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Consistency with Rpy 1 and NumPy packages and tools, e.g. linear_regression

Aperta
  • Qualcosa non va?
#415 4 commenti 0 reazioni 0 assegnatari Vedi su GitHub

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Valutazione

Difficoltà
4/5
Tempo stimato
3-5 giorni
Idoneità per principianti
35/100
Tipo di issue
Bug
Chiarezza
Abbastanza chiara
Stato di attività
Ferma
Stack tecnologico
numpy, python, r
Ambito
build-system, tooling

Direzione di ricerca

Confronta packages/package_rpy_1_0_3/tool_dependencies.xml con la versione GitHub collegata, quindi esamina tools/linear_regression e le relative dipendenze R, rpy e NumPy. Riproduci la discrepanza della versione dell’API segnalata e traccia quali versioni delle dipendenze sono installate. Il lavoro è completato quando la catena di dipendenze rpy e gli strumenti interessati utilizzano versioni compatibili di NumPy senza requisiti duplicati e in conflitto.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

bug

These tools and dependency chains are broken. But will work if you have numpy 1.7 available locally. Detailed analysis follows.

Rpy requires NumPy, but the current version of rpy 1.0.3 in the toolshed (https://toolshed.g2.bx.psu.edu/repos/devteam/package_rpy_1_0_3/file/82170c94ca7c/tool_dependencies.xml https://toolshed.g2.bx.psu.edu/view/devteam/package_rpy_1_0_3/82170c94ca7c) does not have a repository dependency defined.

However, the current version in github, https://github.com/galaxyproject/tools-devteam/blob/fbc219afb27b57b7a7aabbf2936439273753664e/packages/package_rpy_1_0_3/tool_dependencies.xml, has a dependency on numpy 1.9, added in fbc219afb27b57b7a7aabbf2936439273753664e.

But I don't think we can or should 'just update' this package in the toolshed, due to inconsistencies when digging into tools.

The linear_regression tool (https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://toolshed.g2.bx.psu.edu/view/devteam/linear_regression/cf431604ec3e) has dependencies on rpy 1.0.3, R 2.11.0, and numpy 1.7.

This causes an error with linear_regression (and possibly other tools), when Rpy is built against NumPy 1.9, but given NumPy 1.7:

RuntimeError: module compiled against API version 9 but this version of numpy is 7

I was able to hack the Rpy 1.0.3 package locally to get these tools to work, with this:

shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/package_rpy_1_0_3/82170c94ca7c/package_rpy_1_0_3$ hg diff
diff -r 82170c94ca7c tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 01 10:47:51 2014 -0400
+++ b/tool_dependencies.xml	Tue Nov 22 10:35:19 2016 -0500
@@ -3,6 +3,9 @@
   <package name="R" version="2.11.0">
       <repository changeset_revision="6e1b17857732" name="package_r_2_11_0" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
+  <package name="numpy" version="1.7.1">
+      <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
     <package name="rpy" version="1.0.3">
       <install version="1.0">
           <actions>
@@ -15,6 +18,9 @@
                   <repository changeset_revision="6e1b17857732" name="package_r_2_11_0" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
                       <package name="R" version="2.11.0" />
                     </repository>
+                  <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
+                      <package name="numpy" version="1.7.1" />
+                    </repository>
                 </action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">

and then uninstalling/reinstalling rpy 1.0.3.

This was the path of least resistance given the current state of the packages in the toolshed (rpy not requiring numpy).

However, the correct fix is most likely to have rpy require numpy (like in current github-only copy, numpy version is up for debate), and simultaneously update any tools using rpy to not manually require their own version of numpy, thereby getting the version inherited through the rpy dependency chain.

Lingua principale
Python
Stelle
37
Fork
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