Problem with /usr/local/include

[KirkGrubbs]

Hello,
I am very interested in using clustermerge, but unfortunately I am not that familiar with bazel. As such I'm not sure if this is a bazel issue or clustermerge issue. But after beating my head against the wall for a few days I figured I'd ask to see if you had any incite on this issue. At any rate, every time I try to install clustermerge I get the following:

[easybuild@by0ox3] clustermerge-master $ bazel build -c dbg src:clustermerge --verbose_failures
DEBUG: Rule 'com_google_absl' indicated that a canonical reproducible form can be obtained by modifying arguments commit = "fcb104594b0bb4b8ac306cb2f55ecdad40974683", shallow_since = "1543960480 -0500" and dropping ["branch"]
DEBUG: Call stack for the definition of repository 'com_google_absl' which is a git_repository (rule definition at /home/easybuild/.cache/bazel/_bazel_easybuild/e153421d89851bce73d386ece21107a5/external/bazel_tools/tools/build_defs/repo/git.bzl:195:18):

• /gpfs/rtp/.filesets/biogrid_root/tools/eb/easyconfigs/custom/c/clustermerge/clustermerge-master/WORKSPACE:31:1
  INFO: Analyzed target //src:clustermerge (0 packages loaded, 0 targets configured).
  INFO: Found 1 target...
  ERROR: /gpfs/rtp/.filesets/biogrid_root/tools/eb/easyconfigs/custom/c/clustermerge/clustermerge-master/src/common/BUILD:38:1: The include path '/usr/local/include' references a path outside of the execution root.
  Target //src:clustermerge failed to build
  INFO: Elapsed time: 1.529s, Critical Path: 1.22s
  INFO: 0 processes.
  FAILED: Build did NOT complete successfully

[sbyma]

I'm somewhat new to Bazel as well and I have never encountered this issue. I don't know what "outside the execution root" is supposed to mean. Are you on a machine that doesn't use a standard Linux filesystem structure? Sorry, I'm really not sure what the solution is here.

[KirkGrubbs]

We are kicking around some possibilities. To that end I was wondering if you have root and/or super user privileges on your machines/cluster? Kirk Grubbs Bioinformatics Scientist II Mobile: +1 (984) 999-5999, Email: [email protected] Postal Address: BASF Corporation, Innovation Center, 3500 Paramount Parkway, 27560 Morrisville, United States [cid:[email protected]] From: Stuart <[email protected]> Sent: Friday, February 7, 2020 8:26 AM To: epfl-vlsc/clustermerge <[email protected]> Cc: Kirk Grubbs <[email protected]>; Author <[email protected]> Subject: Re: [epfl-vlsc/clustermerge] Problem with /usr/local/include (#13) I'm somewhat new to Bazel as well and I have never encountered this issue. I don't know what "outside the execution root" is supposed to mean. Are you on a machine that doesn't use a standard Linux filesystem structure? Sorry, I'm really not sure what the solution is here. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#13?email_source=notifications&email_token=AOO3ZQOG3A2IVNHZEIZQ3KTRBVOORA5CNFSM4KP4IW4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELC4V3A#issuecomment-583387884>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AOO3ZQINM6OLOMPRITZV6RTRBVOORANCNFSM4KP4IW4A>.

[KirkGrubbs]

Also, are there different instructions in a share drive environment? Kirk Grubbs Bioinformatics Scientist II Mobile: +1 (984) 999-5999, Email: [email protected] Postal Address: BASF Corporation, Innovation Center, 3500 Paramount Parkway, 27560 Morrisville, United States [cid:[email protected]] From: Stuart <[email protected]> Sent: Friday, February 7, 2020 8:26 AM To: epfl-vlsc/clustermerge <[email protected]> Cc: Kirk Grubbs <[email protected]>; Author <[email protected]> Subject: Re: [epfl-vlsc/clustermerge] Problem with /usr/local/include (#13) I'm somewhat new to Bazel as well and I have never encountered this issue. I don't know what "outside the execution root" is supposed to mean. Are you on a machine that doesn't use a standard Linux filesystem structure? Sorry, I'm really not sure what the solution is here. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#13?email_source=notifications&email_token=AOO3ZQOG3A2IVNHZEIZQ3KTRBVOORA5CNFSM4KP4IW4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELC4V3A#issuecomment-583387884>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AOO3ZQINM6OLOMPRITZV6RTRBVOORANCNFSM4KP4IW4A>.

[sbyma]

I don't use root or sudo to build clustermerge. It is definitely not required. However, I have never tried building it in a shared drive environment and this is probably the issue here. Bazel seems to have a problem with it for some reason. Perhaps look for similar issues or post on stack overflow or similar?