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install-deps.pl fails to build libsodium with gcc 11.2.1 #1114

@DMRobertson

Description

@DMRobertson

Describe the bug
Unable to install sytest's perl dependencies following step 3 in README.md.

To Reproduce

  1. Clone sytest repo. Setup perl env vars as in the readme.
  2. ./install-deps.pl
  3. This fails when installing Alien::Sodium. There's a complaint when building libsodium about alignment.
make[3]: Entering directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/src/libsodium'

[...]

  CC       crypto_generichash/blake2/ref/libsodium_la-blake2b-compress-ref.lo
In file included from crypto_generichash/blake2/ref/blake2b-compress-ref.c:5:
crypto_generichash/blake2/ref/blake2.h:118:5: error: size of array element is not a multiple of its alignment
  118 |     blake2s_state S[8][1];
      |     ^~~~~~~~~~~~~
crypto_generichash/blake2/ref/blake2.h:119:5: error: size of array element is not a multiple of its alignment
  119 |     blake2s_state R[1];
      |     ^~~~~~~~~~~~~
crypto_generichash/blake2/ref/blake2.h:126:5: error: size of array element is not a multiple of its alignment
  126 |     blake2b_state S[4][1];
      |     ^~~~~~~~~~~~~
crypto_generichash/blake2/ref/blake2.h:127:5: error: size of array element is not a multiple of its alignment
  127 |     blake2b_state R[1];
      |     ^~~~~~~~~~~~~
make[3]: *** [Makefile:2284: crypto_generichash/blake2/ref/libsodium_la-blake2b-compress-ref.lo] Error 1
Gory details
dmr on titan in sytest on  develop via 🐪 v5.32.1 
2021-08-09 16:32:06 ✔  $ ./install-deps.pl 

**** install-deps.pl: Installing Alien::Sodium ****
CPAN: Storable loaded ok (v3.21)
Reading '/home/dmr/.local/share/.cpan/Metadata'
  Database was generated on Mon, 09 Aug 2021 14:41:03 GMT
CPAN: Digest::SHA loaded ok (v6.02)
CPAN: Compress::Zlib loaded ok (v2.102)
Checksum for /home/dmr/.local/share/.cpan/sources/authors/id/A/AJ/AJGB/Alien-Sodium-1.0.8.0.tar.gz ok
'YAML' not installed, will not store persistent state
CPAN: CPAN::Meta::Requirements loaded ok (v2.140)
CPAN: Parse::CPAN::Meta loaded ok (v2.150010)
CPAN: CPAN::Meta loaded ok (v2.150010)
CPAN: Module::Build loaded ok (v0.4231)
CPAN: Module::CoreList loaded ok (v5.20210620)
Configuring A/AJ/AJGB/Alien-Sodium-1.0.8.0.tar.gz with Build.PL
+ pkg-config --exists 'libsodium = 1.0.8' && pkg-config --modversion libsodium
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Alien-Sodium' version '1.0.8.0'
  AJGB/Alien-Sodium-1.0.8.0.tar.gz
  /usr/bin/perl Build.PL -- OK
Running Build for A/AJ/AJGB/Alien-Sodium-1.0.8.0.tar.gz
Building Alien-Sodium
+ pkg-config --exists 'libsodium = 1.0.8' && pkg-config --modversion libsodium
Downloading File: libsodium-1.0.8.tar.gz ... Done
Extracting Archive ... Done
Building library ... 
+ cd /home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8
+ ./configure --with-pic --prefix=/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/blib/lib/auto/share/dist/Alien-Sodium --with-pic
configure: loading site script /home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/config.site
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '1000' is supported by ustar format... yes
checking whether GID '1000' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for gcc option to accept ISO C99... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for __native_client__ defined... no
checking for _FORTIFY_SOURCE defined... yes
checking whether C compiler accepts -fvisibility=hidden... yes
checking whether C compiler accepts -fPIC... yes
checking whether the linker accepts -fPIC... yes
checking whether C compiler accepts -fPIE... yes
checking whether the linker accepts -fPIE... yes
checking whether the linker accepts -pie... yes
checking whether C compiler accepts -fno-strict-aliasing... yes
checking whether C compiler accepts -fno-strict-overflow... yes
checking whether C compiler accepts -fstack-protector... yes
checking whether the linker accepts -fstack-protector... yes
checking whether C compiler accepts -Winit-self... yes
checking whether C compiler accepts -Wwrite-strings... yes
checking whether C compiler accepts -Wdiv-by-zero... yes
checking whether C compiler accepts -Wsometimes-uninitialized... no
checking whether C compiler accepts  -Wall... yes
checking whether C compiler accepts  -Wall -Wextra... yes
checking for clang... no
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2 -Wimplicit... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2 -Wimplicit -Wmissing-declarations... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2 -Wimplicit -Wmissing-declarations -Wmissing-prototypes... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2 -Wimplicit -Wmissing-declarations -Wmissing-prototypes -Wnormalized=id... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2 -Wimplicit -Wmissing-declarations -Wmissing-prototypes -Wnormalized=id -Woverride-init... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2 -Wimplicit -Wmissing-declarations -Wmissing-prototypes -Wnormalized=id -Woverride-init -Wparentheses... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2 -Wimplicit -Wmissing-declarations -Wmissing-prototypes -Wnormalized=id -Woverride-init -Wparentheses -Wpointer-arith... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2 -Wimplicit -Wmissing-declarations -Wmissing-prototypes -Wnormalized=id -Woverride-init -Wparentheses -Wpointer-arith -Wredundant-decls... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2 -Wimplicit -Wmissing-declarations -Wmissing-prototypes -Wnormalized=id -Woverride-init -Wparentheses -Wpointer-arith -Wredundant-decls -Wstrict-prototypes... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2 -Wimplicit -Wmissing-declarations -Wmissing-prototypes -Wnormalized=id -Woverride-init -Wparentheses -Wpointer-arith -Wredundant-decls -Wstrict-prototypes -Wswitch-enum... yes
checking whether C compiler accepts  -Wall -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat=2 -Wimplicit -Wmissing-declarations -Wmissing-prototypes -Wnormalized=id -Woverride-init -Wparentheses -Wpointer-arith -Wredundant-decls -Wstrict-prototypes -Wswitch-enum -Wvariable-decl... no
checking whether the linker accepts -Wl,-z,relro... yes
checking whether the linker accepts -Wl,-z,now... yes
checking whether the linker accepts -Wl,-z,noexecstack... yes
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for ar... (cached) ar
checking for MMX instructions set... checking whether C compiler accepts -mmmx... yes
yes
checking whether C compiler accepts -mmmx... (cached) yes
checking for SSE2 instructions set... checking whether C compiler accepts -msse2... yes
yes
checking whether C compiler accepts -msse2... (cached) yes
checking whether C compiler accepts -msse3... yes
checking for SSE3 instructions set... yes
checking whether C compiler accepts -msse3... (cached) yes
checking whether C compiler accepts -mssse3... yes
checking for SSSE3 instructions set... yes
checking whether C compiler accepts -mssse3... (cached) yes
checking whether C compiler accepts -msse4.1... yes
checking for SSE4.1 instructions set... yes
checking whether C compiler accepts -msse4.1... (cached) yes
checking whether C compiler accepts -mavx... yes
checking for AVX instructions set... yes
checking whether C compiler accepts -mavx... (cached) yes
checking whether C compiler accepts -maes... yes
checking whether C compiler accepts -mpclmul... yes
checking for AESNI instructions set and PCLMULQDQ... yes
checking whether C compiler accepts -maes... (cached) yes
checking whether C compiler accepts -mpclmul... (cached) yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking for inline... inline
checking whether byte ordering is bigendian... no
checking whether __STDC_LIMIT_MACROS is required... no
checking whether we can use x86_64 asm code... yes
checking whether we can assemble AVX opcodes... yes
checking for 128-bit arithmetic... yes
checking for cpuid instruction... yes
checking if weak symbols are supported... yes
checking if data alignment is required... no
checking for arc4random... no
checking for arc4random_buf... no
checking for mmap... yes
checking for mlock... yes
checking for madvise... yes
checking for mprotect... yes
checking for explicit_bzero... yes
checking for posix_memalign... yes
checking for getpid... yes
checking if gcc/ld supports -Wl,--output-def... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating dist-build/Makefile
config.status: creating libsodium.pc
config.status: creating libsodium-uninstalled.pc
config.status: creating msvc-scripts/Makefile
config.status: creating src/Makefile
config.status: creating src/libsodium/Makefile
config.status: creating src/libsodium/include/Makefile
config.status: creating src/libsodium/include/sodium/version.h
config.status: creating test/default/Makefile
config.status: creating test/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands
+ make
Making all in dist-build
make[1]: Entering directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/dist-build'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/dist-build'
Making all in msvc-scripts
make[1]: Entering directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/msvc-scripts'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/msvc-scripts'
Making all in src
make[1]: Entering directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/src'
Making all in libsodium
make[2]: Entering directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/src/libsodium'
Making all in include
make[3]: Entering directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/src/libsodium/include'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/src/libsodium/include'
make[3]: Entering directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/src/libsodium'
  CC       crypto_aead/chacha20poly1305/sodium/libsodium_la-aead_chacha20poly1305.lo
  CC       crypto_auth/libsodium_la-crypto_auth.lo
  CC       crypto_auth/hmacsha256/libsodium_la-auth_hmacsha256_api.lo
  CC       crypto_auth/hmacsha256/cp/libsodium_la-hmac_hmacsha256.lo
  CC       crypto_auth/hmacsha256/cp/libsodium_la-verify_hmacsha256.lo
  CC       crypto_auth/hmacsha512/libsodium_la-auth_hmacsha512_api.lo
  CC       crypto_auth/hmacsha512/cp/libsodium_la-hmac_hmacsha512.lo
  CC       crypto_auth/hmacsha512/cp/libsodium_la-verify_hmacsha512.lo
  CC       crypto_auth/hmacsha512256/libsodium_la-auth_hmacsha512256_api.lo
  CC       crypto_auth/hmacsha512256/cp/libsodium_la-hmac_hmacsha512256.lo
  CC       crypto_auth/hmacsha512256/cp/libsodium_la-verify_hmacsha512256.lo
  CC       crypto_box/libsodium_la-crypto_box.lo
  CC       crypto_box/libsodium_la-crypto_box_easy.lo
  CC       crypto_box/libsodium_la-crypto_box_seal.lo
  CC       crypto_box/curve25519xsalsa20poly1305/libsodium_la-box_curve25519xsalsa20poly1305_api.lo
  CC       crypto_box/curve25519xsalsa20poly1305/ref/libsodium_la-after_curve25519xsalsa20poly1305.lo
  CC       crypto_box/curve25519xsalsa20poly1305/ref/libsodium_la-before_curve25519xsalsa20poly1305.lo
  CC       crypto_box/curve25519xsalsa20poly1305/ref/libsodium_la-box_curve25519xsalsa20poly1305.lo
  CC       crypto_box/curve25519xsalsa20poly1305/ref/libsodium_la-keypair_curve25519xsalsa20poly1305.lo
  CC       crypto_core/curve25519/ref10/libsodium_la-curve25519_ref10.lo
  CC       crypto_core/hsalsa20/ref2/libsodium_la-core_hsalsa20.lo
  CC       crypto_core/hsalsa20/libsodium_la-core_hsalsa20_api.lo
  CC       crypto_core/salsa20/ref/libsodium_la-core_salsa20.lo
  CC       crypto_core/salsa20/libsodium_la-core_salsa20_api.lo
  CC       crypto_generichash/libsodium_la-crypto_generichash.lo
  CC       crypto_generichash/blake2/libsodium_la-generichash_blake2_api.lo
  CC       crypto_generichash/blake2/ref/libsodium_la-blake2b-compress-ref.lo
In file included from crypto_generichash/blake2/ref/blake2b-compress-ref.c:5:
crypto_generichash/blake2/ref/blake2.h:118:5: error: size of array element is not a multiple of its alignment
  118 |     blake2s_state S[8][1];
      |     ^~~~~~~~~~~~~
crypto_generichash/blake2/ref/blake2.h:119:5: error: size of array element is not a multiple of its alignment
  119 |     blake2s_state R[1];
      |     ^~~~~~~~~~~~~
crypto_generichash/blake2/ref/blake2.h:126:5: error: size of array element is not a multiple of its alignment
  126 |     blake2b_state S[4][1];
      |     ^~~~~~~~~~~~~
crypto_generichash/blake2/ref/blake2.h:127:5: error: size of array element is not a multiple of its alignment
  127 |     blake2b_state R[1];
      |     ^~~~~~~~~~~~~
make[3]: *** [Makefile:2284: crypto_generichash/blake2/ref/libsodium_la-blake2b-compress-ref.lo] Error 1
make[3]: Leaving directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/src/libsodium'
make[2]: *** [Makefile:2967: all-recursive] Error 1
make[2]: Leaving directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/src/libsodium'
make[1]: Leaving directory '/home/dmr/.local/share/.cpan/build/Alien-Sodium-1.0.8.0-2/_alien/libsodium-1.0.8/src'
make[1]: *** [Makefile:377: all-recursive] Error 1
make: *** [Makefile:491: all-recursive] Error 1
External command (make) failed! Error: 512
 at ./Build line 64.
Failed
Build not completed at ./Build line 64.
  AJGB/Alien-Sodium-1.0.8.0.tar.gz
  ./Build -- NOT OK
Stopping: 'install' failed for 'A/AJ/AJGB/Alien-Sodium-1.0.8.0.tar.gz'.
Failed to import Alien::Sodium even after installing: unable to import Alien::Sodium: Can't locate Alien/Sodium.pm in @INC (you may need to install the Alien::Sodium module) (@INC contains: /home/dmr/lib/perl5/x86_64-linux-thread-multi /home/dmr/lib/perl5 /usr/local/lib64/perl5/5.32 /usr/local/share/perl5/5.32 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5).
BEGIN failed--compilation aborted.

Expected behavior
Successful installation.

Desktop (please complete the following information):

  • OS: Fedora 34
  • CC: gcc (GCC) 11.2.1 20210728 (Red Hat 11.2.1-1)

Additional context
Discussed in various places:

GCC's behaviour apparently changed with https://gcc.gnu.org/git/?p=gcc.git;a=commitdiff;h=50bc94898fac1bd9cc1dabf227208fb5d369c4c4

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