Lancet won't use cmake3, although it is required

Question

Lancet won't use cmake3, although it is required

jbsysadmin opened this issue 6 years ago · 4 comments

Greetings. Prior sucessful builds of lancet involved specifying PATH to a custom build of cmake3.
However, cmake does not build when we install 3.12.1-1.el7 by yum. (Specifically: yum install cmake3.x86_64)

When I try to compile this, I get error "CMake 3.0 or higher is required. You are running version 2.8.12.2"
What needs to happen so that your build process sees an in-OS cmake3 ? ( Yum installs that in universal PATH, /usr/bin/ccmake3.)

Note: the new compilation context is re-building this as an RPM. We have a directive to move away from non-RPM builds.

Answer 1 · 2018-10-10T15:21:16.000Z

Since specifying the path to cmake worked in the past. Can you specify the new path to the Yum cmake installation? Otherwise you could try creating a new "cmake" symlink to ccmake3. My guess is that the configure script looks for a "cmake" binary and cannot find it in the universal path.

Answer 2 · 2018-10-10T15:37:38.000Z

We may not create RPMS resulting in disruptive changes to main system items. Yum install of the distro package puts cmake3 in /usr/bin, same place as cmake (2.x) Lancet build worked in past because we built cmake from source, then pre-empted use of cmake 2.x with a PATH. That won’t be possible here, we need to work within the constraints of the provided cmake3. The lancet build instructions simply call for a “make.” I don’t see in MakeFile or that README a reference to cmake. I’m wondering what can be changed to reference /usr/bin/cmake3.

…

-John From: Giuseppe Narzisi <notifications@github.com> Sent: Wednesday, October 10, 2018 11:21 AM To: nygenome/lancet <lancet@noreply.github.com> Cc: Burns, W. J. <wjb2130@cumc.columbia.edu>; Author <author@noreply.github.com> Subject: Re: [nygenome/lancet] Lancet won't use cmake3, although it is required (#35) Since specifying the path to cmake worked in the past. Can you specify the new path to the Yum cmake installation? Otherwise you could try creating a new "cmake" symlink to ccmake3. My guess is that the configure script looks for a "cmake" binary and cannot find it in the universal path. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_nygenome_lancet_issues_35-23issuecomment-2D428615076&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=Lcm_WqJ_rUVrU3IQt7ALp57NrOU09lZVgNzJYrKHguE&m=j_uYcd0UjXb3vBzkToYe0ZsrewI-TYANTHcc_IC_omQ&s=vU6UhYSwUnMJbv9TDXLE-U18a7UIBTdvhs16abUxVAs&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AZsIo0xEL0-2DpBm7b-2DfXG7xwXbn2GjKoQks5ujhBtgaJpZM4XUAkO&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=Lcm_WqJ_rUVrU3IQt7ALp57NrOU09lZVgNzJYrKHguE&m=j_uYcd0UjXb3vBzkToYe0ZsrewI-TYANTHcc_IC_omQ&s=h07XEcXHDGWX9LmmrU4aJJwbSLoN-aigI9yKFddpQH0&e=>.

Answer 3 · 2018-10-10T15:43:46.000Z

Lancet specific source code does not require cmake for compilation. CMake is needed to compile the bamtools API which is included in the lancet distribution: https://github.com/pezmaster31/bamtools/wiki/Building-and-installing

I would recommend asking for support directly to the bamtools developers.

Answer 4 · 2018-10-10T16:22:44.000Z

I was looking at the wrong makefile, “lancet-master/src/Makefile.” Another file has an actual call to cmake, “lancet-master/Makefile” I’ll start from there. Systems admins may see the whole build proceess being under one product. The lancet build process fails because of a dependency requirement, but we contact the lancet support. Thanks for your time, -John From: Giuseppe Narzisi <notifications@github.com> Sent: Wednesday, October 10, 2018 11:44 AM To: nygenome/lancet <lancet@noreply.github.com> Cc: Burns, W. J. <wjb2130@cumc.columbia.edu>; Author <author@noreply.github.com> Subject: Re: [nygenome/lancet] Lancet won't use cmake3, although it is required (#35) Lancet specific source code does not require cmake for compilation. CMake is needed to compile the bamtools API which is included in the lancet distribution: https://github.com/pezmaster31/bamtools/wiki/Building-and-installing<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pezmaster31_bamtools_wiki_Building-2Dand-2Dinstalling&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=Lcm_WqJ_rUVrU3IQt7ALp57NrOU09lZVgNzJYrKHguE&m=3b6ZwK-S9yzGFScUaz9egctCZdYraHQ_LX_WIgqLWw0&s=qxApsZoUs5DXcYocgg4XVTPCIKdOPY7fNg0Tv-qrWt8&e=> I would recommend asking for support directly to the bamtools developers. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_nygenome_lancet_issues_35-23issuecomment-2D428623807&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=Lcm_WqJ_rUVrU3IQt7ALp57NrOU09lZVgNzJYrKHguE&m=3b6ZwK-S9yzGFScUaz9egctCZdYraHQ_LX_WIgqLWw0&s=olJYWiJSPBB_NMtlku4lJ0R2Z0Z1ySA75jQjvNmIzoY&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AZsIoznVcps6-5FUcFbavyvMAmPj9JEmm4ks5ujhWzgaJpZM4XUAkO&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=Lcm_WqJ_rUVrU3IQt7ALp57NrOU09lZVgNzJYrKHguE&m=3b6ZwK-S9yzGFScUaz9egctCZdYraHQ_LX_WIgqLWw0&s=MdWS5h-6ARerS_r6RjEPg_DQIgZFd2YQgLr-O_ITBTo&e=>.