[Bug 1979247] [NEW] plink segfault with LTO enabled

[Paride Legovini]

Public bug reported:

Steps to reproduce:

1. Build the package with LTO enabled
2. From the source tree run: `plink --file toy --freq`
   (this needs the toy.map which is part of the src package)
3. Check that it segfaults:

------------------------------------------------------------

PLINK v1.90b6.22 64-bit (3 Nov 2020)           www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to plink.log.
Options in effect:
  --file toy
  --freq


23918 MB RAM detected; reserving 11959 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (2 variants, 2 people).
--file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
written.
2 variants loaded from .bim file.
2 people (2 males, 0 females) loaded from .fam.
2 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 2 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.75.
Segmentation fault (core dumped)

------------------------------------------------------------

4. Add optimize=-lto to DEB_BUILD_MAINT_OPTION
5. Rebuild, test again, verify that it doesn't segfault.

This is also causing autopkgtest failures.

** Affects: lto-disabled-list (Ubuntu)
     Importance: Undecided
     Assignee: Paride Legovini (paride)
         Status: New

** Affects: plink1.9 (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: lto

** Also affects: lto-disabled-list (Ubuntu)
   Importance: Undecided
       Status: New

** Changed in: lto-disabled-list (Ubuntu)
     Assignee: (unassigned) => Paride Legovini (paride)

** Tags added: lto

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https://bugs.launchpad.net/bugs/1979247

Title:
  plink segfault with LTO enabled

Status in lto-disabled-list package in Ubuntu:
  New
Status in plink1.9 package in Ubuntu:
  New

Bug description:
  Steps to reproduce:

  1. Build the package with LTO enabled
  2. From the source tree run: `plink --file toy --freq`
     (this needs the toy.map which is part of the src package)
  3. Check that it segfaults:

  ------------------------------------------------------------

  PLINK v1.90b6.22 64-bit (3 Nov 2020)           www.cog-genomics.org/plink/1.9/
  (C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
  Logging to plink.log.
  Options in effect:
    --file toy
    --freq

  
  23918 MB RAM detected; reserving 11959 MB for main workspace.
  .ped scan complete (for binary autoconversion).
  Performing single-pass .bed write (2 variants, 2 people).
  --file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
  written.
  2 variants loaded from .bim file.
  2 people (2 males, 0 females) loaded from .fam.
  2 phenotype values loaded from .fam.
  Using 1 thread (no multithreaded calculations invoked).
  Before main variant filters, 2 founders and 0 nonfounders present.
  Calculating allele frequencies... done.
  Total genotyping rate is 0.75.
  Segmentation fault (core dumped)

  ------------------------------------------------------------

  4. Add optimize=-lto to DEB_BUILD_MAINT_OPTION
  5. Rebuild, test again, verify that it doesn't segfault.

  This is also causing autopkgtest failures.

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