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chemicalkinetics.jl's Issues

[PkgEval] ChemicalKinetics may have a testing issue on Julia 0.4 (2014-08-15)

PackageEvaluator.jl is a script that runs nightly. It attempts to load all Julia packages and run their tests (if available) on both the stable version of Julia (0.3) and the nightly build of the unstable version (0.4). The results of this script are used to generate a package listing enhanced with testing results.

On Julia 0.4

  • On 2014-08-14 the testing status was Tests pass.
  • On 2014-08-15 the testing status changed to Tests fail, but package loads.

Tests pass. means that PackageEvaluator found the tests for your package, executed them, and they all passed.

Tests fail, but package loads. means that PackageEvaluator found the tests for your package, executed them, and they didn't pass. However, trying to load your package with using worked.

This issue was filed because your testing status became worse. No additional issues will be filed if your package remains in this state, and no issue will be filed if it improves. If you'd like to opt-out of these status-change messages, reply to this message saying you'd like to and @IainNZ will add an exception. If you'd like to discuss PackageEvaluator.jl please file an issue at the repository. For example, your package may be untestable on the test machine due to a dependency - an exception can be added.

Test log:

>>> 'Pkg.add("ChemicalKinetics")' log
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 8102k    0 13329    0     0  75396      0  0:01:50 --:--:--  0:01:50 75305
  3 8102k    3  312k    0     0   255k      0  0:00:31  0:00:01  0:00:30  255k
 26 8102k   26 2151k    0     0  1002k      0  0:00:08  0:00:02  0:00:06 1002k
100 8102k  100 8102k    0     0  2712k      0  0:00:02  0:00:02 --:--:-- 2711k

---------------------------------
Running SUNDIALS Configure Script
---------------------------------

Initialization
--------------

checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... /usr/bin/install -c

C Compiler Settings
-------------------

checking for cc... cc
... truncated ...
/usr/bin/install -c -m 644 ./../../include/kinsol/kinsol_direct.h  /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/usr/include/kinsol/
/usr/bin/install -c -m 644 ./../../include/kinsol/kinsol_dense.h   /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/usr/include/kinsol/
/usr/bin/install -c -m 644 ./../../include/kinsol/kinsol_band.h    /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/usr/include/kinsol/
/usr/bin/install -c -m 644 ./../../include/kinsol/kinsol_spgmr.h   /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/usr/include/kinsol/
/usr/bin/install -c -m 644 ./../../include/kinsol/kinsol_spbcgs.h  /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/usr/include/kinsol/
/usr/bin/install -c -m 644 ./../../include/kinsol/kinsol_sptfqmr.h /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/usr/include/kinsol/
/usr/bin/install -c -m 644 ./../../include/kinsol/kinsol_bbdpre.h  /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/usr/include/kinsol/
/usr/bin/install -c -m 644 ./../../include/kinsol/kinsol_spils.h   /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/usr/include/kinsol/
/usr/bin/install -c -m 644 ./../../src/kinsol/kinsol_impl.h        /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/usr/include/kinsol/
make[1]: Leaving directory '/home/idunning/pkgtest/.julia/v0.4/Sundials/deps/src/sundials-2.5.0/src/kinsol'

INFO: Installing ArrayViews v0.4.6
INFO: Installing BinDeps v0.2.14
INFO: Installing ChemicalKinetics v0.1.0
INFO: Installing Distributions v0.5.4
INFO: Installing PDMats v0.2.3
INFO: Installing StatsBase v0.6.3
INFO: Installing Sundials v0.1.0
INFO: Installing URIParser v0.0.2
INFO: Building Sundials
INFO: Attempting to Create directory /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/downloads
INFO: Downloading file http://computation.llnl.gov/casc/sundials/download/code/sundials-2.5.0.tar.gz
INFO: Done downloading file http://computation.llnl.gov/casc/sundials/download/code/sundials-2.5.0.tar.gz
INFO: Attempting to Create directory /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/src
INFO: Attempting to Create directory /home/idunning/pkgtest/.julia/v0.4/Sundials/deps
INFO: Directory /home/idunning/pkgtest/.julia/v0.4/Sundials/deps already created
INFO: Attempting to Create directory /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/src/sundials-2.5.0
INFO: Changing Directory to /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/src/sundials-2.5.0
INFO: Changing Directory to /home/idunning/pkgtest/.julia/v0.4/Sundials/deps/src/sundials-2.5.0
INFO: Package database updated

>>> 'using ChemicalKinetics' log

>>> test log
Running tests:
  * test/simulateFitzhughNagumoODEs.jl *
    Testing simulation from Fitzhugh Nagumo ODEs...

ERROR: type Cholesky has no field uplo
 in _rand! at /home/idunning/pkgtest/.julia/v0.4/Distributions/src/multivariate/mvnormal.jl:131
 in simulate_ck_cvode_data at /home/idunning/pkgtest/.julia/v0.4/ChemicalKinetics/src/ode_solver.jl:98
 in anonymous at no file:23
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in anonymous at no file:8
 in include at ./boot.jl:245
 in include_from_node1 at loading.jl:128
 in process_options at ./client.jl:285
 in _start at ./client.jl:354
 in _start_3B_1724 at /home/idunning/julia04/usr/bin/../lib/julia/sys.so
while loading /home/idunning/pkgtest/.julia/v0.4/ChemicalKinetics/test/simulateFitzhughNagumoODEs.jl, in expression starting on line 15
while loading /home/idunning/pkgtest/.julia/v0.4/ChemicalKinetics/run_tests.jl, in expression starting on line 5

>>> end of log

Create a master test file

We're trying to make a master package listing that has more information about package quality and status at http://status.julialang.org/

Part of this is running the tests in your package. To do so, we look for a "master" test file that will run all the tests in your package. Many people choose to go with test/runtests.jl but we support quite a few "guesses": https://github.com/IainNZ/PackageEvaluator.jl/blob/master/src/package.jl#L144

It'd be great if you could add one, and update your package version in METADATA.

[PkgEval] Your package doesn't have a test/runtests.jl file

PackageEvaluator.jl is a script that runs nightly.
It attempts to load all Julia packages and run their tests (if available) on both the stable
version of Julia (0.3) and the nightly build of the unstable version (0.4).
The results of this script are used to generate a package listing
enhanced with testing results. This service also benefits package developers by notifying them if
their package breaks for some reason (caused by e.g. changes in Julia, changes in dependencies,
or broken binary dependencies.)

Currently PackageEvaluator attempts to find your test scripts using a heuristic, preferring the
standarized test/runtests.jl whenever present. Using test/runtests.jl allows people to test
your package using simply Pkg.test("ChemicalKinetics"), with any testing-only dependencies being
installed by looking at test/REQUIRE.

Your package doesn't appear to have a test/runtests.jl file. PackageEvaluator is going to move
away from auto-detecting tests and will instead only test packages with a test/runtests.jl
file. This change will take place in about a month.

You can:

  • Add the file and tag a new version. You may in fact have already added this file but not
    tagged a new version. PackageEvaluator only tests your latest tagged verison, so you must tag
    for the file to be detected.
  • Chose to do nothing. PackageEvaluator will stop attempting to test your package, and the testing
    status will be reported as "not possible".

If you'd like help or more information, please just reply to this issue.

Info about upcoming removal of packages in the General registry

As described in https://discourse.julialang.org/t/ann-plans-for-removing-packages-that-do-not-yet-support-1-0-from-the-general-registry/ we are planning on removing packages that do not support 1.0 from the General registry. This package has been detected to not support 1.0 and is thus slated to be removed. The removal of packages from the registry will happen approximately a month after this issue is open.

To transition to the new Pkg system using Project.toml, see https://github.com/JuliaRegistries/Registrator.jl#transitioning-from-require-to-projecttoml.
To then tag a new version of the package, see https://github.com/JuliaRegistries/Registrator.jl#via-the-github-app.

If you believe this package has erroneously been detected as not supporting 1.0 or have any other questions, don't hesitate to discuss it here or in the thread linked at the top of this post.

[PackageEvaluator.jl] Your package ChemicalKinetics may have a testing issue.

This issue is being filed by a script, but if you reply, I will see it.

PackageEvaluator.jl is a script that runs nightly. It attempts to load all Julia packages and run their test (if available) on both the stable version of Julia (0.2) and the nightly build of the unstable version (0.3).

The results of this script are used to generate a package listing enhanced with testing results.

The status of this package, ChemicalKinetics, on...

  • Julia 0.2 is 'Tests fail, but package loads.' PackageEvaluator.jl
  • Julia 0.3 is 'Tests fail, but package loads.' PackageEvaluator.jl

'No tests, but package loads.' can be due to their being no tests (you should write some if you can!) but can also be due to PackageEvaluator not being able to find your tests. Consider adding a test/runtests.jl file.

'Package doesn't load.' is the worst-case scenario. Sometimes this arises because your package doesn't have BinDeps support, or needs something that can't be installed with BinDeps. If this is the case for your package, please file an issue and an exception can be made so your package will not be tested.

This automatically filed issue is a one-off message. Starting soon, issues will only be filed when the testing status of your package changes in a negative direction (gets worse). If you'd like to opt-out of these status-change messages, reply to this message.

[PkgEval] ChemicalKinetics may have a testing issue on Julia 0.3 (2014-07-15)

PackageEvaluator.jl is a script that runs nightly. It attempts to load all Julia packages and run their tests (if available) on both the stable version of Julia (0.2) and the nightly build of the unstable version (0.3). The results of this script are used to generate a package listing enhanced with testing results.

On Julia 0.3

  • On 2014-07-14 the testing status was Tests pass.
  • On 2014-07-15 the testing status changed to Package doesn't load.

Tests pass. means that PackageEvaluator found the tests for your package, executed them, and they all passed.

Package doesn't load. means that PackageEvaluator did not find tests for your package. Additionally, trying to load your package with using failed.

This issue was filed because your testing status became worse. No additional issues will be filed if your package remains in this state, and no issue will be filed if it improves. If you'd like to opt-out of these status-change messages, reply to this message saying you'd like to and @IainNZ will add an exception. If you'd like to discuss PackageEvaluator.jl please file an issue at the repository. For example, your package may be untestable on the test machine due to a dependency - an exception can be added.

Test log:

INFO: Installing ArrayViews v0.4.6
INFO: Installing BinDeps v0.2.14
INFO: Installing ChemicalKinetics v0.1.0
INFO: Installing Distributions v0.5.2
INFO: Installing PDMats v0.2.1
INFO: Installing StatsBase v0.5.3
INFO: Installing Sundials v0.1.0
INFO: Installing URIParser v0.0.2
INFO: Building Sundials
INFO: Attempting to Create directory /home/idunning/pkgtest/.julia/v0.3/Sundials/deps/downloads
INFO: Downloading file http://computation.llnl.gov/casc/sundials/download/code/sundials-2.5.0.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 8102k    1  109k    0     0   153k      0  0:00:52 --:--:--  0:00:52  153k
  7 8102k    7  642k    0     0   375k      0  0:00:21  0:00:01  0:00:20  375k
 97 8102k   97 7913k    0     0  2927k      0  0:00:02  0:00:02 --:--:-- 2926k
100 8102k  100 8102k    0     0  2978k      0  0:00:02  0:00:02 --:--:-- 2977k
INFO: Done downloading file http://computation.llnl.gov/casc/sundials/download/code/sundials-2.5.0.tar.gz
INFO: Attempting to Create directory /home/idunning/pkgtest/.julia/v0.3/Sundials/deps/src
INFO: Attempting to Create directory /home/idunning/pkgtest/.julia/v0.3/Sundials/deps
INFO: Directory /home/idunning/pkgtest/.julia/v0.3/Sundials/deps already created
INFO: Attempting to Create directory /home/idunning/pkgtest/.julia/v0.3/Sundials/deps/src/sundials-2.5.0
INFO: Changing Directory to /home/idunning/pkgtest/.julia/v0.3/Sundials/deps/src/sundials-2.5.0
..truncated..
/usr/bin/install -c -m 644 ./../../include/kinsol/kinsol_spils.h   /home/idunning/pkgtest/.julia/v0.3/Sundials/deps/usr/include/kinsol/
/usr/bin/install -c -m 644 ./../../src/kinsol/kinsol_impl.h        /home/idunning/pkgtest/.julia/v0.3/Sundials/deps/usr/include/kinsol/
make[1]: Leaving directory '/home/idunning/pkgtest/.julia/v0.3/Sundials/deps/src/sundials-2.5.0/src/kinsol'

INFO: Package database updated
ERROR: NumericExtensions not found
 in require at loading.jl:47
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in reload_path at loading.jl:152
 in _require at loading.jl:67
 in require at loading.jl:54
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in reload_path at loading.jl:152
 in _require at loading.jl:67
 in require at loading.jl:54
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in reload_path at loading.jl:152
 in _require at loading.jl:67
 in require at loading.jl:51
 in include at ./boot.jl:245
 in include_from_node1 at loading.jl:128
 in process_options at ./client.jl:285
 in _start at ./client.jl:354
while loading /home/idunning/pkgtest/.julia/v0.3/PDMats/src/PDMats.jl, in expression starting on line 9
while loading /home/idunning/pkgtest/.julia/v0.3/Distributions/src/Distributions.jl, in expression starting on line 4
while loading /home/idunning/pkgtest/.julia/v0.3/ChemicalKinetics/src/ChemicalKinetics.jl, in expression starting on line 2
while loading /home/idunning/pkgtest/.julia/v0.3/ChemicalKinetics/testusing.jl, in expression starting on line 1
INFO: Package database updated

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