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Adapting to gcc 15 #767

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jennybc opened this issue Feb 25, 2025 · 4 comments
Open

Adapting to gcc 15 #767

jennybc opened this issue Feb 25, 2025 · 4 comments
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upkeep maintenance, infrastructure, and similar

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@jennybc
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jennybc commented Feb 25, 2025

From CRAN's gcc 15 results:

* installing *source* package ‘readxl’ ...
** this is package ‘readxl’ version ‘1.4.3’
** package ‘readxl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (GCC) 15.0.1 20250223 (experimental)’
using C++ compiler: ‘g++-15 (GCC) 15.0.1 20250223 (experimental)’
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-gcc15/readxl/src'
g++-15 -std=gnu++17 -I"/data/gannet/ripley/R/gcc15/include" -DNDEBUG -Iunix -I. -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/progress/include' -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c cpp11.cpp -o cpp11.o
g++-15 -std=gnu++17 -I"/data/gannet/ripley/R/gcc15/include" -DNDEBUG -Iunix -I. -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/progress/include' -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c XlsWorkBook.cpp -o XlsWorkBook.o
In file included from ./libxls/xlstypes.h:44,
                 from libxls/xls.h:42,
                 from ColSpec.h:6,
                 from XlsWorkBook.h:3,
                 from XlsWorkBook.cpp:1:
/usr/local/gcc15/include/c++/15.0.1/cstdint:58:11: error: 'int_fast8_t' has not been declared in '::'
   58 |   using ::int_fast8_t;
      |           ^~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:59:11: error: 'int_fast16_t' has not been declared in '::'
   59 |   using ::int_fast16_t;
      |           ^~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:60:11: error: 'int_fast32_t' has not been declared in '::'
   60 |   using ::int_fast32_t;
      |           ^~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:61:11: error: 'int_fast64_t' has not been declared in '::'
   61 |   using ::int_fast64_t;
      |           ^~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:63:11: error: 'int_least8_t' has not been declared in '::'
   63 |   using ::int_least8_t;
      |           ^~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:64:11: error: 'int_least16_t' has not been declared in '::'
   64 |   using ::int_least16_t;
      |           ^~~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:65:11: error: 'int_least32_t' has not been declared in '::'
   65 |   using ::int_least32_t;
      |           ^~~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:66:11: error: 'int_least64_t' has not been declared in '::'
   66 |   using ::int_least64_t;
      |           ^~~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:68:11: error: 'intmax_t' has not been declared in '::'
   68 |   using ::intmax_t;
      |           ^~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:69:11: error: 'intptr_t' has not been declared in '::'
   69 |   using ::intptr_t;
      |           ^~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:71:11: error: 'uint8_t' has not been declared in '::'
   71 |   using ::uint8_t;
      |           ^~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:72:11: error: 'uint16_t' has not been declared in '::'
   72 |   using ::uint16_t;
      |           ^~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:73:11: error: 'uint32_t' has not been declared in '::'
   73 |   using ::uint32_t;
      |           ^~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:74:11: error: 'uint64_t' has not been declared in '::'
   74 |   using ::uint64_t;
      |           ^~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:76:11: error: 'uint_fast8_t' has not been declared in '::'
   76 |   using ::uint_fast8_t;
      |           ^~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:77:11: error: 'uint_fast16_t' has not been declared in '::'
   77 |   using ::uint_fast16_t;
      |           ^~~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:78:11: error: 'uint_fast32_t' has not been declared in '::'
   78 |   using ::uint_fast32_t;
      |           ^~~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:79:11: error: 'uint_fast64_t' has not been declared in '::'
   79 |   using ::uint_fast64_t;
      |           ^~~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:81:11: error: 'uint_least8_t' has not been declared in '::'
   81 |   using ::uint_least8_t;
      |           ^~~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:82:11: error: 'uint_least16_t' has not been declared in '::'
   82 |   using ::uint_least16_t;
      |           ^~~~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:83:11: error: 'uint_least32_t' has not been declared in '::'
   83 |   using ::uint_least32_t;
      |           ^~~~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:84:11: error: 'uint_least64_t' has not been declared in '::'
   84 |   using ::uint_least64_t;
      |           ^~~~~~~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:86:11: error: 'uintmax_t' has not been declared in '::'
   86 |   using ::uintmax_t;
      |           ^~~~~~~~~
/usr/local/gcc15/include/c++/15.0.1/cstdint:87:11: error: 'uintptr_t' has not been declared in '::'
   87 |   using ::uintptr_t;
      |           ^~~~~~~~~
make[2]: *** [/data/gannet/ripley/R/gcc15/etc/Makeconf:208: XlsWorkBook.o] Error 1
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-gcc15/readxl/src'
ERROR: compilation failed for package ‘readxl’
* removing ‘/data/gannet/ripley/R/packages/tests-strict/Libs/readxl-lib/readxl’
Command exited with non-zero status 1
Time 0:07.66, 6.83 + 0.71

I have a similar report via email from @eddelbuettel in his role as Debian maintainer.

The issue appears to be header changes, described in the Porting to GCC 15 guide:

Some C++ Standard Library headers have been changed to no longer include other headers that were being used internally by the library. As such, C++ programs that used standard library components without including the right headers will no longer compile.

In particular, the following headers are used less widely within libstdc++ and may need to be included explicitly when compiling with GCC 15:

  • <stdint.h> (for int8_t, int32_t etc.) and <cstdint> (for std::int8_t, std::int32_t etc.)
  • <ostream> (for std::endl, std::flush etc.)
@jennybc jennybc added the upkeep maintenance, infrastructure, and similar label Feb 25, 2025
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jennybc commented Feb 25, 2025

This doesn't appear to be a simple lack of use of <cstdint>, because I am already including it. All the errors seem to be related to this #ifdef _GLIBCXX_USE_C99_STDINT block:

https://github.com/gcc-mirror/gcc/blob/fffe14f045df597bf5ab50730eebe0977eea7090/libstdc%2B%2B-v3/include/c_global/cstdint#L52

@jennybc jennybc mentioned this issue Feb 25, 2025
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jennybc commented Feb 25, 2025 •
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From the debian log:

DC-Build-Header: r-cran-readxl 1.4.3-1 / 2025-02-16 03:22:22 +0000
DC-Task: type:rebuild-binarch-only source:r-cran-readxl version:1.4.3-1 chroot:unstable esttime:81 logfile:/tmp/r-cran-readxl_1.4.3-1_unstable_gccexp.log modes:gcc-exp:binarch-only
DC-System-Info: 8 cores (Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz), 32516492 kB RAM
DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/gcc-exp r-cran-readxl_1.4.3-1'
sbuild (Debian sbuild) 0.88.1~bpo12+1 (29 December 2024) on ip-10-84-234-117

+==============================================================================+
| r-cran-readxl 1.4.3-1 (amd64)                Sun, 16 Feb 2025 03:22:22 +0000 |
+==============================================================================+

Package: r-cran-readxl
Version: 1.4.3-1
Source Version: 1.4.3-1
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: binary

I: Unpacking /home/user42/.cache/sbuild/unstable-amd64.tar.gz to /tmp/tmp.sbuild.NMQHBUeXeo...
I: Setting up the chroot...
I: Creating chroot session...
I: Setting up log color...

(... JENNYBRYAN deleted lots of output ...)


User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=user42
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=user42

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -us -uc -b
dpkg-buildpackage: info: source package r-cran-readxl
dpkg-buildpackage: info: source version 1.4.3-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Dirk Eddelbuettel <[email protected]>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --buildsystem R
   dh_auto_clean -O--buildsystem=R
   dh_autoreconf_clean -O--buildsystem=R
   dh_clean -O--buildsystem=R
 debian/rules binary
dh binary --buildsystem R
   dh_update_autotools_config -O--buildsystem=R
   dh_autoreconf -O--buildsystem=R
   dh_auto_configure -O--buildsystem=R
   dh_auto_build -O--buildsystem=R
   dh_auto_test -O--buildsystem=R
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=R
   dh_prep -O--buildsystem=R
   dh_auto_install --destdir=debian/r-cran-readxl/ -O--buildsystem=R
I: R Package: readxl Version: 1.4.3
I: Building using R version 4.4.2-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 07 Jul 2023 11:54:50 -0500
	mkdir -p /build/reproducible-path/r-cran-readxl-1.4.3/debian/r-cran-readxl/usr/lib/R/site-library
	R CMD INSTALL -l /build/reproducible-path/r-cran-readxl-1.4.3/debian/r-cran-readxl/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 07 Jul 2023 11:54:50 -0500'"
* installing *source* package ‘readxl’ ...
** package ‘readxl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Debian 15-20250213-1) 15.0.1 20250213 (experimental) [master r15-7502-g26baa2c09b3]’
using C++ compiler: ‘g++ (Debian 15-20250213-1) 15.0.1 20250213 (experimental) [master r15-7502-g26baa2c09b3]’
make[1]: Entering directory '/build/reproducible-path/r-cran-readxl-1.4.3/src'
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/usr/lib/R/site-library/cpp11/include' -I'/usr/lib/R/site-library/progress/include'    -fvisibility=hidden -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/usr/lib/R/site-library/cpp11/include' -I'/usr/lib/R/site-library/progress/include'    -fvisibility=hidden -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c XlsWorkBook.cpp -o XlsWorkBook.o
In file included from ./libxls/xlstypes.h:44,
                 from libxls/xls.h:42,
                 from ColSpec.h:6,
                 from XlsWorkBook.h:3,
                 from XlsWorkBook.cpp:1:
/usr/include/c++/15/cstdint:58:11: error: ‘int_fast8_t’ has not been declared in ‘::’
   58 |   using ::int_fast8_t;
      |           ^~~~~~~~~~~
/usr/include/c++/15/cstdint:59:11: error: ‘int_fast16_t’ has not been declared in ‘::’
   59 |   using ::int_fast16_t;
      |           ^~~~~~~~~~~~
/usr/include/c++/15/cstdint:60:11: error: ‘int_fast32_t’ has not been declared in ‘::’
   60 |   using ::int_fast32_t;
      |           ^~~~~~~~~~~~
/usr/include/c++/15/cstdint:61:11: error: ‘int_fast64_t’ has not been declared in ‘::’
   61 |   using ::int_fast64_t;
      |           ^~~~~~~~~~~~
/usr/include/c++/15/cstdint:63:11: error: ‘int_least8_t’ has not been declared in ‘::’
   63 |   using ::int_least8_t;
      |           ^~~~~~~~~~~~
/usr/include/c++/15/cstdint:64:11: error: ‘int_least16_t’ has not been declared in ‘::’
   64 |   using ::int_least16_t;
      |           ^~~~~~~~~~~~~
/usr/include/c++/15/cstdint:65:11: error: ‘int_least32_t’ has not been declared in ‘::’
   65 |   using ::int_least32_t;
      |           ^~~~~~~~~~~~~
/usr/include/c++/15/cstdint:66:11: error: ‘int_least64_t’ has not been declared in ‘::’
   66 |   using ::int_least64_t;
      |           ^~~~~~~~~~~~~
/usr/include/c++/15/cstdint:68:11: error: ‘intmax_t’ has not been declared in ‘::’
   68 |   using ::intmax_t;
      |           ^~~~~~~~
/usr/include/c++/15/cstdint:69:11: error: ‘intptr_t’ has not been declared in ‘::’
   69 |   using ::intptr_t;
      |           ^~~~~~~~
/usr/include/c++/15/cstdint:71:11: error: ‘uint8_t’ has not been declared in ‘::’
   71 |   using ::uint8_t;
      |           ^~~~~~~
/usr/include/c++/15/cstdint:72:11: error: ‘uint16_t’ has not been declared in ‘::’
   72 |   using ::uint16_t;
      |           ^~~~~~~~
/usr/include/c++/15/cstdint:73:11: error: ‘uint32_t’ has not been declared in ‘::’
   73 |   using ::uint32_t;
      |           ^~~~~~~~
/usr/include/c++/15/cstdint:74:11: error: ‘uint64_t’ has not been declared in ‘::’
   74 |   using ::uint64_t;
      |           ^~~~~~~~
/usr/include/c++/15/cstdint:76:11: error: ‘uint_fast8_t’ has not been declared in ‘::’
   76 |   using ::uint_fast8_t;
      |           ^~~~~~~~~~~~
/usr/include/c++/15/cstdint:77:11: error: ‘uint_fast16_t’ has not been declared in ‘::’
   77 |   using ::uint_fast16_t;
      |           ^~~~~~~~~~~~~
/usr/include/c++/15/cstdint:78:11: error: ‘uint_fast32_t’ has not been declared in ‘::’
   78 |   using ::uint_fast32_t;
      |           ^~~~~~~~~~~~~
/usr/include/c++/15/cstdint:79:11: error: ‘uint_fast64_t’ has not been declared in ‘::’
   79 |   using ::uint_fast64_t;
      |           ^~~~~~~~~~~~~
/usr/include/c++/15/cstdint:81:11: error: ‘uint_least8_t’ has not been declared in ‘::’
   81 |   using ::uint_least8_t;
      |           ^~~~~~~~~~~~~
/usr/include/c++/15/cstdint:82:11: error: ‘uint_least16_t’ has not been declared in ‘::’
   82 |   using ::uint_least16_t;
      |           ^~~~~~~~~~~~~~
/usr/include/c++/15/cstdint:83:11: error: ‘uint_least32_t’ has not been declared in ‘::’
   83 |   using ::uint_least32_t;
      |           ^~~~~~~~~~~~~~
/usr/include/c++/15/cstdint:84:11: error: ‘uint_least64_t’ has not been declared in ‘::’
   84 |   using ::uint_least64_t;
      |           ^~~~~~~~~~~~~~
/usr/include/c++/15/cstdint:86:11: error: ‘uintmax_t’ has not been declared in ‘::’
   86 |   using ::uintmax_t;
      |           ^~~~~~~~~
/usr/include/c++/15/cstdint:87:11: error: ‘uintptr_t’ has not been declared in ‘::’
   87 |   using ::uintptr_t;
      |           ^~~~~~~~~
make[1]: *** [/usr/lib/R/etc/Makeconf:204: XlsWorkBook.o] Error 1
make[1]: Leaving directory '/build/reproducible-path/r-cran-readxl-1.4.3/src'
make[1]: Entering directory '/build/reproducible-path/r-cran-readxl-1.4.3/src'
make[1]: Leaving directory '/build/reproducible-path/r-cran-readxl-1.4.3/src'
ERROR: compilation failed for package ‘readxl’
* removing ‘/build/reproducible-path/r-cran-readxl-1.4.3/debian/r-cran-readxl/usr/lib/R/site-library/readxl’
dh_auto_install: error: R CMD INSTALL -l /build/reproducible-path/r-cran-readxl-1.4.3/debian/r-cran-readxl/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 07 Jul 2023 11:54:50 -0500'" returned exit code 1
make: *** [debian/rules:7: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-02-16T03:23:33Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                      Sun, 16 Feb 2025 03:23:33 +0000 |
+------------------------------------------------------------------------------+

Purging /build/reproducible-path
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died with exit 2)

+------------------------------------------------------------------------------+
| Summary                                      Sun, 16 Feb 2025 03:23:34 +0000 |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Type: binary
Build-Space: 4720
Build-Time: 7
Distribution: unstable
Fail-Stage: build
Host Architecture: amd64
Install-Time: 38
Job: r-cran-readxl_1.4.3-1
Machine Architecture: amd64
Package: r-cran-readxl
Package-Time: 71
Source-Version: 1.4.3-1
Space: 4720
Status: attempted
Version: 1.4.3-1
--------------------------------------------------------------------------------
Finished at 2025-02-16T03:23:33Z
Build needed 00:01:11, 4720k disk space
E: Build failure (dpkg-buildpackage died with exit 2)
DC-Status: Failed 72.519312051s

jennybc added a commit that referenced this issue Feb 25, 2025
@jennybc
Reapply a diff in libxls 1.6.3
9e02842 
I should not have reversed this when I applied our "usual patches" to libxls. This was a real and desirable change.

Addresses (I hope) #767

See libxls/libxls#118, libxls/libxls#127, libxls/libxls#125.
@jennybc
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jennybc commented Feb 25, 2025

I don't have a great way to quickly prove that this is fixed, so I'll leave this open until some proof rolls in. But I am hopeful.

@eddelbuettel
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eddelbuettel commented Feb 26, 2025 •
edited
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If you start from a Debian-based container (such as the rocker/r-base aka r-base I stand behind) then you can get gcc-15 and friends from the 'experimental' flavour you can opt-in.

If you start from an Ubuntu-based container (such as rocker/r2u:noble that I stand behind) then you can opt-into the newer 25.04 pre-release that also has gcc-15 and friends. That is usually easy: you don't need to update the whole container, it will just pick and choose what is needed. And in a container you risk little relative to your outer system, and it is quicker than firing up a VM or alike.

I am sure there are other containers too that are suitable because people also tried to match what Brian Ripley uses on Fedora. I personally get by with the ones I look after so I am less au courant relative to the Fedora-based approaches but they also exist.

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