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#3597 closed defect

Can't install bundles with circular dependencies — at Version 1

Reported by:	goddard@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Build System	Version:
Keywords:		Cc:	Eric Pettersen
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description (last modified by Tom Goddard)

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.1.dev202008050141 (2020-08-05 01:41:49 UTC)
Description
Make install in mmcif fails saying it can't satisfy connect_structure dependency, and make install in connect_structure fails saying it can't satisfy mmcif dependency.  We need a way to do these installs, maybe "make DEPENDENCY_ERRORS=0 install" that just warns about unsatisfied dependencies and installs anyways.

$ cd ../mmcif/
$ make install
make -C mmcif_cpp source
make[1]: Entering directory '/home/goddard/ucsf/chimerax/src/bundles/mmcif/mmcif_cpp'
cd readcif_cpp; make install
make[2]: Entering directory '/home/goddard/ucsf/chimerax/src/bundles/mmcif/mmcif_cpp/readcif_cpp'
/home/goddard/ucsf/chimerax/build/bin/rsync.convert -rlptWv readcif.h ../include
sending incremental file list

sent 47 bytes  received 12 bytes  118.00 bytes/sec
total size is 13,557  speedup is 229.78
/home/goddard/ucsf/chimerax/build/bin/rsync.convert -rlptWv libreadcif.lib ../lib
sending incremental file list

sent 52 bytes  received 12 bytes  128.00 bytes/sec
total size is 787,536  speedup is 12,305.25
#cp libreadcif.dll /home/goddard/ucsf/chimerax/build/bin
#if [ -d "/home/goddard/ucsf/chimerax/ChimeraX.app/include" ]; then \
#       /home/goddard/ucsf/chimerax/build/bin/rsync.convert -rlptWv readcif.h /home/goddard/ucsf/chimerax/ChimeraX.app/include; \
#fi
#if [ -d "/home/goddard/ucsf/chimerax/ChimeraX.app/lib" ]; then \
#       /home/goddard/ucsf/chimerax/build/bin/rsync.convert -rlptWv libreadcif.lib /home/goddard/ucsf/chimerax/ChimeraX.app/lib; \
#fi
#if [ -d "/home/goddard/ucsf/chimerax/ChimeraX.app/bin" ]; then /home/goddard/ucsf/chimerax/build/bin/rsync.convert -rlptWv libreadcif.dll /home/goddard/ucsf/chimerax/ChimeraX.app/bin; fi
make[2]: Leaving directory '/home/goddard/ucsf/chimerax/src/bundles/mmcif/mmcif_cpp/readcif_cpp'
make[1]: Leaving directory '/home/goddard/ucsf/chimerax/src/bundles/mmcif/mmcif_cpp'
../../../ChimeraX.app/bin/ChimeraX-console.exe --nogui --safemode --exit --cmd "devel install . user false exit true  "
0.00% done: Initializing core
50.00% done: Initializing bundles
Executing: devel install . user false exit true
running build
running build_py
running build_ext
No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
running bdist_wheel
installing to build\bdist.win-amd64\wheel
running install
running install_lib
running build_ext
No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
creating build\bdist.win-amd64\wheel
creating build\bdist.win-amd64\wheel\chimerax
creating build\bdist.win-amd64\wheel\chimerax\atomic
creating build\bdist.win-amd64\wheel\chimerax\atomic\mmcif
copying build\lib.win-amd64-3.7\chimerax\atomic\mmcif\mmcif.py -> build\bdist.win-amd64\wheel\.\chimerax\atomic
\mmcif
copying build\lib.win-amd64-3.7\chimerax\atomic\mmcif\mmcif_write.py -> build\bdist.win-amd64\wheel\.\chimerax\
atomic\mmcif
copying build\lib.win-amd64-3.7\chimerax\atomic\mmcif\stdresidues.cif -> build\bdist.win-amd64\wheel\.\chimerax
\atomic\mmcif
copying build\lib.win-amd64-3.7\chimerax\atomic\mmcif\_mmcif.cp37-win_amd64.pyd -> build\bdist.win-amd64\wheel\
.\chimerax\atomic\mmcif
copying build\lib.win-amd64-3.7\chimerax\atomic\mmcif\__init__.py -> build\bdist.win-amd64\wheel\.\chimerax\ato
mic\mmcif
creating build\bdist.win-amd64\wheel\chimerax\mmcif
copying build\lib.win-amd64-3.7\chimerax\mmcif\mmcif.py -> build\bdist.win-amd64\wheel\.\chimerax\mmcif
copying build\lib.win-amd64-3.7\chimerax\mmcif\mmcif_write.py -> build\bdist.win-amd64\wheel\.\chimerax\mmcif
copying build\lib.win-amd64-3.7\chimerax\mmcif\stdresidues.cif -> build\bdist.win-amd64\wheel\.\chimerax\mmcif
copying build\lib.win-amd64-3.7\chimerax\mmcif\_mmcif.cp37-win_amd64.pyd -> build\bdist.win-amd64\wheel\.\chime
rax\mmcif
copying build\lib.win-amd64-3.7\chimerax\mmcif\__init__.py -> build\bdist.win-amd64\wheel\.\chimerax\mmcif
running install_egg_info
running egg_info
writing ChimeraX_mmCIF.egg-info\PKG-INFO
writing dependency_links to ChimeraX_mmCIF.egg-info\dependency_links.txt
writing requirements to ChimeraX_mmCIF.egg-info\requires.txt
writing top-level names to ChimeraX_mmCIF.egg-info\top_level.txt
reading manifest file 'ChimeraX_mmCIF.egg-info\SOURCES.txt'
writing manifest file 'ChimeraX_mmCIF.egg-info\SOURCES.txt'
Copying ChimeraX_mmCIF.egg-info to build\bdist.win-amd64\wheel\.\ChimeraX_mmCIF-2.2-py3.7.egg-info
running install_scripts
creating build\bdist.win-amd64\wheel\ChimeraX_mmCIF-2.2.dist-info\WHEEL
creating 'dist\ChimeraX_mmCIF-2.2-cp37-cp37m-win_amd64.whl' and adding 'build\bdist.win-amd64\wheel' to it
adding 'chimerax/atomic/mmcif/__init__.py'
adding 'chimerax/atomic/mmcif/_mmcif.cp37-win_amd64.pyd'
adding 'chimerax/atomic/mmcif/mmcif.py'
adding 'chimerax/atomic/mmcif/mmcif_write.py'
adding 'chimerax/atomic/mmcif/stdresidues.cif'
adding 'chimerax/mmcif/__init__.py'
adding 'chimerax/mmcif/_mmcif.cp37-win_amd64.pyd'
adding 'chimerax/mmcif/mmcif.py'
adding 'chimerax/mmcif/mmcif_write.py'
adding 'chimerax/mmcif/stdresidues.cif'
adding 'ChimeraX_mmCIF-2.2.dist-info/METADATA'
adding 'ChimeraX_mmCIF-2.2.dist-info/WHEEL'
adding 'ChimeraX_mmCIF-2.2.dist-info/top_level.txt'
adding 'ChimeraX_mmCIF-2.2.dist-info/RECORD'
removing build\bdist.win-amd64\wheel
Distribution is in .\dist\ChimeraX_mmCIF-2.2-cp37-cp37m-win_amd64.whl
Executing: toolshed install ".\\dist\\ChimeraX_mmCIF-2.2-cp37-cp37m-win_amd64.whl" userOnly false
Traceback (most recent call last):
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\toolshed\__init
__.py", line 1181, in _pip_install
    results = self._run_pip(command, logger)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\toolshed\__init
__.py", line 1227, in _run_pip
    raise RuntimeError(s)
RuntimeError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing c:\cygwin64\home\goddard\ucsf\chimerax\src\bundles\mmcif\dist\chimerax_mmcif-2.2-cp37-cp37m-win_amd6
4.whl
Requirement already satisfied, skipping upgrade: ChimeraX-PDB~=2.0 in c:\cygwin64\home\goddard\ucsf\chimerax\ch
imerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (2.1)
Requirement already satisfied, skipping upgrade: ChimeraX-SaveCommand~=1.0 in c:\cygwin64\home\goddard\ucsf\chi
merax\chimerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.1)
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic~=1.5 in c:\cygwin64\home\goddard\ucsf\chimerax
\chimerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.6)
Requirement already satisfied, skipping upgrade: ChimeraX-OpenCommand~=1.0 in c:\cygwin64\home\goddard\ucsf\chi
merax\chimerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.2.1)
Requirement already satisfied, skipping upgrade: ChimeraX-Core~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax\c
himerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.1.dev202006302005)
Requirement already satisfied, skipping upgrade: ChimeraX-DataFormats~=1.0 in c:\cygwin64\home\goddard\ucsf\chi
merax\chimerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Arrays~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax
\chimerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-IO~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax\chi
merax.app\bin\lib\site-packages (from ChimeraX-SaveCommand~=1.0->ChimeraX-mmCIF==2.2) (1.0)
ERROR: Could not find a version that satisfies the requirement ChimeraX-ConnectStructure~=2.0 (from ChimeraX-At
omic~=1.5->ChimeraX-mmCIF==2.2) (from versions: none)
ERROR: No matching distribution found for ChimeraX-ConnectStructure~=2.0 (from ChimeraX-Atomic~=1.5->ChimeraX-m
mCIF==2.2)
WARNING: You are using pip version 20.1.1; however, version 20.2.1 is available.
You should consider upgrading via the 'C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\ChimeraX-console
.exe -m pip install --upgrade pip' command.


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\devel.
py", line 162, in _run
    unbound_method(bb, *args, **kw)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\bundle_builder\bundl
e_builder.py", line 102, in make_install
    run(session, cmd)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\run.py
", line 31, in run
    results = command.run(text, log=log)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\cli.py
", line 2805, in run
    result = ci.function(session, **kw_args)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\toolsh
ed.py", line 258, in toolshed_install
    ts.install_bundle(bi, logger, **kw)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\toolshed\__init
__.py", line 679, in install_bundle
    per_user=per_user, reinstall=reinstall, no_deps=no_deps)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\toolshed\__init
__.py", line 1184, in _pip_install
    raise UserError(str(e))
chimerax.core.errors.UserError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/p
ypi/
Processing c:\cygwin64\home\goddard\ucsf\chimerax\src\bundles\mmcif\dist\chimerax_mmcif-2.2-cp37-cp37m-win_amd6
4.whl
Requirement already satisfied, skipping upgrade: ChimeraX-PDB~=2.0 in c:\cygwin64\home\goddard\ucsf\chimerax\ch
imerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (2.1)
Requirement already satisfied, skipping upgrade: ChimeraX-SaveCommand~=1.0 in c:\cygwin64\home\goddard\ucsf\chi
merax\chimerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.1)
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic~=1.5 in c:\cygwin64\home\goddard\ucsf\chimerax
\chimerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.6)
Requirement already satisfied, skipping upgrade: ChimeraX-OpenCommand~=1.0 in c:\cygwin64\home\goddard\ucsf\chi
merax\chimerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.2.1)
Requirement already satisfied, skipping upgrade: ChimeraX-Core~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax\c
himerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.1.dev202006302005)
Requirement already satisfied, skipping upgrade: ChimeraX-DataFormats~=1.0 in c:\cygwin64\home\goddard\ucsf\chi
merax\chimerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Arrays~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax
\chimerax.app\bin\lib\site-packages (from ChimeraX-mmCIF==2.2) (1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-IO~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax\chi
merax.app\bin\lib\site-packages (from ChimeraX-SaveCommand~=1.0->ChimeraX-mmCIF==2.2) (1.0)
ERROR: Could not find a version that satisfies the requirement ChimeraX-ConnectStructure~=2.0 (from ChimeraX-At
omic~=1.5->ChimeraX-mmCIF==2.2) (from versions: none)
ERROR: No matching distribution found for ChimeraX-ConnectStructure~=2.0 (from ChimeraX-Atomic~=1.5->ChimeraX-m
mCIF==2.2)
WARNING: You are using pip version 20.1.1; however, version 20.2.1 is available.
You should consider upgrading via the 'C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\ChimeraX-console
.exe -m pip install --upgrade pip' command.



make: *** [../Makefile.bundle:48: install] Error 1


$ cd ../connect_structure/
$ make install
../../../ChimeraX.app/bin/ChimeraX-console.exe --nogui --safemode --exit --cmd "devel install . user false exit true  "
0.00% done: Initializing core
50.00% done: Initializing bundles
Executing: devel install . user false exit true
running build
running build_py
creating build\lib.win-amd64-3.7\chimerax\connect_structure
copying src\__init__.py -> build\lib.win-amd64-3.7\chimerax\connect_structure
running build_ext
No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
building 'chimerax.connect_structure._cs' extension
C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\bin\HostX64\x64\cl.exe
/c /nologo /Ox /W3 /GL /DNDEBUG /MD -DMAJOR_VERSION=0 -DMINOR_VERSION=1 -IC:\cygwin64\home\goddard\ucsf\chimera
x\ChimeraX.app\include -IC:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\ato
mic\include -IC:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\atom_search\in
clude -IC:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\include -IC:\cygwin64\home\goddard\ucsf\chimera
x\ChimeraX.app\bin\include -IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\ucrt -IC:\Program File
s (x86)\Windows Kits\10\include\10.0.17763.0\shared -IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763
.0\um -IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\winrt -IC:\Program Files (x86)\Windows Kits
\10\include\10.0.17763.0\cppwinrt -Ic:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC
\14.16.27023\include -Ic:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\
atlmfc\include -Ic:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\ucrt -Ic:\Program Files (x86)\Wind
ows Kits\10\include\10.0.17763.0\shared -Ic:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\um -Ic:\P
rogram Files (x86)\Windows Kits\10\include\10.0.17763.0\winrt -Ic:\Program Files (x86)\Windows Kits\10\include\
10.0.17763.0\cppwinrt /EHsc /Tpconnect_cpp/connect.cpp /Fobuild\temp.win-amd64-3.7\Release\connect_cpp/connect.
obj
C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\bin\HostX64\x64\link.ex
e /nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:C:\cygwin64\home\goddard\ucs
f\chimerax\ChimeraX.app\lib /LIBPATH:C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\
chimerax\atomic\lib /LIBPATH:C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax
\atom_search\lib /LIBPATH:C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\libs /LIBPATH:C:\cygwin64\hom
e\goddard\ucsf\chimerax\ChimeraX.app\bin\PCbuild\amd64 /LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0
.17763.0\ucrt\x64 /LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.17763.0\um\x64 /LIBPATH:c:\Program F
iles (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\lib\\x64 /LIBPATH:c:\Program Files
(x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\atlmfc\lib\\x64 /LIBPATH:c:\Program File
s (x86)\Windows Kits\10\lib\10.0.17763.0\ucrt\x64 /LIBPATH:c:\Program Files (x86)\Windows Kits\10\lib\10.0.1776
3.0\um\x64 libatomstruct.lib libelement.lib libpyinstance.lib libatomsearch.lib /EXPORT:PyInit__cs build\temp.w
in-amd64-3.7\Release\connect_cpp/connect.obj /OUT:build\lib.win-amd64-3.7\chimerax\connect_structure\_cs.cp37-w
in_amd64.pyd /IMPLIB:build\temp.win-amd64-3.7\Release\connect_cpp\_cs.cp37-win_amd64.lib
running bdist_wheel
installing to build\bdist.win-amd64\wheel
running install
running install_lib
running build_ext
No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
creating build\bdist.win-amd64\wheel
creating build\bdist.win-amd64\wheel\chimerax
creating build\bdist.win-amd64\wheel\chimerax\atomic
creating build\bdist.win-amd64\wheel\chimerax\atomic\connect_structure
copying build\lib.win-amd64-3.7\chimerax\atomic\connect_structure\_cs.cp37-win_amd64.pyd -> build\bdist.win-amd
64\wheel\.\chimerax\atomic\connect_structure
copying build\lib.win-amd64-3.7\chimerax\atomic\connect_structure\__init__.py -> build\bdist.win-amd64\wheel\.\
chimerax\atomic\connect_structure
creating build\bdist.win-amd64\wheel\chimerax\connect_structure
copying build\lib.win-amd64-3.7\chimerax\connect_structure\_cs.cp37-win_amd64.pyd -> build\bdist.win-amd64\whee
l\.\chimerax\connect_structure
copying build\lib.win-amd64-3.7\chimerax\connect_structure\__init__.py -> build\bdist.win-amd64\wheel\.\chimera
x\connect_structure
running install_egg_info
running egg_info
writing ChimeraX_ConnectStructure.egg-info\PKG-INFO
writing dependency_links to ChimeraX_ConnectStructure.egg-info\dependency_links.txt
writing requirements to ChimeraX_ConnectStructure.egg-info\requires.txt
writing top-level names to ChimeraX_ConnectStructure.egg-info\top_level.txt
reading manifest file 'ChimeraX_ConnectStructure.egg-info\SOURCES.txt'
writing manifest file 'ChimeraX_ConnectStructure.egg-info\SOURCES.txt'
Copying ChimeraX_ConnectStructure.egg-info to build\bdist.win-amd64\wheel\.\ChimeraX_ConnectStructure-2.0-py3.7
.egg-info
running install_scripts
creating build\bdist.win-amd64\wheel\ChimeraX_ConnectStructure-2.0.dist-info\WHEEL
creating 'dist\ChimeraX_ConnectStructure-2.0-cp37-cp37m-win_amd64.whl' and adding 'build\bdist.win-amd64\wheel'
 to it
adding 'chimerax/atomic/connect_structure/__init__.py'
adding 'chimerax/atomic/connect_structure/_cs.cp37-win_amd64.pyd'
adding 'chimerax/connect_structure/__init__.py'
adding 'chimerax/connect_structure/_cs.cp37-win_amd64.pyd'
adding 'ChimeraX_ConnectStructure-2.0.dist-info/METADATA'
adding 'ChimeraX_ConnectStructure-2.0.dist-info/WHEEL'
adding 'ChimeraX_ConnectStructure-2.0.dist-info/top_level.txt'
adding 'ChimeraX_ConnectStructure-2.0.dist-info/RECORD'
removing build\bdist.win-amd64\wheel
Distribution is in .\dist\ChimeraX_ConnectStructure-2.0-cp37-cp37m-win_amd64.whl
Executing: toolshed install ".\\dist\\ChimeraX_ConnectStructure-2.0-cp37-cp37m-win_amd64.whl" userOnly false
Traceback (most recent call last):
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\toolshed\__init
__.py", line 1181, in _pip_install
    results = self._run_pip(command, logger)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\toolshed\__init
__.py", line 1227, in _run_pip
    raise RuntimeError(s)
RuntimeError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing c:\cygwin64\home\goddard\ucsf\chimerax\src\bundles\connect_structure\dist\chimerax_connectstructure-
2.0-cp37-cp37m-win_amd64.whl
Requirement already satisfied, skipping upgrade: ChimeraX-Core~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax\c
himerax.app\bin\lib\site-packages (from ChimeraX-ConnectStructure==2.0) (1.1.dev202006302005)
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax
\chimerax.app\bin\lib\site-packages (from ChimeraX-ConnectStructure==2.0) (1.6)
Requirement already satisfied, skipping upgrade: ChimeraX-AtomSearch~=2.0 in c:\cygwin64\home\goddard\ucsf\chim
erax\chimerax.app\bin\lib\site-packages (from ChimeraX-ConnectStructure==2.0) (2.0)
Requirement already satisfied, skipping upgrade: ChimeraX-PDB~=2.0 in c:\cygwin64\home\goddard\ucsf\chimerax\ch
imerax.app\bin\lib\site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-ConnectStructure==2.0) (2.1)
Requirement already satisfied, skipping upgrade: ChimeraX-Arrays~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax
\chimerax.app\bin\lib\site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-ConnectStructure==2.0) (1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Graphics~=1.0 in c:\cygwin64\home\goddard\ucsf\chimer
ax\chimerax.app\bin\lib\site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-ConnectStructure==2.0) (1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Geometry~=1.0 in c:\cygwin64\home\goddard\ucsf\chimer
ax\chimerax.app\bin\lib\site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-ConnectStructure==2.0) (1.1)
ERROR: Could not find a version that satisfies the requirement ChimeraX-mmCIF~=2.0 (from ChimeraX-Atomic~=1.0->
ChimeraX-ConnectStructure==2.0) (from versions: none)
ERROR: No matching distribution found for ChimeraX-mmCIF~=2.0 (from ChimeraX-Atomic~=1.0->ChimeraX-ConnectStruc
ture==2.0)
WARNING: You are using pip version 20.1.1; however, version 20.2.1 is available.
You should consider upgrading via the 'C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\ChimeraX-console
.exe -m pip install --upgrade pip' command.


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\devel.
py", line 162, in _run
    unbound_method(bb, *args, **kw)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\bundle_builder\bundl
e_builder.py", line 102, in make_install
    run(session, cmd)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\run.py
", line 31, in run
    results = command.run(text, log=log)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\cli.py
", line 2805, in run
    result = ci.function(session, **kw_args)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\toolsh
ed.py", line 258, in toolshed_install
    ts.install_bundle(bi, logger, **kw)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\toolshed\__init
__.py", line 679, in install_bundle
    per_user=per_user, reinstall=reinstall, no_deps=no_deps)
  File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\toolshed\__init
__.py", line 1184, in _pip_install
    raise UserError(str(e))
chimerax.core.errors.UserError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/p
ypi/
Processing c:\cygwin64\home\goddard\ucsf\chimerax\src\bundles\connect_structure\dist\chimerax_connectstructure-
2.0-cp37-cp37m-win_amd64.whl
Requirement already satisfied, skipping upgrade: ChimeraX-Core~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax\c
himerax.app\bin\lib\site-packages (from ChimeraX-ConnectStructure==2.0) (1.1.dev202006302005)
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax
\chimerax.app\bin\lib\site-packages (from ChimeraX-ConnectStructure==2.0) (1.6)
Requirement already satisfied, skipping upgrade: ChimeraX-AtomSearch~=2.0 in c:\cygwin64\home\goddard\ucsf\chim
erax\chimerax.app\bin\lib\site-packages (from ChimeraX-ConnectStructure==2.0) (2.0)
Requirement already satisfied, skipping upgrade: ChimeraX-PDB~=2.0 in c:\cygwin64\home\goddard\ucsf\chimerax\ch
imerax.app\bin\lib\site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-ConnectStructure==2.0) (2.1)
Requirement already satisfied, skipping upgrade: ChimeraX-Arrays~=1.0 in c:\cygwin64\home\goddard\ucsf\chimerax
\chimerax.app\bin\lib\site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-ConnectStructure==2.0) (1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Graphics~=1.0 in c:\cygwin64\home\goddard\ucsf\chimer
ax\chimerax.app\bin\lib\site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-ConnectStructure==2.0) (1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Geometry~=1.0 in c:\cygwin64\home\goddard\ucsf\chimer
ax\chimerax.app\bin\lib\site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-ConnectStructure==2.0) (1.1)
ERROR: Could not find a version that satisfies the requirement ChimeraX-mmCIF~=2.0 (from ChimeraX-Atomic~=1.0->
ChimeraX-ConnectStructure==2.0) (from versions: none)
ERROR: No matching distribution found for ChimeraX-mmCIF~=2.0 (from ChimeraX-Atomic~=1.0->ChimeraX-ConnectStruc
ture==2.0)
WARNING: You are using pip version 20.1.1; however, version 20.2.1 is available.
You should consider upgrading via the 'C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\ChimeraX-console
.exe -m pip install --upgrade pip' command.



make: *** [../Makefile.bundle:48: install] Error 1



Log:
UCSF ChimeraX version: 1.1.dev202008050141 (2020-08-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 442.19
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z270X-Gaming K7
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 17,129,693,184
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.0
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.2
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.dev202008050141
    ChimeraX-CoreFormats: 1.0
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-RealSense: 1.5
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.2
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.5
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    pyrealsense2: 2.35.2.1937
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 47.3.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 4.3.3
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (1)

comment:1 by Tom Goddard, 5 years ago

Cc:	Eric Pettersen added
Component:	Unassigned → Build System
Description:	modified (diff)
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Can't install bundles with circular dependencies

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