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channotation / chap

CHAP is a tool for the functional annotation of ion channel structures:
http://www.channotation.org
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Issue with Make chap-version_0_9_1 #15

Open BDehury85 opened 4 years ago

BDehury85 commented 4 years ago

make Scanning dependencies of target googletest [ 0%] Creating directories for 'googletest' [ 1%] Performing download step (download, verify and extract) for 'googletest' -- Downloading... dst='/home/bd422/chap-version_0_9_1/build/googletest-prefix/src/release-1.7.0.zip' timeout='none' -- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip' -- Retrying... -- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip' -- Retry after 5 seconds (attempt #2) ... -- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip' -- Retry after 5 seconds (attempt #3) ... -- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip' -- Retry after 15 seconds (attempt #4) ... -- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip' -- Retry after 60 seconds (attempt #5) ... -- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip' CMake Error at googletest-stamp/download-googletest.cmake:159 (message): Each download failed!

error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
     status_code: 1
     status_string: "Unsupported protocol"
     log:
     --- LOG BEGIN ---
     Protocol "https" not supported or disabled in libcurl

Closing connection -1

     --- LOG END ---
     error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
     status_code: 1
     status_string: "Unsupported protocol"
     log:
     --- LOG BEGIN ---
     Protocol "https" not supported or disabled in libcurl

Closing connection -1

     --- LOG END ---
     error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
     status_code: 1
     status_string: "Unsupported protocol"
     log:
     --- LOG BEGIN ---
     Protocol "https" not supported or disabled in libcurl

Closing connection -1

     --- LOG END ---
     error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
     status_code: 1
     status_string: "Unsupported protocol"
     log:
     --- LOG BEGIN ---
     Protocol "https" not supported or disabled in libcurl

Closing connection -1

     --- LOG END ---
     error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
     status_code: 1
     status_string: "Unsupported protocol"
     log:
     --- LOG BEGIN ---
     Protocol "https" not supported or disabled in libcurl

Closing connection -1

     --- LOG END ---
     error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
     status_code: 1
     status_string: "Unsupported protocol"
     log:
     --- LOG BEGIN ---
     Protocol "https" not supported or disabled in libcurl

Closing connection -1

     --- LOG END ---

CMakeFiles/googletest.dir/build.make:90: recipe for target 'googletest-prefix/src/googletest-stamp/googletest-download' failed make[2]: [googletest-prefix/src/googletest-stamp/googletest-download] Error 1 CMakeFiles/Makefile2:404: recipe for target 'CMakeFiles/googletest.dir/all' failed make[1]: [CMakeFiles/googletest.dir/all] Error 2 Makefile:140: recipe for target 'all' failed make: *** [all] Error 2

Inniag commented 4 years ago

The installer fails to download a prerequisite library (GoogleTest), which should be downloaded automatically. As far as I can see, this is due to missing support for the https protocol.

When installing cmake, you need to make sure to link it to a version of libcurl that supports https. In case you have so far installed cmake from your system repositories, this may help get you started with compiling from source:

git clone -b v3.5.2 https://cmake.org/cmake.git cmake
cd cmake
./bootstrap --system-curl
make
sudo make install

(I found this solution here and can not guarantee it will work.)

An alternative workaround may be to change the URL in line 101 of CHAP's CMakeLists.txt to

http://github.com/google/googletest/archive/release-1.7.0.zip

i.e. without the "s". I have not tried this and it may well be that GitHub rejects unsecure (s = secure) HTTP connections.

BDehury85 commented 4 years ago

Hi,

I have tried to run Cmake, through it was successful, I could not able to install chap properly in my system. I am still having the issue with cmake: [----------] 3 tests from InplaneOptimisedProbePathFinderTest 1: [ RUN ] InplaneOptimisedProbePathFinderTest.InplaneOptimisedProbePathFinderXDirTest 1: unknown file: Failure 1: C++ exception with description "Pore radius at initial probe position is infinite. Consider increasing the maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for neighbourhood searches explicitly with -pf-cutoff." thrown in the test body. 1: [ FAILED ] InplaneOptimisedProbePathFinderTest.InplaneOptimisedProbePathFinderXDirTest (20 ms) 1: [ RUN ] InplaneOptimisedProbePathFinderTest.InplaneOptimisedProbePathFinderYDirTest 1: unknown file: Failure 1: C++ exception with description "Pore radius at initial probe position is infinite. Consider increasing the maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for neighbourhood searches explicitly with -pf-cutoff." thrown in the test body. 1: [ FAILED ] InplaneOptimisedProbePathFinderTest.InplaneOptimisedProbePathFinderYDirTest (6 ms) 1: [ RUN ] InplaneOptimisedProbePathFinderTest.InplaneOptimisedProbePathFinderZDirTest 1: unknown file: Failure 1: C++ exception with description "Pore radius at initial probe position is infinite. Consider increasing the maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for neighbourhood searches explicitly with -pf-cutoff." thrown in the test body. 1: [ FAILED ] InplaneOptimisedProbePathFinderTest.InplaneOptimisedProbePathFinderZDirTest (1 ms) 1: [----------] 3 tests from InplaneOptimisedProbePathFinderTest (27 ms total) 1: 1: [----------] 3 tests from MolecularPathTest 1: [ RUN ] MolecularPathTest.MolecularPathLengthTest 1: [ OK ] MolecularPathTest.MolecularPathLengthTest (43 ms) 1: [ RUN ] MolecularPathTest.MolecularPathMinRadiusTest 1: [ OK ] MolecularPathTest.MolecularPathMinRadiusTest (43 ms) 1: [ RUN ] MolecularPathTest.MolecularPathVolumeTest 1: [ OK ] MolecularPathTest.MolecularPathVolumeTest (53 ms) 1: [----------] 3 tests from MolecularPathTest (139 ms total) 1: 1: [----------] 2 tests from MolecularPathObjExporterTest 1: [ RUN ] MolecularPathObjExporterTest.MolecularPathObjExporterOrthogonalVectorTest 1: [ OK ] MolecularPathObjExporterTest.MolecularPathObjExporterOrthogonalVectorTest (0 ms) 1: [ RUN ] MolecularPathObjExporterTest.MolecularPathObjExporterAxisRotationTest 1: [ OK ] MolecularPathObjExporterTest.MolecularPathObjExporterAxisRotationTest (0 ms) 1: [----------] 2 tests from MolecularPathObjExporterTest (0 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 62 tests from 19 test cases ran. (3238 ms total) 1: [ PASSED ] 59 tests. 1: [ FAILED ] 3 tests, listed below: 1: [ FAILED ] InplaneOptimisedProbePathFinderTest.InplaneOptimisedProbePathFinderXDirTest 1: [ FAILED ] InplaneOptimisedProbePathFinderTest.InplaneOptimisedProbePathFinderYDirTest 1: [ FAILED ] InplaneOptimisedProbePathFinderTest.InplaneOptimisedProbePathFinderZDirTest 1: 1: 3 FAILED TESTS 1/1 Test #1: runAllTests ......................***Failed 3.49 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 3.49 sec

The following tests FAILED: 1 - runAllTests (Failed) Errors while running CTest test/CMakeFiles/check.dir/build.make:57: recipe for target 'test/CMakeFiles/check' failed make[3]: [test/CMakeFiles/check] Error 8 CMakeFiles/Makefile2:1056: recipe for target 'test/CMakeFiles/check.dir/all' failed make[2]: [test/CMakeFiles/check.dir/all] Error 2 CMakeFiles/Makefile2:1063: recipe for target 'test/CMakeFiles/check.dir/rule' failed make[1]: [test/CMakeFiles/check.dir/rule] Error 2 Makefile:563: recipe for target 'check' failed make: [check] Error 2

Inniag commented 4 years ago

It looks like the error you are seeing is originating from make check rather than from cmake. You have already successfully compiled CHAP and only some of the unit tests seem to fail.

Could you try to run CHAP on the bundled examples as described in the documentation? If this works, you might be able to run CHAP on your own systems, as passing make check is not strictly required (only make is).

The unit test failure is still disconcerting and may be hard to diagnose from afar. What operating system are you using? Could you please post the output from running chap -version?

BDehury85 commented 4 years ago

Thanks for quick and prompt reply. I am using Ubuntu 18.04.3 LTS 64 bit OS. While I try to run chap -help or chap -version

It says Command 'chap' not found, did you mean:

command 'chat' from deb ppp command 'czap' from deb dvb-apps command 'mhap' from deb mhap command 'cap' from deb capistrano command 'chcp' from deb nilfs-tools

Try: sudo apt install Which suggest it has not been installed properly.

Inniag commented 4 years ago

You need to run make install prior to calling chap -version or alternatively specify the complete path to the CHAP binary created when running make.

BDehury85 commented 4 years ago

bd422@support-OptiPlex-9020:~/chap-version_0_9_1/build$ sudo make install [sudo] password for bd422: [ 6%] Built target googletest [ 45%] Built target chap [100%] Built target runAllTests Install the project... -- Install configuration: "RELEASE" -- Up-to-date: /usr/local/chap/bin/chap -- Up-to-date: /usr/local/chap/share -- Up-to-date: /usr/local/chap/share/data -- Up-to-date: /usr/local/chap/share/data/palettes -- Up-to-date: /usr/local/chap/share/data/palettes/default.json -- Up-to-date: /usr/local/chap/share/data/vdwradii -- Up-to-date: /usr/local/chap/share/data/vdwradii/hole_amberuni.json -- Up-to-date: /usr/local/chap/share/data/vdwradii/hole_bondi.json -- Up-to-date: /usr/local/chap/share/data/vdwradii/hole_hardcore.json -- Up-to-date: /usr/local/chap/share/data/vdwradii/hole_simple.json -- Up-to-date: /usr/local/chap/share/data/vdwradii/hole_xplor.json -- Up-to-date: /usr/local/chap/share/data/hydrophobicity -- Up-to-date: /usr/local/chap/share/data/hydrophobicity/memprotmd.json -- Up-to-date: /usr/local/chap/share/data/hydrophobicity/wimley_white_1996.json -- Up-to-date: /usr/local/chap/share/data/hydrophobicity/hessa_2005.json -- Up-to-date: /usr/local/chap/share/data/hydrophobicity/zhu_2016.json -- Up-to-date: /usr/local/chap/share/data/hydrophobicity/monera_1995.json -- Up-to-date: /usr/local/chap/share/data/hydrophobicity/moon_2011.json -- Up-to-date: /usr/local/chap/share/data/hydrophobicity/kyte_doolittle_1982.json -- Up-to-date: /usr/local/chap/scripts -- Up-to-date: /usr/local/chap/scripts/visualisation -- Up-to-date: /usr/local/chap/scripts/visualisation/PyMOL -- Up-to-date: /usr/local/chap/scripts/visualisation/PyMOL/wobj.py -- Up-to-date: /usr/local/chap/scripts/visualisation/PyMOL/visualise_pathway.py -- Up-to-date: /usr/local/chap/scripts/visualisation/VMD -- Up-to-date: /usr/local/chap/scripts/visualisation/VMD/wobj.tcl -- Up-to-date: /usr/local/chap/scripts/visualisation/VMD/visualise_pathway.tcl -- Up-to-date: /usr/local/chap/scripts/plotting -- Up-to-date: /usr/local/chap/scripts/plotting/Python -- Up-to-date: /usr/local/chap/scripts/plotting/Python/chap_plot_pathway_profile.py -- Up-to-date: /usr/local/chap/scripts/plotting/Python/chap_plot_scalar_time_series.py -- Up-to-date: /usr/local/chap/scripts/plotting/Python/chap_plot_profile_time_series.py -- Up-to-date: /usr/local/chap/scripts/plotting/R -- Up-to-date: /usr/local/chap/scripts/plotting/R/chap_plot_profile_time_series.R -- Up-to-date: /usr/local/chap/scripts/plotting/R/chap_plot_pathway_profile.R -- Up-to-date: /usr/local/chap/scripts/plotting/R/chap_plot_scalar_time_series.R bd422@support-OptiPlex-9020:~/chap-version_0_9_1/build$ chap -h

Command 'chap' not found, did you mean:

I ran sudo make install ..It is successful, but after that while I tried to run chap -version or chap -h...its not working...

Inniag commented 4 years ago

After running sudo make install, run /usr/local/chap/bin/chap -h. Does that work? If so, make sure the CHAP binary is in your PATH when attempting to call chap without absolute path.

BDehury85 commented 4 years ago

@Inniag Thank you so much for your valuable feedback. Its working now..

Thanks and regards Budheswar