New issues with install #60
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was able to get past by adding prefix to cmake cmake -DBOOST_ROOT=/software/boost/1.60/x86_64-linux-ubuntu14.04 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/share/biocore/software BUT whats the deal with all the _test bins msettles@ganesh: build$ll /share/biocore/software/bin/ something tells me the process still isn't quite right Matt |
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oh and then make test fails |
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It probably would be good to default the install directory to "./bin/" (e.g. HTStream/build/bin/). Also it does seem like building (or at least installing) the "*test" binaries should probably not be done on a release build. Those are all the google-test unit tests however, which is a GOOD thing because it means the code is being tested and has a testing framework! |
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agreed, build/bin and then maybe a 'make install' to send it to the system (or specified install location) if one so chooses, unit tests are great, but weird to coexist with regular binaries in the final install directory (unless maybe in the build/bin), shouldn't 'make test' then execute and verify install works correctly? |
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I agree, |
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My result of ’make test’
msettles@ganesh: build$make test
Running tests...
Test project /share/biocore/software/src/HTStream/build
Start 1: test_common
1/8 Test #1: test_common ......................***Failed 0.08 sec
Start 2: test_superd
2/8 Test #2: test_superd ......................***Failed 0.06 sec
Start 3: test_polyATtrim
3/8 Test #3: test_polyATtrim ..................***Failed 0.06 sec
Start 4: test_q_window_trim
4/8 Test #4: test_q_window_trim ...............***Failed 0.04 sec
Start 5: test_cut_trim
5/8 Test #5: test_cut_trim ....................***Failed 0.06 sec
Start 6: test_phix_remover
6/8 Test #6: test_phix_remover ................***Failed 0.04 sec
Start 7: test_overlapper
7/8 Test #7: test_overlapper ..................***Failed 0.03 sec
Start 8: test_n_remover
8/8 Test #8: test_n_remover ...................***Failed 0.00 sec
0% tests passed, 8 tests failed out of 8
Total Test time (real) = 0.49 sec
The following tests FAILED:
1 - test_common (Failed)
2 - test_superd (Failed)
3 - test_polyATtrim (Failed)
4 - test_q_window_trim (Failed)
5 - test_cut_trim (Failed)
6 - test_phix_remover (Failed)
7 - test_overlapper (Failed)
8 - test_n_remover (Failed)
Errors while running CTest
make: *** [test] Error 8
From: Joe Angell <notifications@github.com>
Reply-To: ibest/HTStream <reply@reply.github.com>
Date: Monday, February 20, 2017 at 9:25 AM
To: ibest/HTStream <HTStream@noreply.github.com>
Cc: Matt Settles <mattsettles@gmail.com>, Author <author@noreply.github.com>
Subject: Re: [ibest/HTStream] New issues with install (#60)
I agree, make should build all the binaries in the build dir (the default behavior of cmake), make install should not install the test binaries. Does make test currently not work?
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pr to fix install issues: https://github.com/ibest/HTStream/pull/65
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I can run the test executables yes, but they didn’t run from make test, not sure why, nor how to check for wrong libraries. Also not ideal to run each test app ;)
Matt
From: Joe Angell <notifications@github.com>
Reply-To: ibest/HTStream <reply@reply.github.com>
Date: Monday, February 20, 2017 at 10:33 AM
To: ibest/HTStream <HTStream@noreply.github.com>
Cc: Matt Settles <mattsettles@gmail.com>, Author <author@noreply.github.com>
Subject: Re: [ibest/HTStream] New issues with install (#60)
pr to fix install issues: #65
make test works for me, your runtime is probably pulling in the wrong libraries or something. You can run the test executables directly to see why they are failing.
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`make test` runs each executable, that is the output you posted. I'm
suggesting you run the individual test to get more output on what is
failing.
…On Mon, Feb 20, 2017 at 11:14 AM, Matt Settles ***@***.***> wrote:
I can run the test executables yes, but they didn’t run from make test,
not sure why, nor how to check for wrong libraries. Also not ideal to run
each test app ;)
Matt
From: Joe Angell ***@***.***>
Reply-To: ibest/HTStream ***@***.***>
Date: Monday, February 20, 2017 at 10:33 AM
To: ibest/HTStream ***@***.***>
Cc: Matt Settles ***@***.***>, Author <
***@***.***>
Subject: Re: [ibest/HTStream] New issues with install (#60)
pr to fix install issues: #65
make test works for me, your runtime is probably pulling in the wrong
libraries or something. You can run the test executables directly to see
why they are failing.
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<https://github.com/ibest/HTStream/issues/60#issuecomment-281160750>, or mute
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fixed in #65 |
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FYI: shunter@zen:/bio/HTStream/build$ make test 100% tests passed, 0 tests failed out of 8 |
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So I checked all the individual test apps, and they all complete successfully, looks to me like none of them run with make test. I think this has to do with me redirecting install path to somewhere else and the test apps go along with it. It looks like ‘make test’ assumes the apps to be in the build? Sam are your executables in /bio/HTStream/build?
I just pulled down changes, Joe’s changes to CMakes, this time looks like executables are built under the build dir with ‘make’ and ‘make test’ works. Then ‘make install’ puts only the app executables (no test executables) to the right place.
So things seem to be fine now, but you may want to add ‘make install’ to the install documentations.
Matt
From: Sam Hunter <notifications@github.com>
Reply-To: ibest/HTStream <reply@reply.github.com>
Date: Monday, February 20, 2017 at 9:48 PM
To: ibest/HTStream <HTStream@noreply.github.com>
Cc: Matt Settles <mattsettles@gmail.com>, Author <author@noreply.github.com>
Subject: Re: [ibest/HTStream] New issues with install (#60)
FYI:
shunter@zen:/bio/HTStream/build$ make test
Running tests...
Test project /bio/HTStream/build
Start 1: test_common
1/8 Test #1: test_common ...................... Passed 0.01 sec
Start 2: test_superd
2/8 Test #2: test_superd ...................... Passed 0.01 sec
Start 3: test_polyATtrim
3/8 Test #3: test_polyATtrim .................. Passed 0.01 sec
Start 4: test_q_window_trim
4/8 Test #4: test_q_window_trim ............... Passed 0.01 sec
Start 5: test_cut_trim
5/8 Test #5: test_cut_trim .................... Passed 0.01 sec
Start 6: test_phix_remover
6/8 Test #6: test_phix_remover ................ Passed 0.01 sec
Start 7: test_overlapper
7/8 Test #7: test_overlapper .................. Passed 0.01 sec
Start 8: test_n_remover
8/8 Test #8: test_n_remover ................... Passed 0.00 sec
100% tests passed, 0 tests failed out of 8
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after loading module cmake/boost AND
cmake -DBOOST_ROOT=/software/boost/1.60/x86_64-linux-ubuntu14.04 -DCMAKE_BUILD_TYPE=Release -DBoost_NO_SYSTEM_PATHS=TRUE -DBoost_NO_BOOST_CMAKE=TRUE ..
[ 16%] Built target googletest
[ 18%] Linking CXX executable /usr/local/bin/hts_common_test
/usr/bin/ld: cannot open output file /usr/local/bin/hts_common_test: Permission denied
collect2: error: ld returned 1 exit status
make[2]: *** [/usr/local/bin/hts_common_test] Error 1
make[1]: *** [common/CMakeFiles/hts_common_test.dir/all] Error 2
make: *** [all] Error 2
Looks like its trying to reference /usr/local/bin which contains nothing I as a user I don't have access to write to
Matt
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