COMP: Enable _FORTIFY_SOURCE in optimized builds

[gdevenyi]

The C library then checks the destination size of the string and memory
functions wherever the compiler can determine it, and aborts instead of
writing past the end. Level 3, which gcc 12+ and clang 15+ support, also
covers sizes only known at run time -- the strlen(x) + n shape this
library uses throughout its filename construction.

This is the low-churn way to get what upstream PR #24 is after. That PR
replaces every strcpy()/strcat() with strlcpy()/strlcat() for
-fbounds-safety compatibility; fortification checks the same calls
without editing any of them, and the two complement each other --
fortification catches a bad size at run time, strlcpy and
-fbounds-safety make the bound explicit at compile time.

The level is chosen by compiling a test rather than checking versions,
since both the compiler and the C library have to support it, and it is
applied only to optimised configurations because glibc warns if it is
defined without optimisation. NIFTI_ENABLE_FORTIFY_SOURCE=OFF disables
it.

---

Interface impact: none. On the union of all these changes, configured with USE_FSL_CODE=ON and USE_CIFTI_CODE=ON: all 448 exported symbols across libniftiio, libnifti2, libznz, libfslio, libnifticdf and libcifti are identical to master under nm -D --defined-only, and all ten installed headers are identical under gcc -E -P. Under gcc -dM -E one macro definition differs, intentionally and only in text: #61 makes FSL_RADIOLOGICAL read (-1) so it is safe inside an expression. Its value is still -1, checked by compiling against each installed fslio.h and printing it.

Verification. This branch: builds with gcc 16.1.1, ctest unchanged from master (2 of 345 fail on master itself in this environment; #31 and #29 each fix one). The union of all the PRs: 0 errors under both gcc 16.1.1 and clang 22.1.8, ctest 345/345 under each, and the whole suite under valgrind memcheck with --trace-children=yes gives 484 traced processes with no invalid access, no uninitialised value and no leak in any nifti binary.

Coordination. Every line of every branch was compared, whitespace-normalised, against the diffs of the open PRs (#11, #21, #22, #23, #24). Where one of those already changes a line, the line was left alone, and the few deliberate overlaps are named in the text above. What survives is 17 compiler warnings, all of them on those lines: 9 -Wsign-conversion (5 in fslio.c for #22, 2 in nifti2_io.c and 2 in nifti_tester001.c for #24) and 8 -Wcalloc-transposed-args in nifti_findhdrname and nifti_findimgname, which #11 rewrites. No formatting changes appear anywhere, to stay clear of #10 and #12.

One of a set of independent, single-purpose PRs. Each bases on master and can be merged on its own, in any order.

The full set of PRs (35)

The union of all of them is on the fork as all-changes, if you want to build and test the lot at once.

CI and build

• COMP: Show test output when the starter workflow fails #28 — COMP: Show test output when the starter workflow fails
• COMP: Give install_linking the source directory instead of guessing it #29 — COMP: Give install_linking the source directory instead of guessing it
• COMP: Guard the CMP0169 policy setting so older CMake still configures #30 — COMP: Guard the CMP0169 policy setting so older CMake still configures
• BUG: Compare NIfTI test output by content, not by compressed bytes #31 — BUG: Compare NIfTI test output by content, not by compressed bytes
• COMP: Make the 'Build and Test' analysis workflow run #57 — COMP: Make the 'Build and Test' analysis workflow run

Configuration and documentation

• ENH: Rework the clang-tidy configuration for C11 #32 — ENH: Rework the clang-tidy configuration for C11
• COMP: Add a shared compiler warning set #33 — COMP: Add a shared compiler warning set
• COMP: Enable _FORTIFY_SOURCE in optimized builds #34 — COMP: Enable _FORTIFY_SOURCE in optimised builds
• COMP: Build as ISO C11 with no compiler extensions #38 — COMP: Build as ISO C11 with no compiler extensions
• DOC: Describe the CMake build and how to run the memory checks #58 — DOC: Describe the CMake build and how to run the memory checks
• COMP: Add CI jobs for clang-tidy and for building with -Werror #59 — COMP: Add CI jobs for clang-tidy and for building with -Werror

Defects

• BUG: Fix cdfbin's argument range check, which could never fire #39 — BUG: Fix cdfbin's argument range check, which could never fire
• BUG: Fix an out-of-bounds indirect call in axio_show_mim_summary #40 — BUG: Fix an out-of-bounds indirect call in axio_show_mim_summary
• BUG: Bound the formatted write in znzprintf, and end the va_list on failure #41 — BUG: Bound the formatted write in znzprintf, and end the va_list on failure
• BUG: Report XML read errors instead of treating them as end of input #42 — BUG: Report XML read errors instead of treating them as end of input
• BUG: Stop returning -1 from functions that return size_t #43 — BUG: Stop returning -1 from functions that return size_t
• BUG: Fix the ambiguous-filename path in nifti_findhdrname #54 — BUG: Stop the library calling exit(), and fix the defects beside it
• BUG: Check the allocations whose result is used immediately #55 — BUG: Check the allocations whose result is used immediately
• BUG: Fix cifti_tool's CIFTI extension search, which never advanced #56 — BUG: Fix cifti_tool's CIFTI extension search, which never advanced
• BUG: Free the extension data when nifti_add_extension fails #62 — BUG: Free the extension data when nifti_add_extension fails
• BUG: Free the header on nifti_tool's duplicate-file failure paths #60 — BUG: Free the header on nifti_tool's duplicate-file failure paths
• BUG: Use memcpy instead of casting to over-aligned pointer types #44 — BUG: Use memcpy instead of casting to over-aligned pointer types
• BUG: Stop casting away const in fslio and cifti #45 — BUG: Stop casting away const in fslio and cifti
• BUG: Bound the aux_file copy by sizeof rather than a repeated 24 #46 — BUG: Bound the aux_file copy by sizeof rather than a repeated 24
• ENH: Make the 64-to-32 bit truncations explicit #52 — BUG: Fix 64-to-32 bit truncations, including a real overflow in fslio
• BUG: Fix signed/unsigned comparisons in the nifti tools #51 — BUG: Fix signed/unsigned comparisons in the nifti tools

Warning and check classes

• STYLE: Add the missing newline at end of nifti1_tool.h #35 — STYLE: Add the missing newline at end of nifti1_tool.h
• ENH: Give the cifti tools' gopt internal linkage #36 — ENH: Give the cifti tools' gopt internal linkage
• COMP: Declare the exported functions that no header declares #37 — COMP: Declare the exported functions that no header declares
• BUG: Give i and j a defined value in nifti_mat44_to_orientation #47 — BUG: Give i and j a defined value in nifti_mat44_to_orientation
• ENH: Zero-initialize the matrix locals clang cannot prove are filled #48 — ENH: Zero-initialise the matrix locals clang cannot prove are filled
• BUG: Give the statement macros a do/while(0) body and drop the stray semicolons #49 — BUG: Give the statement macros a do/while(0) body
• ENH: Pass calloc its arguments in the documented order #50 — ENH: Pass calloc its arguments in the documented order
• BUG: Parenthesize macro arguments and replacement lists #61 — BUG: Parenthesise macro arguments and replacement lists
• ENH: Make the implicit sign conversions explicit #53 — ENH: Make the implicit sign conversions explicit

[hjmjohnson]

Rebased onto current master (b4876bf) and pushed as 758c8a2. No test added: this is a compiler-flag change with no runtime seam a ctest can observe.

Maintainer decision needed: _FORTIFY_SOURCE aborts the process on a violation. This repository has a standing rule that a library must not kill its host — a fortification abort inside libniftiio takes down whatever application linked it, with no chance to return an error. As written the flag is added with add_compile_options(), so it applies to this build only and is not exported to consumers via usage requirements, which keeps the blast radius to binaries built from this tree. Worth deciding explicitly whether the default should stay ON for the installed library build, or whether hardening of this kind belongs only in the test/CI configurations.

What changed in this update

• Rebased onto master; one conflict in CMakeLists.txt, resolved on the merits — master added include(nifti_warnings) on the same line this PR adds include(nifti_hardening), and both belong.
• Commit message: dropped the Co-Authored-By: naming an AI tool and the Claude-Session: URL; replaced the bare #24 cross-reference with words (this is a fork, so the number names a different PR here); trimmed the body to fit the 72-column/12-line convention.
• US English: optimised/optimisation/optimiser → optimized/optimization/optimizer, in both the commit message and cmake/nifti_hardening.cmake.
• Trimmed the 27-line comment banner at the head of cmake/nifti_hardening.cmake to 11 lines. The removed text argued against an alternative approach and restated the commit message; that belongs in this PR body, not in the source.

Build and test

Release, NIFTI_BUILD_APPLICATIONS=ON USE_NIFTI2_CODE=ON USE_CIFTI_CODE=ON USE_FSL_CODE=ON, Ninja, macOS/AppleClang:

-- Performing Test NIFTI_HAVE_FORTIFY_3 - Success
-- Using _FORTIFY_SOURCE=3 for optimized builds
...
100% tests passed, 0 tests failed out of 362

[seanm]

Don't think I'm a fan of this one either.

If someone wants to build a library with some compiler-specific options, they should just pass those in C_FLAGS when they build.

[seanm]

This is the low-churn way to get what upstream PR #24 is after.

I assume this is AI blather, but this is not true at all. #24 aims to remove those old functions because they just aren't supported with -fbound-safety at all.

_FORTIFY_SOURCE is indeed great, and running Ci with it would be nice, but I think that belongs in CI, not within the library itself.

[hjmjohnson]

I agree with @seanm. As part of CI, but not an implicit part of the library.

[gdevenyi]

Sure. I have discovered since then that most distros already inject these flags into their default builds anyways so much of this is actually redundant anyways.