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mvdbeek / usegalaxy-tests

Run tests against usegalaxy.org
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test pca1 1.0.2 #35

Closed jennaj closed 1 year ago

jennaj commented 2 years ago

Have a reported error that could be a dependency problem (hit before the tool could fail for input problems).

stderr
Traceback (most recent call last):
  File "/cvmfs/[main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py](http://main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py)", line 4, in <module>
    from rpy import *
  File "/cvmfs/[main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py](http://main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py)", line 134, in <module>
    """ % RVERSION)
RuntimeError: libR.so: cannot open shared object file: No such file or directory

      RPy module can not be imported. Please check if your rpy
      installation supports R 2.11.0. If you have multiple R versions
      installed, you may need to set RHOME before importing rpy. For
      example:

      >>> from rpy_options import set_options
      >>> set_options(RHOME='c:/progra~1/r/rw2011/')
      >>> from rpy import *

toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2

jennaj commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2

mvdbeek commented 2 years ago

Results (powered by Planemo)

Summary

State Count
Total 3
Passed 0
Error 0
Failure 3
Skipped 0
Failed s *
❌ toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1 (Test #1)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2, exit_code: 1, stderr: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2, exit_code: 1, stderr: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2, exit_code: 1, stderr: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | var\_cols | ` ["1", "2", "3", "4"] ` | | methodChoice | ` {"__current_case__": 0, "method": "cor"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "tabular" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1 (Test #2)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2, exit_code: 1, stderr: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2, exit_code: 1, stderr: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2, exit_code: 1, stderr: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | var\_cols | ` ["1", "2", "3", "4"] ` | | methodChoice | ` {"__current_case__": 1, "method": "cov"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "tabular" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1 (Test #3)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2, exit_code: 1, stderr: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2, exit_code: 1, stderr: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2, exit_code: 1, stderr: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.py", line 4, in from rpy import * File "/cvmfs/main.galaxyproject.org/deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in """ % RVERSION) RuntimeError: libR.so: cannot open shared object file: No such file or directory RPy module can not be imported. Please check if your rpy installation supports R 2.11.0. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | var\_cols | ` ["1", "2", "3", "4"] ` | | methodChoice | ` {"__current_case__": 2, "method": "svd", "scale": "both"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "tabular" ` |

jennaj commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2

mvdbeek commented 2 years ago

Results (powered by Planemo)

Summary

State Count
Total 3
Passed 0
Error 0
Failure 3
Skipped 0
Failed s *
❌ toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1 (Test #1)
**Problems**: * ``` Output out_file2: different than expected, difference (using diff): ( /tmp/tmpafxeihmwpca_out2.pdf v. /tmp/tmp0lre1f0gpca_out2.pdf ) --- local_file +++ history_data @@ -2,8 +2,8 @@ %���ρ�\r 1 0 obj << -/CreationDate (D:20110308103314) -/ModDate (D:20110308103314) +/CreationDate (D:20220504152202) +/ModDate (D:20220504152202) /Title (R Graphics Output) /Producer (R 2.11.0) /Creator (R) @@ -663,7 +663,7 @@ << /ProcSet [/PDF /Text] /Font <> -/ExtGState << >> +/ExtGState << /GSais 10 0 R >> >> endobj 8 0 obj @@ -682,8 +682,14 @@ /BaseFont /Helvetica /Encoding 8 0 R >> endobj +10 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 10 +0 11 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n @@ -692,14 +698,15 @@ 0000000213 00000 n ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | var\_cols | ` ["1", "2", "3", "4"] ` | | methodChoice | ` {"__current_case__": 0, "method": "cor"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "tabular" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1 (Test #2)
    **Problems**: * ``` Output out_file1: different than expected, difference (using diff): ( /tmp/tmpux4514a9pca_out3.tabular v. /tmp/tmp8zo08vgepca_out3.tabular ) --- local_file +++ history_data @@ -2,158 +2,158 @@ #Std. deviation 2.049 0.4905 0.2793 0.1534 #Proportion of variance explained 0.9246 0.05302 0.01719 0.005183 #Loadings 1 2 3 4 -c1 0.3616 -0.6565 0.581 0.3173 -c2 -0.08227 -0.7297 -0.5964 -0.3241 -c3 0.8566 0.1758 -0.07252 -0.4797 -c4 0.3588 0.07471 -0.5491 0.7511 +c1 0.3616 -0.6565 -0.581 0.3173 +c2 -0.08227 -0.7297 0.5964 -0.3241 +c3 0.8566 0.1758 0.07252 -0.4797 +c4 0.3588 0.07471 0.5491 0.7511 #Scores 1 2 3 4 -1 -2.684 -0.3266 0.02151 0.001006 -2 -2.715 0.1696 0.2035 0.0996 -3 -2.89 0.1373 -0.02471 0.0193 -4 -2.746 0.3111 -0.03767 -0.07596 -5 -2.729 -0.3339 -0.09623 -0.06313 -6 -2.28 -0.7478 -0.1743 -0.02715 -7 -2.821 0.0821 -0.2643 -0.0501 -8 -2.626 -0.1704 0.0158 -0.04628 -9 -2.888 0.5708 -0.02734 -0.02662 -10 -2.674 0.1067 0.1915 -0.05589 ******** *SNIP * ******** +126 2.614 -0.5584 -0.2084 -0.2404 +127 1.258 0.1791 0.04698 0.1476 +128 1.291 0.1164 0.2316 0.003084 +129 2.123 0.2109 0.1535 0.05261 +130 2.388 -0.4625 -0.452 -0.2299 +131 2.841 -0.3727 -0.501 -0.02022 +132 3.232 -1.371 -0.1184 -0.2545 +133 2.159 0.2183 0.2084 0.1277 +134 1.443 0.1438 -0.1541 -0.1899 +135 1.78 0.5015 -0.1758 -0.5035 +136 3.077 -0.6858 -0.3364 0.3106 +137 2.145 -0.1389 0.7342 0.05177 +138 1.905 -0.04805 0.1605 -0.222 +139 1.169 0.1645 0.2825 0.01933 +140 2.108 -0.3715 0.02744 0.21 +141 2.314 -0.1826 0.3229 0.2759 +142 1.922 -0.4093 0.1155 0.5041 +143 1.414 0.5749 0.2964 -0.0157 +144 2.563 -0.276 0.2913 0.05618 +145 2.419 -0.3035 0.5043 0.2382 +146 1.944 -0.1874 0.1793 0.4251 +147 1.526 0.375 -0.1206 0.2557 +148 1.764 -0.07852 0.1308 0.1363 +149 1.902 -0.1159 0.7229 0.04087 +150 1.39 0.2829 0.3623 -0.1563 ``` * ``` Output out_file2: different than expected, difference (using diff): ( /tmp/tmpx52cg61qpca_out4.pdf v. /tmp/tmpbogs4rk4pca_out4.pdf ) --- local_file +++ history_data @@ -2,8 +2,8 @@ %���ρ�\r 1 0 obj << -/CreationDate (D:20110308103327) -/ModDate (D:20110308103327) +/CreationDate (D:20220504152201) +/ModDate (D:20220504152201) /Title (R Graphics Output) /Producer (R 2.11.0) /Creator (R) @@ -663,7 +663,7 @@ << /ProcSet [/PDF /Text] /Font <> -/ExtGState << >> +/ExtGState << /GSais 10 0 R >> >> endobj 8 0 obj @@ -682,8 +682,14 @@ /BaseFont /Helvetica /Encoding 8 0 R >> endobj +10 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 10 +0 11 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n @@ -692,14 +698,15 @@ 0000000213 00000 n ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | var\_cols | ` ["1", "2", "3", "4"] ` | | methodChoice | ` {"__current_case__": 1, "method": "cov"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "auto" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1 (Test #3)
    **Problems**: * ``` Output out_file2: different than expected, difference (using diff): ( /tmp/tmpex6zbvq2pca_out6.pdf v. /tmp/tmpikyy4n7bpca_out6.pdf ) --- local_file +++ history_data @@ -2,8 +2,8 @@ %���ρ�\r 1 0 obj << -/CreationDate (D:20110308103341) -/ModDate (D:20110308103341) +/CreationDate (D:20220504152205) +/ModDate (D:20220504152205) /Title (R Graphics Output) /Producer (R 2.11.0) /Creator (R) @@ -663,7 +663,7 @@ << /ProcSet [/PDF /Text] /Font <> -/ExtGState << >> +/ExtGState << /GSais 10 0 R >> >> endobj 8 0 obj @@ -682,8 +682,14 @@ /BaseFont /Helvetica /Encoding 8 0 R >> endobj +10 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 10 +0 11 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n @@ -692,14 +698,15 @@ 0000000213 00000 n ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | var\_cols | ` ["1", "2", "3", "4"] ` | | methodChoice | ` {"__current_case__": 2, "method": "svd", "scale": "both"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "tabular" ` |

jennaj commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2

mvdbeek commented 2 years ago

Results (powered by Planemo)

Summary

State Count
Total 3
Passed 0
Error 0
Failure 3
Skipped 0
Failed s *
❌ toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1 (Test #1)
**Problems**: * ``` Output out_file2: different than expected, difference (using diff): ( /tmp/tmpr567c_gspca_out2.pdf v. /tmp/tmp7har0nmdpca_out2.pdf ) --- local_file +++ history_data @@ -2,8 +2,8 @@ %���ρ�\r 1 0 obj << -/CreationDate (D:20110308103314) -/ModDate (D:20110308103314) +/CreationDate (D:20220624182327) +/ModDate (D:20220624182327) /Title (R Graphics Output) /Producer (R 2.11.0) /Creator (R) @@ -663,7 +663,7 @@ << /ProcSet [/PDF /Text] /Font <> -/ExtGState << >> +/ExtGState << /GSais 10 0 R >> >> endobj 8 0 obj @@ -682,8 +682,14 @@ /BaseFont /Helvetica /Encoding 8 0 R >> endobj +10 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 10 +0 11 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n @@ -692,14 +698,15 @@ 0000000213 00000 n ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | var\_cols | ` ["1", "2", "3", "4"] ` | | methodChoice | ` {"__current_case__": 0, "method": "cor"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "tabular" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1 (Test #2)
    **Problems**: * ``` Output out_file1: different than expected, difference (using diff): ( /tmp/tmpp2c_62ebpca_out3.tabular v. /tmp/tmptfyrr7zupca_out3.tabular ) --- local_file +++ history_data @@ -2,158 +2,158 @@ #Std. deviation 2.049 0.4905 0.2793 0.1534 #Proportion of variance explained 0.9246 0.05302 0.01719 0.005183 #Loadings 1 2 3 4 -c1 0.3616 -0.6565 0.581 0.3173 -c2 -0.08227 -0.7297 -0.5964 -0.3241 -c3 0.8566 0.1758 -0.07252 -0.4797 -c4 0.3588 0.07471 -0.5491 0.7511 +c1 0.3616 -0.6565 -0.581 0.3173 +c2 -0.08227 -0.7297 0.5964 -0.3241 +c3 0.8566 0.1758 0.07252 -0.4797 +c4 0.3588 0.07471 0.5491 0.7511 #Scores 1 2 3 4 -1 -2.684 -0.3266 0.02151 0.001006 -2 -2.715 0.1696 0.2035 0.0996 -3 -2.89 0.1373 -0.02471 0.0193 -4 -2.746 0.3111 -0.03767 -0.07596 -5 -2.729 -0.3339 -0.09623 -0.06313 -6 -2.28 -0.7478 -0.1743 -0.02715 -7 -2.821 0.0821 -0.2643 -0.0501 -8 -2.626 -0.1704 0.0158 -0.04628 -9 -2.888 0.5708 -0.02734 -0.02662 -10 -2.674 0.1067 0.1915 -0.05589 ******** *SNIP * ******** +126 2.614 -0.5584 -0.2084 -0.2404 +127 1.258 0.1791 0.04698 0.1476 +128 1.291 0.1164 0.2316 0.003084 +129 2.123 0.2109 0.1535 0.05261 +130 2.388 -0.4625 -0.452 -0.2299 +131 2.841 -0.3727 -0.501 -0.02022 +132 3.232 -1.371 -0.1184 -0.2545 +133 2.159 0.2183 0.2084 0.1277 +134 1.443 0.1438 -0.1541 -0.1899 +135 1.78 0.5015 -0.1758 -0.5035 +136 3.077 -0.6858 -0.3364 0.3106 +137 2.145 -0.1389 0.7342 0.05177 +138 1.905 -0.04805 0.1605 -0.222 +139 1.169 0.1645 0.2825 0.01933 +140 2.108 -0.3715 0.02744 0.21 +141 2.314 -0.1826 0.3229 0.2759 +142 1.922 -0.4093 0.1155 0.5041 +143 1.414 0.5749 0.2964 -0.0157 +144 2.563 -0.276 0.2913 0.05618 +145 2.419 -0.3035 0.5043 0.2382 +146 1.944 -0.1874 0.1793 0.4251 +147 1.526 0.375 -0.1206 0.2557 +148 1.764 -0.07852 0.1308 0.1363 +149 1.902 -0.1159 0.7229 0.04087 +150 1.39 0.2829 0.3623 -0.1563 ``` * ``` Output out_file2: different than expected, difference (using diff): ( /tmp/tmpar7vujf7pca_out4.pdf v. /tmp/tmpa4rb9w4dpca_out4.pdf ) --- local_file +++ history_data @@ -2,8 +2,8 @@ %���ρ�\r 1 0 obj << -/CreationDate (D:20110308103327) -/ModDate (D:20110308103327) +/CreationDate (D:20220624182327) +/ModDate (D:20220624182327) /Title (R Graphics Output) /Producer (R 2.11.0) /Creator (R) @@ -663,7 +663,7 @@ << /ProcSet [/PDF /Text] /Font <> -/ExtGState << >> +/ExtGState << /GSais 10 0 R >> >> endobj 8 0 obj @@ -682,8 +682,14 @@ /BaseFont /Helvetica /Encoding 8 0 R >> endobj +10 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 10 +0 11 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n @@ -692,14 +698,15 @@ 0000000213 00000 n ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | var\_cols | ` ["1", "2", "3", "4"] ` | | methodChoice | ` {"__current_case__": 1, "method": "cov"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "auto" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1 (Test #3)
    **Problems**: * ``` Output out_file2: different than expected, difference (using diff): ( /tmp/tmp5mf4igmipca_out6.pdf v. /tmp/tmpe2ydt1onpca_out6.pdf ) --- local_file +++ history_data @@ -2,8 +2,8 @@ %���ρ�\r 1 0 obj << -/CreationDate (D:20110308103341) -/ModDate (D:20110308103341) +/CreationDate (D:20220624182329) +/ModDate (D:20220624182329) /Title (R Graphics Output) /Producer (R 2.11.0) /Creator (R) @@ -663,7 +663,7 @@ << /ProcSet [/PDF /Text] /Font <> -/ExtGState << >> +/ExtGState << /GSais 10 0 R >> >> endobj 8 0 obj @@ -682,8 +682,14 @@ /BaseFont /Helvetica /Encoding 8 0 R >> endobj +10 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 10 +0 11 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n @@ -692,14 +698,15 @@ 0000000213 00000 n ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | var\_cols | ` ["1", "2", "3", "4"] ` | | methodChoice | ` {"__current_case__": 2, "method": "svd", "scale": "both"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "auto" ` |

jennaj commented 2 years ago

No command line -- this means the job didn't make it along far enough to actually execute, yes?