eval('LoadPackage("{0}")'.format(pkg))
+      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
+        return make_any_gap_element(self, gap_eval(gap_command))
+      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
+        raise ValueError('libGAP: '+str(msg).strip())
+    ValueError: libGAP: 
+**********************************************************************
+File "src/sage/tests/gap_packages.py", line 54, in sage.tests.gap_packages.test_packages
+Failed example:
+    pkgs = all_installed_packages()
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.tests.gap_packages.test_packages[2]>", line 1, in <module>
+        pkgs = all_installed_packages()
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 109, in all_installed_packages
+        for path in libgap.eval('GAP_ROOT_PATHS').sage():
+      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
+        return make_any_gap_element(self, gap_eval(gap_command))
+      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
+        raise ValueError('libGAP: '+str(msg).strip())
+    ValueError: libGAP: 
+**********************************************************************
+File "src/sage/tests/gap_packages.py", line 55, in sage.tests.gap_packages.test_packages
+Failed example:
+    test_packages(pkgs)    # random output
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.tests.gap_packages.test_packages[3]>", line 1, in <module>
+        test_packages(pkgs)    # random output
+    NameError: name 'pkgs' is not defined
+**********************************************************************
+File "src/sage/tests/gap_packages.py", line 105, in sage.tests.gap_packages.all_installed_packages
+Failed example:
+    all_installed_packages()
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.tests.gap_packages.all_installed_packages[1]>", line 1, in <module>
+        all_installed_packages()
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 109, in all_installed_packages
+        for path in libgap.eval('GAP_ROOT_PATHS').sage():
+      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
+        return make_any_gap_element(self, gap_eval(gap_command))
+      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
+        raise ValueError('libGAP: '+str(msg).strip())
+    ValueError: libGAP: 
+**********************************************************************
+3 items had failures:
+   1 of   4 in sage.tests.gap_packages
+   1 of   3 in sage.tests.gap_packages.all_installed_packages
+   3 of   5 in sage.tests.gap_packages.test_packages
+    [9 tests, 5 failures, 4.49 s]
+sage -t --long src/sage/coding/linear_code.py
+**********************************************************************
+File "src/sage/coding/linear_code.py", line 3284, in sage.coding.linear_code.AbstractLinearCode.spectrum
+Failed example:
+    C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[8]>", line 1, in <module>
+        C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
+        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
+        process = Popen(stdout=PIPE, *popenargs, **kwargs)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
+        errread, errwrite)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
+        raise child_exception
+    OSError: [Errno 2] No such file or directory
+**********************************************************************
+File "src/sage/coding/linear_code.py", line 3292, in sage.coding.linear_code.AbstractLinearCode.spectrum
+Failed example:
+    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[12]>", line 1, in <module>
+        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
+        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
+        process = Popen(stdout=PIPE, *popenargs, **kwargs)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
+        errread, errwrite)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
+        raise child_exception
+    OSError: [Errno 2] No such file or directory
+**********************************************************************
+File "src/sage/coding/linear_code.py", line 3296, in sage.coding.linear_code.AbstractLinearCode.spectrum
+Failed example:
+    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[14]>", line 1, in <module>
+        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
+        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
+        process = Popen(stdout=PIPE, *popenargs, **kwargs)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
+        errread, errwrite)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
+        raise child_exception
+    OSError: [Errno 2] No such file or directory
+**********************************************************************
+File "src/sage/coding/linear_code.py", line 3300, in sage.coding.linear_code.AbstractLinearCode.spectrum
+Failed example:
+    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[16]>", line 1, in <module>
+        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
+        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
+        process = Popen(stdout=PIPE, *popenargs, **kwargs)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
+        errread, errwrite)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
+        raise child_exception
+    OSError: [Errno 2] No such file or directory
+**********************************************************************
+1 item had failures:
+   4 of  18 in sage.coding.linear_code.AbstractLinearCode.spectrum
+    [634 tests, 4 failures, 26.04 s]
+----------------------------------------------------------------------
+sage -t --long src/sage/tests/gap_packages.py  # 5 doctests failed
+sage -t --long src/sage/coding/linear_code.py  # 4 doctests failed
+----------------------------------------------------------------------
+```
kwankyu commented 8 years ago
comment:11

Automatic testing of all installed optional packages was introduced in #18558

kwankyu commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,193 +1,4 @@
 Since #20182 there are some failing doctests related to optional packages

-```
-sage -t --long src/sage/tests/gap_packages.py
-**********************************************************************
-File "src/sage/tests/gap_packages.py", line 8, in sage.tests.gap_packages
-Failed example:
-    test_packages(pkgs, only_failures=True)    # optional - gap_packages
-Exception raised:
-    Traceback (most recent call last):
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
-        self.compile_and_execute(example, compiler, test.globs)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
-        exec(compiled, globs)
-      File "<doctest sage.tests.gap_packages[2]>", line 1, in <module>
-        test_packages(pkgs, only_failures=True)    # optional - gap_packages
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 77, in test_packages
-        output = libgap.eval('LoadPackage("{0}")'.format(pkg))
-      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
-        return make_any_gap_element(self, gap_eval(gap_command))
-      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
-        raise ValueError('libGAP: '+str(msg).strip())
-    ValueError: libGAP: Error, <opr> is not an operation
-**********************************************************************
-File "src/sage/tests/gap_packages.py", line 47, in sage.tests.gap_packages.test_packages
-Failed example:
-    test_packages(['GAPDoc'])
-Exception raised:
-    Traceback (most recent call last):
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
-        self.compile_and_execute(example, compiler, test.globs)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
-        exec(compiled, globs)
-      File "<doctest sage.tests.gap_packages.test_packages[1]>", line 1, in <module>
-        test_packages(['GAPDoc'])
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 77, in test_packages
-        output = libgap.eval('LoadPackage("{0}")'.format(pkg))
-      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
-        return make_any_gap_element(self, gap_eval(gap_command))
-      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
-        raise ValueError('libGAP: '+str(msg).strip())
-    ValueError: libGAP: 
-**********************************************************************
-File "src/sage/tests/gap_packages.py", line 54, in sage.tests.gap_packages.test_packages
-Failed example:
-    pkgs = all_installed_packages()
-Exception raised:
-    Traceback (most recent call last):
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
-        self.compile_and_execute(example, compiler, test.globs)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
-        exec(compiled, globs)
-      File "<doctest sage.tests.gap_packages.test_packages[2]>", line 1, in <module>
-        pkgs = all_installed_packages()
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 109, in all_installed_packages
-        for path in libgap.eval('GAP_ROOT_PATHS').sage():
-      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
-        return make_any_gap_element(self, gap_eval(gap_command))
-      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
-        raise ValueError('libGAP: '+str(msg).strip())
-    ValueError: libGAP: 
-**********************************************************************
-File "src/sage/tests/gap_packages.py", line 55, in sage.tests.gap_packages.test_packages
-Failed example:
-    test_packages(pkgs)    # random output
-Exception raised:
-    Traceback (most recent call last):
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
-        self.compile_and_execute(example, compiler, test.globs)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
-        exec(compiled, globs)
-      File "<doctest sage.tests.gap_packages.test_packages[3]>", line 1, in <module>
-        test_packages(pkgs)    # random output
-    NameError: name 'pkgs' is not defined
-**********************************************************************
-File "src/sage/tests/gap_packages.py", line 105, in sage.tests.gap_packages.all_installed_packages
-Failed example:
-    all_installed_packages()
-Exception raised:
-    Traceback (most recent call last):
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
-        self.compile_and_execute(example, compiler, test.globs)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
-        exec(compiled, globs)
-      File "<doctest sage.tests.gap_packages.all_installed_packages[1]>", line 1, in <module>
-        all_installed_packages()
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 109, in all_installed_packages
-        for path in libgap.eval('GAP_ROOT_PATHS').sage():
-      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
-        return make_any_gap_element(self, gap_eval(gap_command))
-      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
-        raise ValueError('libGAP: '+str(msg).strip())
-    ValueError: libGAP: 
-**********************************************************************
-3 items had failures:
-   1 of   4 in sage.tests.gap_packages
-   1 of   3 in sage.tests.gap_packages.all_installed_packages
-   3 of   5 in sage.tests.gap_packages.test_packages
-    [9 tests, 5 failures, 4.49 s]
-sage -t --long src/sage/coding/linear_code.py
-**********************************************************************
-File "src/sage/coding/linear_code.py", line 3284, in sage.coding.linear_code.AbstractLinearCode.spectrum
-Failed example:
-    C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
-Exception raised:
-    Traceback (most recent call last):
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
-        self.compile_and_execute(example, compiler, test.globs)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
-        exec(compiled, globs)
-      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[8]>", line 1, in <module>
-        C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
-        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
-        process = Popen(stdout=PIPE, *popenargs, **kwargs)
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
-        errread, errwrite)
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
-        raise child_exception
-    OSError: [Errno 2] No such file or directory
-**********************************************************************
-File "src/sage/coding/linear_code.py", line 3292, in sage.coding.linear_code.AbstractLinearCode.spectrum
-Failed example:
-    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
-Exception raised:
-    Traceback (most recent call last):
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
-        self.compile_and_execute(example, compiler, test.globs)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
-        exec(compiled, globs)
-      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[12]>", line 1, in <module>
-        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
-        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
-        process = Popen(stdout=PIPE, *popenargs, **kwargs)
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
-        errread, errwrite)
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
-        raise child_exception
-    OSError: [Errno 2] No such file or directory
-**********************************************************************
-File "src/sage/coding/linear_code.py", line 3296, in sage.coding.linear_code.AbstractLinearCode.spectrum
-Failed example:
-    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
-Exception raised:
-    Traceback (most recent call last):
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
-        self.compile_and_execute(example, compiler, test.globs)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
-        exec(compiled, globs)
-      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[14]>", line 1, in <module>
-        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
-        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
-        process = Popen(stdout=PIPE, *popenargs, **kwargs)
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
-        errread, errwrite)
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
-        raise child_exception
-    OSError: [Errno 2] No such file or directory
-**********************************************************************
-File "src/sage/coding/linear_code.py", line 3300, in sage.coding.linear_code.AbstractLinearCode.spectrum
-Failed example:
-    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
-Exception raised:
-    Traceback (most recent call last):
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
-        self.compile_and_execute(example, compiler, test.globs)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
-        exec(compiled, globs)
-      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[16]>", line 1, in <module>
-        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
-      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
-        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
-        process = Popen(stdout=PIPE, *popenargs, **kwargs)
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
-        errread, errwrite)
-      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
-        raise child_exception
-    OSError: [Errno 2] No such file or directory
-**********************************************************************
-1 item had failures:
-   4 of  18 in sage.coding.linear_code.AbstractLinearCode.spectrum
-    [634 tests, 4 failures, 26.04 s]
-----------------------------------------------------------------------
-sage -t --long src/sage/tests/gap_packages.py  # 5 doctests failed
-sage -t --long src/sage/coding/linear_code.py  # 4 doctests failed
-----------------------------------------------------------------------
-```
+- `coding/linear_code.py`: related to Guava (gap package) (see [failing_doctests-librae.log](https://github.com/sagemath/sage-prod/files/10658881/failing_doctests-librae.log))
+- `tests/gap_packages.py`: related to gap packages (see [failing_doctests-librae.log](https://github.com/sagemath/sage-prod/files/10658881/failing_doctests-librae.log))
jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,4 +1,193 @@
-Since #20182 there are some failing doctests related to optional packages
+With Sage 7.2.beta6:

-- `coding/linear_code.py`: related to Guava (gap package) (see [failing_doctests-librae.log](https://github.com/sagemath/sage-prod/files/10658881/failing_doctests-librae.log))
-- `tests/gap_packages.py`: related to gap packages (see [failing_doctests-librae.log](https://github.com/sagemath/sage-prod/files/10658881/failing_doctests-librae.log))
+```
+sage -t --long src/sage/tests/gap_packages.py
+**********************************************************************
+File "src/sage/tests/gap_packages.py", line 8, in sage.tests.gap_packages
+Failed example:
+    test_packages(pkgs, only_failures=True)    # optional - gap_packages
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.tests.gap_packages[2]>", line 1, in <module>
+        test_packages(pkgs, only_failures=True)    # optional - gap_packages
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 77, in test_packages
+        output = libgap.eval('LoadPackage("{0}")'.format(pkg))
+      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
+        return make_any_gap_element(self, gap_eval(gap_command))
+      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
+        raise ValueError('libGAP: '+str(msg).strip())
+    ValueError: libGAP: Error, <opr> is not an operation
+**********************************************************************
+File "src/sage/tests/gap_packages.py", line 47, in sage.tests.gap_packages.test_packages
+Failed example:
+    test_packages(['GAPDoc'])
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.tests.gap_packages.test_packages[1]>", line 1, in <module>
+        test_packages(['GAPDoc'])
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 77, in test_packages
+        output = libgap.eval('LoadPackage("{0}")'.format(pkg))
+      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
+        return make_any_gap_element(self, gap_eval(gap_command))
+      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
+        raise ValueError('libGAP: '+str(msg).strip())
+    ValueError: libGAP: 
+**********************************************************************
+File "src/sage/tests/gap_packages.py", line 54, in sage.tests.gap_packages.test_packages
+Failed example:
+    pkgs = all_installed_packages()
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.tests.gap_packages.test_packages[2]>", line 1, in <module>
+        pkgs = all_installed_packages()
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 109, in all_installed_packages
+        for path in libgap.eval('GAP_ROOT_PATHS').sage():
+      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
+        return make_any_gap_element(self, gap_eval(gap_command))
+      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
+        raise ValueError('libGAP: '+str(msg).strip())
+    ValueError: libGAP: 
+**********************************************************************
+File "src/sage/tests/gap_packages.py", line 55, in sage.tests.gap_packages.test_packages
+Failed example:
+    test_packages(pkgs)    # random output
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.tests.gap_packages.test_packages[3]>", line 1, in <module>
+        test_packages(pkgs)    # random output
+    NameError: name 'pkgs' is not defined
+**********************************************************************
+File "src/sage/tests/gap_packages.py", line 105, in sage.tests.gap_packages.all_installed_packages
+Failed example:
+    all_installed_packages()
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.tests.gap_packages.all_installed_packages[1]>", line 1, in <module>
+        all_installed_packages()
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/tests/gap_packages.py", line 109, in all_installed_packages
+        for path in libgap.eval('GAP_ROOT_PATHS').sage():
+      File "sage/libs/gap/libgap.pyx", line 431, in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4183)
+        return make_any_gap_element(self, gap_eval(gap_command))
+      File "sage/libs/gap/util.pyx", line 288, in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4947)
+        raise ValueError('libGAP: '+str(msg).strip())
+    ValueError: libGAP: 
+**********************************************************************
+3 items had failures:
+   1 of   4 in sage.tests.gap_packages
+   1 of   3 in sage.tests.gap_packages.all_installed_packages
+   3 of   5 in sage.tests.gap_packages.test_packages
+    [9 tests, 5 failures, 4.49 s]
+sage -t --long src/sage/coding/linear_code.py
+**********************************************************************
+File "src/sage/coding/linear_code.py", line 3284, in sage.coding.linear_code.AbstractLinearCode.spectrum
+Failed example:
+    C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[8]>", line 1, in <module>
+        C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
+        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
+        process = Popen(stdout=PIPE, *popenargs, **kwargs)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
+        errread, errwrite)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
+        raise child_exception
+    OSError: [Errno 2] No such file or directory
+**********************************************************************
+File "src/sage/coding/linear_code.py", line 3292, in sage.coding.linear_code.AbstractLinearCode.spectrum
+Failed example:
+    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[12]>", line 1, in <module>
+        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
+        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
+        process = Popen(stdout=PIPE, *popenargs, **kwargs)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
+        errread, errwrite)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
+        raise child_exception
+    OSError: [Errno 2] No such file or directory
+**********************************************************************
+File "src/sage/coding/linear_code.py", line 3296, in sage.coding.linear_code.AbstractLinearCode.spectrum
+Failed example:
+    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[14]>", line 1, in <module>
+        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
+        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
+        process = Popen(stdout=PIPE, *popenargs, **kwargs)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
+        errread, errwrite)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
+        raise child_exception
+    OSError: [Errno 2] No such file or directory
+**********************************************************************
+File "src/sage/coding/linear_code.py", line 3300, in sage.coding.linear_code.AbstractLinearCode.spectrum
+Failed example:
+    C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+Exception raised:
+    Traceback (most recent call last):
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 496, in _run
+        self.compile_and_execute(example, compiler, test.globs)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 858, in compile_and_execute
+        exec(compiled, globs)
+      File "<doctest sage.coding.linear_code.AbstractLinearCode.spectrum[16]>", line 1, in <module>
+        C.spectrum() == C.spectrum(algorithm="leon")   # optional - gap_packages (Guava package)
+      File "/usr/local/src/sage-git/local/lib/python2.7/site-packages/sage/coding/linear_code.py", line 3328, in spectrum
+        lines = subprocess.check_output([os.path.join(guava_bin_dir, 'wtdist'), input])
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 566, in check_output
+        process = Popen(stdout=PIPE, *popenargs, **kwargs)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 710, in __init__
+        errread, errwrite)
+      File "/usr/local/src/sage-git/local/lib/python/subprocess.py", line 1335, in _execute_child
+        raise child_exception
+    OSError: [Errno 2] No such file or directory
+**********************************************************************
+1 item had failures:
+   4 of  18 in sage.coding.linear_code.AbstractLinearCode.spectrum
+    [634 tests, 4 failures, 26.04 s]
+----------------------------------------------------------------------
+sage -t --long src/sage/tests/gap_packages.py  # 5 doctests failed
+sage -t --long src/sage/coding/linear_code.py  # 4 doctests failed
+----------------------------------------------------------------------
+```
jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -191,3 +191,29 @@
 sage -t --long src/sage/coding/linear_code.py  # 4 doctests failed
 ----------------------------------------------------------------------

+ +The failures in gap_packages.py are because of + +``` +sage: libgap.eval('LoadPackage("HAPcryst")') +--------------------------------------------------------------------------- +ValueError Traceback (most recent call last) + in () +----> 1 libgap.eval('LoadPackage("HAPcryst")') + +/usr/local/src/sage-git/src/sage/libs/gap/libgap.pyx in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4168)()

jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -217,3 +217,11 @@

 ValueError: libGAP: Error, <opr> is not an operation

+ +The failures in linear_code.pyx are because of + + +sage: print gap.eval('DirectoriesPackagePrograms("guava")[1]') +dir("/usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13/bin/x86_64-unknown-linux-gnu-gcc-default64/") + +but this directory does not exist!

jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,4 +1,40 @@
 With Sage 7.2.beta6:
+
+```
+sage: libgap.eval('LoadPackage("HAPcryst")')
+---------------------------------------------------------------------------
+ValueError                                Traceback (most recent call last)
+<ipython-input-1-90cb9d4fcac6> in <module>()
+----> 1 libgap.eval('LoadPackage("HAPcryst")')
+
+/usr/local/src/sage-git/src/sage/libs/gap/libgap.pyx in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4168)()
+    429         if not isinstance(gap_command, basestring):
+    430             gap_command = str(gap_command._gap_init_())
+--> 431         return make_any_gap_element(self, gap_eval(gap_command))
+    432 
+    433     @cached_method
+
+/usr/local/src/sage-git/src/sage/libs/gap/util.pyx in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4932)()
+    286             sig_off()
+    287         except RuntimeError as msg:
+--> 288             raise ValueError('libGAP: '+str(msg).strip())
+    289 
+    290         if libGAP_Symbol != libGAP_S_SEMICOLON:
+
+ValueError: libGAP: Error, <opr> is not an operation
+```
+
+A second issue is a mis-installation of guava:
+
+```
+sage: print gap.eval('DirectoriesPackagePrograms("guava")[1]')
+dir("/usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13/bin/x86_64-unknown-linux-gnu-gcc-default64/")
+```
+but this directory does not exist!
+
+---
+
+This causes doctest failures

sage -t --long src/sage/tests/gap_packages.py @@ -191,37 +227,3 @@ sage -t --long src/sage/coding/linear_code.py # 4 doctests failed

-
-The failures in `gap_packages.py` are because of
-
-```
-sage: libgap.eval('LoadPackage("HAPcryst")')
----------------------------------------------------------------------------
-ValueError                                Traceback (most recent call last)
-<ipython-input-1-90cb9d4fcac6> in <module>()
-----> 1 libgap.eval('LoadPackage("HAPcryst")')
-
-/usr/local/src/sage-git/src/sage/libs/gap/libgap.pyx in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4168)()
-    429         if not isinstance(gap_command, basestring):
-    430             gap_command = str(gap_command._gap_init_())
---> 431         return make_any_gap_element(self, gap_eval(gap_command))
-    432 
-    433     @cached_method
-
-/usr/local/src/sage-git/src/sage/libs/gap/util.pyx in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4932)()
-    286             sig_off()
-    287         except RuntimeError as msg:
---> 288             raise ValueError('libGAP: '+str(msg).strip())
-    289 
-    290         if libGAP_Symbol != libGAP_S_SEMICOLON:
-
-ValueError: libGAP: Error, <opr> is not an operation
-```
-
-The failures in `linear_code.pyx` are because of
-
-```
-sage: print gap.eval('DirectoriesPackagePrograms("guava")[1]')
-dir("/usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13/bin/x86_64-unknown-linux-gnu-gcc-default64/")
-```
-but this directory does not exist!
dimpase commented 8 years ago
comment:16

these tests work for me. Must be patchbot madness...

dimpase commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,40 +1,4 @@
 With Sage 7.2.beta6:
-
-```
-sage: libgap.eval('LoadPackage("HAPcryst")')
----------------------------------------------------------------------------
-ValueError                                Traceback (most recent call last)
-<ipython-input-1-90cb9d4fcac6> in <module>()
-----> 1 libgap.eval('LoadPackage("HAPcryst")')
-
-/usr/local/src/sage-git/src/sage/libs/gap/libgap.pyx in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4168)()
-    429         if not isinstance(gap_command, basestring):
-    430             gap_command = str(gap_command._gap_init_())
---> 431         return make_any_gap_element(self, gap_eval(gap_command))
-    432 
-    433     @cached_method
-
-/usr/local/src/sage-git/src/sage/libs/gap/util.pyx in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4932)()
-    286             sig_off()
-    287         except RuntimeError as msg:
---> 288             raise ValueError('libGAP: '+str(msg).strip())
-    289 
-    290         if libGAP_Symbol != libGAP_S_SEMICOLON:
-
-ValueError: libGAP: Error, <opr> is not an operation
-```
-
-A second issue is a mis-installation of guava:
-
-```
-sage: print gap.eval('DirectoriesPackagePrograms("guava")[1]')
-dir("/usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13/bin/x86_64-unknown-linux-gnu-gcc-default64/")
-```
-but this directory does not exist!
-
----
-
-This causes doctest failures

sage -t --long src/sage/tests/gap_packages.py

jdemeyer commented 8 years ago
comment:18

Replying to @dimpase:

these tests work for me.

Not for me.

Must be patchbot madness...

No, this is unrelated to the patchbot.

jdemeyer commented 8 years ago
comment:19

Please don't revert the changes I make to the ticket :-)

jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,4 +1,39 @@
 With Sage 7.2.beta6:
+
+```
+sage: libgap.eval('LoadPackage("HAPcryst")')
+---------------------------------------------------------------------------
+ValueError                                Traceback (most recent call last)
+<ipython-input-1-90cb9d4fcac6> in <module>()
+----> 1 libgap.eval('LoadPackage("HAPcryst")')
+
+/usr/local/src/sage-git/src/sage/libs/gap/libgap.pyx in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4168)()
+    429         if not isinstance(gap_command, basestring):
+    430             gap_command = str(gap_command._gap_init_())
+--> 431         return make_any_gap_element(self, gap_eval(gap_command))
+    432 
+    433     @cached_method
+
+/usr/local/src/sage-git/src/sage/libs/gap/util.pyx in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:4932)()
+    286             sig_off()
+    287         except RuntimeError as msg:
+--> 288             raise ValueError('libGAP: '+str(msg).strip())
+    289 
+    290         if libGAP_Symbol != libGAP_S_SEMICOLON:
+
+ValueError: libGAP: Error, <opr> is not an operation
+```
+
+A second issue is a mis-installation of guava:
+
+```
+sage: print gap.eval('DirectoriesPackagePrograms("guava")[1]')
+dir("/usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13/bin/x86_64-unknown-linux-gnu-gcc-default64/")
+```
+
+but this directory does not exist!
+
+---

sage -t --long src/sage/tests/gap_packages.py

jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,27 +1,42 @@
 With Sage 7.2.beta6:

-sage: libgap.eval('LoadPackage("HAPcryst")')

-ValueError Traceback (most recent call last) - in () -----> 1 libgap.eval('LoadPackage("HAPcryst")')

-/usr/local/src/sage-git/src/sage/libs/gap/libgap.pyx in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4168)()

jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -42,7 +42,7 @@
 A second issue is a mis-installation of guava:

-sage: print gap.eval('DirectoriesPackagePrograms("guava")[1]') +gap> DirectoriesPackagePrograms("guava")[1]; dir("/usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13/bin/x86_64-unknown-linux-gnu-gcc-default64/")

jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -46,7 +46,29 @@
 dir("/usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13/bin/x86_64-unknown-linux-gnu-gcc-default64/")

-but this directory does not exist! +but this directory does not exist: + + +$ ls -l /usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13 +total 168 +-rw-r--r-- 1 jdemeyer jdemeyer 11775 Mar 19 23:17 CHANGES.guava +-rwxr-xr-x 1 jdemeyer jdemeyer 1918 Mar 19 23:17 configure +-rw-r--r-- 1 jdemeyer jdemeyer 51189 Mar 19 23:17 COPYING.guava +drwxr-xr-x 2 jdemeyer jdemeyer 4096 Mar 30 00:32 doc +-rw-r--r-- 1 jdemeyer jdemeyer 368 Mar 19 23:17 gapdoc.g +-rw-r--r-- 1 jdemeyer jdemeyer 2059 Mar 19 23:17 HISTORY.guava +-rw-r--r-- 1 jdemeyer jdemeyer 1364 Mar 19 23:17 init.g +drwxr-xr-x 2 jdemeyer jdemeyer 4096 Mar 30 00:32 lib +-rw-r--r-- 1 jdemeyer jdemeyer 35120 Mar 19 23:17 LICENSE +-rw-r--r-- 1 jdemeyer jdemeyer 2858 Mar 19 23:17 Makefile.in +-rw-r--r-- 1 jdemeyer jdemeyer 11638 Mar 19 23:17 PackageInfo.g +-rw-r--r-- 1 jdemeyer jdemeyer 1420 Mar 19 23:17 read.g +-rw-r--r-- 1 jdemeyer jdemeyer 4882 Mar 19 23:17 README.guava +-rw-r--r-- 1 jdemeyer jdemeyer 98 Mar 19 23:17 README.md +drwxr-xr-x 4 jdemeyer jdemeyer 4096 Mar 30 00:32 src +drwxr-xr-x 2 jdemeyer jdemeyer 4096 Mar 30 00:32 tbl +drwxr-xr-x 2 jdemeyer jdemeyer 4096 Mar 30 00:32 tst +

jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -46,7 +46,7 @@
 dir("/usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13/bin/x86_64-unknown-linux-gnu-gcc-default64/")

-but this directory does not exist: +but this directory does not exist, bin is missing below:

 $ ls -l /usr/local/src/sage-git/local/gap/latest/pkg/guava-3.13
jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -72,6 +72,8 @@

 ---

+This causes doctest failures:
+

sage -t --long src/sage/tests/gap_packages.py

jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,7 +1,6 @@
-With Sage 7.2.beta6:
-
-```
-$ ./sage --gap
+With Sage 7.2.beta6, within a `sage --gap` session:
+
+```
 gap> LoadPackage("HAPcryst");
 #I  polymake command not found. Please set POLYMAKE_COMMAND by hand
 ----------------------------------------------------------------
jdemeyer commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,4 +1,4 @@
-With Sage 7.2.beta6, within a `sage --gap` session:
+With Sage 7.2.beta6 with `gap_packages` installed, within a `sage --gap` session:

gap> LoadPackage("HAPcryst");

dimpase commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,4 +1,4 @@
-With Sage 7.2.beta6 with `gap_packages` installed, within a `sage --gap` session:
+With Sage 7.2.beta6, within a `sage --gap` session:

gap> LoadPackage("HAPcryst");

dimpase commented 8 years ago
comment:27

ok: ./spkg-install: line 72: cd: /home/scratch/dimpase/sage/sage/local/gap/latest/pkg/guava-3*: No such file or directory

but why?! This is expansion of cd "$PKG_DIR/guava-3*". And it seems to work:

$ cd /home/scratch/dimpase/sage/sage/local/gap/latest/pkg/guava-3*
clpc171[/home/scratch/dimpase/sage/sage/local/gap/latest/pkg/guava-3.13]$
dimpase commented 8 years ago

Commit: 8860e47

dimpase commented 8 years ago

Branch: public/20525

dimpase commented 8 years ago
comment:28

guava issue fix - see the commit

New commits:

8860e47guaba path fix
dimpase commented 8 years ago
comment:29

I cannot reproduce the HAPcryst thing though. I get 

$ sage -t --long src/sage/tests/gap_packages.py
Running doctests with ID 2016-05-02-16-39-21-92780109.
Git branch: gappacs
Using --optional=cbc,csdp,database_gap,gap_packages,mpir,python2,sage
Doctesting 1 file.
sage -t --long --warn-long 56.7 src/sage/tests/gap_packages.py
    [10 tests, 3.75 s]
----------------------------------------------------------------------
All tests passed!

As I get 10 tests run as opposed to 9 above, I probably have more packages installed...

and 

$ sage --gap
 ┌───────┐   GAP 4.8.3, 19-Mar-2016, build of 2016-04-06 10:34:11 (BST)
 │  GAP  │   http://www.gap-system.org
 └───────┘   Architecture: x86_64-unknown-linux-gnu-gcc-default64
 Libs used:  gmp, readline
 Loading the library and packages ...
 Components: trans 1.0, prim 2.1, small* 1.0, id* 1.0
 Packages:   Alnuth 3.0.0, AtlasRep 1.5.0, AutPGrp 1.6, CTblLib 1.2.2, FactInt 1.5.3, GAPDoc 1.5.1, LAGUNA 3.7.0, 
             Polycyclic 2.11, TomLib 1.2.5
 Try '?help' for help. See also  '?copyright' and  '?authors'
gap> LoadPackage("HAPcryst");
#I  polymake command not found. Please set POLYMAKE_COMMAND by hand
----------------------------------------------------------------
Loading  polymaking 0.8.1
(A package for using polymake in GAP)
by Marc Roeder
----------------------------------------------------------------
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Loading  Cryst 4.1.12 (Computing with crystallographic groups)
by Bettina Eick (http://www.icm.tu-bs.de/~beick/),
   Franz Gähler (http://www.math.uni-bielefeld.de/~gaehler/), and
   Werner Nickel (http://www.mathematik.tu-darmstadt.de/~nickel/).
Homepage: http://www.math.uni-bielefeld.de/~gaehler/gap45/packages.php
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Loading  CrystCat 1.1.6 (The crystallographic groups catalog)
by Volkmar Felsch (http://www.math.rwth-aachen.de/~Volkmar.Felsch/) and
   Franz Gähler (http://www.math.uni-bielefeld.de/~gaehler/).
Homepage: http://www.math.uni-bielefeld.de/~gaehler/gap45/packages.php
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Loading  AClib 1.2 (Almost Crystallographic Groups - A Library and Algorithms)
by Karel Dekimpe (http://www.kulak.ac.be/~dekimpe) and
   Bettina Eick (http://www.icm.tu-bs.de/~beick).
Homepage: http://www.icm.tu-bs.de/~beick/so.html
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#I  HAP warning: Set POLYMAKE_PATH manually if needed. 
#I  MakeReadOnlyGlobal: GradedAlgebraPresentationType no value bound
Loading HAP 1.11.13 ...
----------------------------------------------------------------
This is HAPcryst version 0.1.11
by Marc Roeder
----------------------------------------------------------------
true
gap>

looks OK to me.

videlec commented 8 years ago
comment:30

I guess you have polymake working on your computer?

jdemeyer commented 8 years ago
comment:31

You need to bump the patchlevel of the gap_packages package to ensure the change has effect.

jdemeyer commented 8 years ago
comment:32

Also, you better check the result of that cd operation, for example

cd "$PKG_DIR"/guava-3* && ./configure "$GAP_DIR"
jdemeyer commented 8 years ago
comment:33

...or use set -e.

dimpase commented 8 years ago
comment:34

Replying to @videlec:

I guess you have polymake working on your computer?

no, I don't have polymake at all.

dimpase commented 8 years ago
comment:35

Replying to @jdemeyer:

You need to bump the patchlevel of the gap_packages package to ensure the change has effect.

why? the tarball is the same, no removed/added/changed patches. Since when a change to spkg-install does need a version change?!

(this is an optional package, so it won't magically rebuild by bumping anything, no?)

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 8 years ago

Branch pushed to git repo; I updated commit sha1. New commits:

ca9607dcheck 'cd.. *' success
7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 8 years ago

Changed commit from 8860e47 to ca9607d

jdemeyer commented 8 years ago
comment:37

Replying to @dimpase:

Since when a change to spkg-install does need a version change?!

Since you need to fix broken installations of gap_packages. People who install gap_packages today have a broken version of it. Just changing spkg-install doesn't fix that: you need to actually reinstall gap_packages.

dimpase commented 8 years ago
comment:38

Replying to @jdemeyer:

Replying to @dimpase:

Since when a change to spkg-install does need a version change?!

Since you need to fix broken installations of gap_packages. People who install gap_packages today have a broken version of it. Just changing spkg-install doesn't fix that: you need to actually reinstall gap_packages.

yes, but it won't happen without human interaction, would it?

jdemeyer commented 8 years ago
comment:39

Replying to @dimpase:

yes, but it won't happen without human interaction, would it?

Installed optional packages are upgraded just like standard packages are. So, running make should be sufficient to rebuild gap_packages if it was built before.

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 8 years ago

Changed commit from ca9607d to 44d9d61

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 8 years ago

Branch pushed to git repo; I updated commit sha1. New commits:

44d9d61bump up the version
dimpase commented 8 years ago

Author: Dima Pasechnik

dimpase commented 8 years ago
comment:41

OK, done.