New issues with install about htstream HOT 12 CLOSED

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/
total 3.9M
drwxrwxr-x 2 msettles biocore 18 Feb 19 16:37 .
drwxrwxr-x 4 msettles biocore 4 Jan 3 15:25 ..
-rwxrwxr-x 1 msettles biocore 274K Feb 19 16:37 cut-trim
-rwxrwxr-x 1 msettles biocore 782K Feb 19 16:36 cut-trim_test
-rwxrwxr-x 1 msettles biocore 931K Feb 19 16:36 hts_common_test
-rwxrwxr-x 1 msettles biocore 270K Feb 19 16:37 n-remover
-rwxrwxr-x 1 msettles biocore 733K Feb 19 16:37 NRemover_test
-rwxrwxr-x 1 msettles biocore 315K Feb 19 16:37 overlapper
-rwxrwxr-x 1 msettles biocore 755K Feb 19 16:37 overlapper_test
-rwxrwxr-x 1 msettles biocore 283K Feb 19 16:37 phix-remover
-rwxrwxr-x 1 msettles biocore 714K Feb 19 16:37 phix_remover_test
-rwxrwxr-x 1 msettles biocore 274K Feb 19 16:36 polyAT-trim
-rwxrwxr-x 1 msettles biocore 792K Feb 19 16:36 polyATtrim_test
-rwxrwxr-x 1 msettles biocore 274K Feb 19 16:36 q-window-trim
-rwxrwxr-x 1 msettles biocore 791K Feb 19 16:36 q-window-trim_test
-rwxrwxr-x 1 msettles biocore 285K Feb 19 16:36 super-deduper
-rwxrwxr-x 1 msettles biocore 793K Feb 19 16:36 super-deduper_test
-rwxrwxr-x 1 msettles biocore 237K Feb 19 16:36 tab-converter

something tells me the process still isn't quite right

Matt

from htstream.

oh and then make test fails

from htstream.

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!

from htstream.

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?

from htstream.

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?

from htstream.

from htstream.

pr to fix install issues: https://github.com/ibest/HTStream/pull/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.

from htstream.

from htstream.

from htstream.

fixed in #65

from htstream.

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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from htstream.