Changes between Initial Version and Version 2 of Ticket #5289


Ignore:
Timestamp:
Sep 27, 2021, 4:59:52 PM (4 years ago)
Author:
Greg Couch
Comment:

Incompatible version of UI bundle was installed. Unfortunately to remove it is complicated because it is in the user customization of ChimeraX.

To fix this, two directories need to be removed. To find out where in the filesystem they are, use the info path}} command to to find the {{{user versioned data directory.

Then use a file browser to go to that directory. On Windows, you might need to check the Hidden Files entry in the View menu. Then go into the site-packages directory and remove the ChimeraX_UI-1.2.1.dist-info directory. And then go into the chimerax directory (inside of site-packages) and remove the ui directory.

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  • Ticket #5289

    • Property Cc Tristan Croll added
    • Property Component Unassigned → Tool Shed
    • Property Owner set to Greg Couch
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → closed
    • Property Summary ChimeraX bug report submission → Dependency conflict trying to install ISOLDE into 1.2.5
    • Property Resolution → limitation

  • Ticket #5289 – Description

    initial v2  
    3131> toolshed install isolde
    3232
    33 Looking in indexes: https://pypi.org/simple,
    34 https://cxtoolshed.rbvi.ucsf.edu/pypi/ Requirement already satisfied:
    35 ChimeraX-ISOLDE==1.2.2 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-
    36 packages (1.2.2) Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in
    37 c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2)
    38 (1.13.2) Collecting ChimeraX-Clipper~=0.16.0 Using cached
    39 https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.16.0/ChimeraX_Clipper-0.16.0-cp38-cp38-win_amd64.whl
    40 (22.9 MB) Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in c:\program
    41 files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.0)
    42 Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in c:\program
    43 files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3)
    44 Requirement already satisfied: ChimeraX-Core~=1.2.0 in c:\program
    45 files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5)
    46 Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
    47 files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-
    48 ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-
    49 ConnectStructure~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from
    50 ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0) Requirement already
    51 satisfied: ChimeraX-Nucleotides~=2.0 in c:\program
    52 files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-
    53 ISOLDE==1.2.2) (2.0.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
    54 c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-
    55 Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3) Requirement already satisfied:
    56 ChimeraX-Graphics~=1.0 in c:\program files\chimerax\bin\lib\site-packages
    57 (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement
    58 already satisfied: ChimeraX-PDB~=2.0 in c:\program
    59 files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-
    60 ISOLDE==1.2.2) (2.4.1) Requirement already satisfied: ChimeraX-
    61 AtomSearchLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages
    62 (from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
    63 ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0
    64 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-
    65 mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1)
    66 Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program
    67 files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
    68 Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.4) Requirement already satisfied:
    69 ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages
    70 (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2)
    71 (1.5) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program
    72 files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
    73 Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied:
    74 ChimeraX-IO~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from
    75 ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-
    76 Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied:
    77 ChimeraX-Surface~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from
    78 ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2)
    79 (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in
    80 c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-
    81 Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.2.1)
    82 INFO: pip is looking at multiple versions of chimerax-pdblibrary to determine
    83 which version is compatible with other requirements. This could take a while.
    84 INFO: pip is looking at multiple versions of chimerax-pdb to determine which
    85 version is compatible with other requirements. This could take a while. INFO:
    86 pip is looking at multiple versions of chimerax-opencommand to determine which
    87 version is compatible with other requirements. This could take a while. INFO:
    88 pip is looking at multiple versions of chimerax-nucleotides to determine which
    89 version is compatible with other requirements. This could take a while. INFO:
    90 pip is looking at multiple versions of chimerax-io to determine which version
    91 is compatible with other requirements. This could take a while. INFO: pip is
    92 looking at multiple versions of chimerax-dataformats to determine which
    93 version is compatible with other requirements. This could take a while. INFO:
    94 pip is looking at multiple versions of chimerax-mmcif to determine which
    95 version is compatible with other requirements. This could take a while. INFO:
    96 pip is looking at multiple versions of chimerax-graphics to determine which
    97 version is compatible with other requirements. This could take a while. INFO:
    98 pip is looking at multiple versions of chimerax-geometry to determine which
    99 version is compatible with other requirements. This could take a while. INFO:
    100 pip is looking at multiple versions of chimerax-core to determine which
    101 version is compatible with other requirements. This could take a while. INFO:
    102 pip is looking at multiple versions of chimerax-atomsearchlibrary to determine
    103 which version is compatible with other requirements. This could take a while.
    104 INFO: pip is looking at multiple versions of chimerax-connectstructure to
    105 determine which version is compatible with other requirements. This could take
    106 a while. INFO: pip is looking at multiple versions of <Python from Requires-
    107 Python> to determine which version is compatible with other requirements. This
    108 could take a while. INFO: pip is looking at multiple versions of chimerax-
    109 clipper to determine which version is compatible with other requirements. This
    110 could take a while. INFO: pip is looking at multiple versions of chimerax-
    111 atomiclibrary to determine which version is compatible with other
    112 requirements. This could take a while. INFO: pip is looking at multiple
    113 versions of chimerax-atomic to determine which version is compatible with
    114 other requirements. This could take a while. INFO: pip is looking at multiple
    115 versions of chimerax-arrays to determine which version is compatible with
    116 other requirements. This could take a while. INFO: pip is looking at multiple
    117 versions of chimerax-isolde to determine which version is compatible with
    118 other requirements. This could take a while. The conflict is caused by:
    119 chimerax-nucleotides 2.0.1 depends on ChimeraX-UI~=1.0 chimerax-opencommand
    120 1.5 depends on ChimeraX-UI~=1.0 chimerax-savecommand 1.4 depends on ChimeraX-
    121 UI~=1.4 To fix this you could try to: 1\. loosen the range of package versions
    122 you've specified 2\. remove package versions to allow pip attempt to solve the
    123 dependency conflict ERROR: Cannot install chimerax-nucleotides==2.0.1,
    124 chimerax-opencommand==1.5 and chimerax-savecommand==1.4 because these package
    125 versions have conflicting dependencies. ERROR: ResolutionImpossible: for help
    126 visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-
    127 dependencies WARNING: You are using pip version 21.0.1; however, version
    128 21.2.4 is available. You should consider upgrading via the 'C:\Program
    129 Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command. 
     33Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
     34Requirement already satisfied:
     35ChimeraX-ISOLDE==1.2.2 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (1.2.2)
     36Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2)
     37Collecting ChimeraX-Clipper~=0.16.0 Using cached https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.16.0/ChimeraX_Clipper-0.16.0-cp38-cp38-win_amd64.whl (22.9 MB)
     38Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.0)
     39Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3)
     40Requirement already satisfied: ChimeraX-Core~=1.2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5)
     41Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1)
     42Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)
     43Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1)
     44Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3)
     45Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax\bin\lib\site-packages(from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0)
     46Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1)
     47Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
     48ISOLDE==1.2.2) (1.0)
     49Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1)
     50Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.4) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.5)
     51Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-IO~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1)
     52Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0)
     53Requirement already satisfied: ChimeraX-UI~=1.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.2.1)
     54INFO: pip is looking at multiple versions of chimerax-pdblibrary to determine which version is compatible with other requirements. This could take a while.
     55INFO: pip is looking at multiple versions of chimerax-pdb to determine which version is compatible with other requirements. This could take a while.
     56INFO: pip is looking at multiple versions of chimerax-opencommand to determine which version is compatible with other requirements. This could take a while.
     57INFO: pip is looking at multiple versions of chimerax-nucleotides to determine which version is compatible with other requirements. This could take a while.
     58INFO: pip is looking at multiple versions of chimerax-io to determine which version is compatible with other requirements. This could take a while.
     59INFO: pip is looking at multiple versions of chimerax-dataformats to determine which version is compatible with other requirements. This could take a while.
     60INFO: pip is looking at multiple versions of chimerax-mmcif to determine which version is compatible with other requirements. This could take a while.
     61INFO: pip is looking at multiple versions of chimerax-graphics to determine which version is compatible with other requirements. This could take a while.
     62INFO:pip is looking at multiple versions of chimerax-geometry to determine which version is compatible with other requirements. This could take a while.
     63INFO: pip is looking at multiple versions of chimerax-core to determine which version is compatible with other requirements. This could take a while.
     64INFO: pip is looking at multiple versions of chimerax-atomsearchlibrary to determine which version is compatible with other requirements. This could take a while.
     65INFO: pip is looking at multiple versions of chimerax-connectstructure to determine which version is compatible with other requirements. This could take a while.
     66INFO: pip is looking at multiple versions of <Python from Requires-Python> to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-clipper to determine which version is compatible with other requirements. This
     67could take a while.
     68INFO: pip is looking at multiple versions of chimerax-atomiclibrary to determine which version is compatible with other requirements. This could take a while.
     69INFO: pip is looking at multiple versions of chimerax-atomic to determine which version is compatible with other requirements. This could take a while.
     70INFO: pip is looking at multiple versions of chimerax-arrays to determine which version is compatible with other requirements. This could take a while.
     71INFO: pip is looking at multiple versions of chimerax-isolde to determine which version is compatible with other requirements. This could take a while. The conflict is caused by: chimerax-nucleotides 2.0.1 depends on ChimeraX-UI~=1.0 chimerax-opencommand 1.5 depends on ChimeraX-UI~=1.0 chimerax-savecommand 1.4 depends on ChimeraX-UI~=1.4 To fix this you could try to: 1\. loosen the range of package versions you've specified 2\. remove package versions to allow pip attempt to solve the
     72dependency conflict
     73ERROR: Cannot install chimerax-nucleotides==2.0.1, chimerax-opencommand==1.5 and chimerax-savecommand==1.4 because these package versions have conflicting dependencies.
     74ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies
     75WARNING: You are using pip version 21.0.1; however, version 21.2.4 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command. 
    13076
    13177> toolshed uninstall chimerax-nucleotides