Windows 11 "Looking for compiler [clang++]: not found"

[SueKim]

Hello, I am trying to install and run mrtrix3 on my computer (Windows 11) and I am getting stuck on the build stage where you run ./configure

This is the error I receive:

MRtrix build type requested: debug version with asserts, nooptim


Detecting OS: windows
Looking for compiler [g++]: g++.exe (Rev8, Built by MSYS2 project) 15.2.0
Checking for C++11 compliance: test failed (see configure.log for details)

Looking for compiler [clang++]: not found

ERROR: no suitable compiler found!



  Set the CXX environment variable to inform 'configure' of the path to the
  compiler on your system, as follows:
    $ export CXX=/usr/bin/g++-5.5
    $./configure
  (amend with the actual path to the compiler on your system)

  If you are using a compiler other than gcc or clang, you can also set the CXX_ARGS
  environment variable to specify how your compiler expects different arguments
  to be presented on the command line, for instance as follows:
    $ export CXX_ARGS="-c CFLAGS SRC -o OBJECT"
    $ ./configure


  See the file 'configure.log' for details. If this doesn't help and you need
  further assistance, please post on the MRtrix3 community forum
  (http://community.mrtrix.org/), and make sure to include the full contents of
  the 'configure.log' file.

I can’t seem to find ‘MinGW-w64 Win64 Shell’ as indicated in the documentation, so I am running the code on MSYS2 MINGW64 as administrator. Furthermore, I cannot find a ‘configure.log’ file in the \mrtrix3 directory, only the original configure.file

I have run the pacman -Syuu code upwards to 6 times at this point.

Running pacman -Q results in this output:

base 2022.06-1
bash 5.2.037-2
bash-completion 2.16.0-1
brotli 1.1.0-2
bsdtar 3.8.1-1
bzip2 1.0.8-4
ca-certificates 20250419-1
coreutils 8.32-5
curl 8.16.0-1
dash 0.5.12-1
db 6.2.32-5
file 5.46-2
filesystem 2025.05.08-2
findutils 4.10.0-2
gawk 5.3.2-1
gcc-libs 15.2.0-1
gdbm 1.26-1
getent 2.18.90-5
gettext 0.22.5-1
git 2.51.0-1
gmp 6.3.0-2
gnupg 2.4.8-1
grep 1~3.0-7
gzip 1.14-1
heimdal 7.8.0-5
heimdal-libs 7.8.0-5
inetutils 2.6-1
info 7.2-2
less 679-1
libargp 20241207-1
libasprintf 0.22.5-1
libassuan 3.0.2-1
libbz2 1.0.8-4
libcbor 0.12.0-1
libcurl 8.16.0-1
libdb 6.2.32-5
libedit 20240808_3.1-1
libexpat 2.7.1-1
libffi 3.5.2-1
libfido2 1.16.0-1
libgcrypt 1.11.2-1
libgdbm 1.26-1
libgettextpo 0.22.5-1
libgnutls 3.8.10-1
libgpg-error 1.55-1
libhogweed 3.10.2-1
libiconv 1.18-1
libidn2 2.3.8-1
libintl 0.22.5-1
libksba 1.6.7-1
liblz4 1.10.0-1
liblzma 5.8.1-1
libnettle 3.10.2-1
libnghttp2 1.67.0-1
libnghttp3 1.11.0-1
libngtcp2 1.15.0-1
libnpth 1.8-1
libopenssl 3.5.2-1
libp11-kit 0.25.7-1
libpcre 8.45-5
libpcre2_8 10.46-1
libpsl 0.21.5-2
libreadline 8.3.001-1
libsqlite 3.50.4-1
libssh2 1.11.1-1
libtasn1 4.20.0-1
libunistring 1.3-1
libutil-linux 2.40.2-2
libxcrypt 4.4.38-1
libzstd 1.5.7-1
mingw-w64-ucrt-x86_64-binutils 2.45-2
mingw-w64-ucrt-x86_64-crt-git 13.0.0.r167.g2e31630bc-1
mingw-w64-ucrt-x86_64-gcc 15.2.0-8
mingw-w64-ucrt-x86_64-gcc-libs 15.2.0-8
mingw-w64-ucrt-x86_64-gettext-runtime 0.26-1
mingw-w64-ucrt-x86_64-gmp 6.3.0-2
mingw-w64-ucrt-x86_64-headers-git 13.0.0.r167.g2e31630bc-1
mingw-w64-ucrt-x86_64-isl 0.27-1
mingw-w64-ucrt-x86_64-libiconv 1.18-1
mingw-w64-ucrt-x86_64-libwinpthread 13.0.0.r167.g2e31630bc-1
mingw-w64-ucrt-x86_64-mpc 1.3.1-2
mingw-w64-ucrt-x86_64-mpfr 4.2.2-1
mingw-w64-ucrt-x86_64-tzdata 2025b-2
mingw-w64-ucrt-x86_64-windows-default-manifest 6.4-4
mingw-w64-ucrt-x86_64-winpthreads 13.0.0.r167.g2e31630bc-1
mingw-w64-ucrt-x86_64-zlib 1.3.1-1
mingw-w64-ucrt-x86_64-zstd 1.5.7-1
mingw-w64-x86_64-assimp 6.0.2-1
mingw-w64-x86_64-binutils 2.45-2
mingw-w64-x86_64-brotli 1.1.0-5
mingw-w64-x86_64-bzip2 1.0.8-3
mingw-w64-x86_64-crt-git 13.0.0.r167.g2e31630bc-1
mingw-w64-x86_64-dbus 1.16.2-3
mingw-w64-x86_64-double-conversion 3.3.1-3
mingw-w64-x86_64-eigen3 3.4.0-1
mingw-w64-x86_64-expat 2.7.1-2
mingw-w64-x86_64-fftw 3.3.10-5
mingw-w64-x86_64-fontconfig 2.17.1-1
mingw-w64-x86_64-freeglut 3.6.0-1
mingw-w64-x86_64-freetype 2.14.1-1
mingw-w64-x86_64-gcc 15.2.0-8
mingw-w64-x86_64-gcc-libs 15.2.0-8
mingw-w64-x86_64-gettext-runtime 0.26-1
mingw-w64-x86_64-giflib 5.2.2-1
mingw-w64-x86_64-glib2 2.86.0-1
mingw-w64-x86_64-gmp 6.3.0-2
mingw-w64-x86_64-graphite2 1.3.14-3
mingw-w64-x86_64-harfbuzz 11.5.0-1
mingw-w64-x86_64-headers-git 13.0.0.r167.g2e31630bc-1
mingw-w64-x86_64-icu 77.1-2
mingw-w64-x86_64-isl 0.27-1
mingw-w64-x86_64-jasper 4.2.8-1
mingw-w64-x86_64-jbigkit 2.1-5
mingw-w64-x86_64-lcms2 2.17-1
mingw-w64-x86_64-lerc 4.0.0-1
mingw-w64-x86_64-libdeflate 1.24-1
mingw-w64-x86_64-libffi 3.5.2-1
mingw-w64-x86_64-libiconv 1.18-1
mingw-w64-x86_64-libjpeg-turbo 3.1.2-1
mingw-w64-x86_64-libmng 2.0.3-7
mingw-w64-x86_64-libmysofa 1.3.1-1
mingw-w64-x86_64-libpng 1.6.50-1
mingw-w64-x86_64-libsystre 1.0.2-1
mingw-w64-x86_64-libtiff 4.7.0-1
mingw-w64-x86_64-libtre 0.9.0-1
mingw-w64-x86_64-libwebp 1.6.0-1
mingw-w64-x86_64-libwinpthread 13.0.0.r167.g2e31630bc-1
mingw-w64-x86_64-libxml2 2.14.6-1
mingw-w64-x86_64-libxslt 1.1.43-3
mingw-w64-x86_64-md4c 0.5.2-1
mingw-w64-x86_64-minizip 1.3.1-1
mingw-w64-x86_64-mpc 1.3.1-2
mingw-w64-x86_64-mpdecimal 4.0.1-1
mingw-w64-x86_64-mpfr 4.2.2-1
mingw-w64-x86_64-mrtrix3 3.0.7-1
mingw-w64-x86_64-ncurses 6.5.20241228-3
mingw-w64-x86_64-openal 1.24.3-2
mingw-w64-x86_64-openjpeg2 2.5.3-1
mingw-w64-x86_64-openssl 3.5.2-2
mingw-w64-x86_64-pcre2 10.46-1
mingw-w64-x86_64-python 3.12.11-3
mingw-w64-x86_64-python-packaging 25.0-1
mingw-w64-x86_64-qt5-3d 5.15.17-2
mingw-w64-x86_64-qt5-activeqt 5.15.17-1
mingw-w64-x86_64-qt5-base 5.15.17+kde+r122-1
mingw-w64-x86_64-qt5-charts 5.15.17-1
mingw-w64-x86_64-qt5-connectivity 5.15.17-1
mingw-w64-x86_64-qt5-datavis3d 5.15.17-1
mingw-w64-x86_64-qt5-declarative 5.15.17+kde+r21-1
mingw-w64-x86_64-qt5-doc 5.15.17-1
mingw-w64-x86_64-qt5-gamepad 5.15.17-1
mingw-w64-x86_64-qt5-graphicaleffects 5.15.17-1
mingw-w64-x86_64-qt5-imageformats 5.15.17-1
mingw-w64-x86_64-qt5-location 5.15.17+kde+r7-1
mingw-w64-x86_64-qt5-lottie 5.15.17-1
mingw-w64-x86_64-qt5-multimedia 5.15.17-1
mingw-w64-x86_64-qt5-networkauth 5.15.17-1
mingw-w64-x86_64-qt5-pdf 5.15.17-1
mingw-w64-x86_64-qt5-purchasing 5.15.17-1
mingw-w64-x86_64-qt5-quick3d 5.15.17-2
mingw-w64-x86_64-qt5-quickcontrols 5.15.17-1
mingw-w64-x86_64-qt5-quickcontrols2 5.15.17+kde+r5-1
mingw-w64-x86_64-qt5-quicktimeline 5.15.17-1
mingw-w64-x86_64-qt5-remoteobjects 5.15.17-1
mingw-w64-x86_64-qt5-script 5.15.17-1
mingw-w64-x86_64-qt5-scxml 5.15.17-1
mingw-w64-x86_64-qt5-sensors 5.15.17-1
mingw-w64-x86_64-qt5-serialbus 5.15.17-1
mingw-w64-x86_64-qt5-serialport 5.15.17-1
mingw-w64-x86_64-qt5-speech 5.15.17-1
mingw-w64-x86_64-qt5-svg 5.15.17+kde+r5-1
mingw-w64-x86_64-qt5-tools 5.15.17-2
mingw-w64-x86_64-qt5-translations 5.15.17-1
mingw-w64-x86_64-qt5-virtualkeyboard 5.15.17-1
mingw-w64-x86_64-qt5-webchannel 5.15.17+kde+r3-1
mingw-w64-x86_64-qt5-webglplugin 5.15.17-1
mingw-w64-x86_64-qt5-websockets 5.15.17+kde+r2-1
mingw-w64-x86_64-qt5-webview 5.15.17-1
mingw-w64-x86_64-qt5-winextras 5.15.17-1
mingw-w64-x86_64-qt5-xmlpatterns 5.15.17-1
mingw-w64-x86_64-readline 8.3.001-1
mingw-w64-x86_64-sqlite3 3.50.4-1
mingw-w64-x86_64-tcl 8.6.16-1
mingw-w64-x86_64-termcap 1.3.1-7
mingw-w64-x86_64-tk 8.6.16-1
mingw-w64-x86_64-tzdata 2025b-2
mingw-w64-x86_64-vulkan-loader 1~1.4.321.0-1
mingw-w64-x86_64-windows-default-manifest 6.4-4
mingw-w64-x86_64-wineditline 2.208-1
mingw-w64-x86_64-winpthreads 13.0.0.r167.g2e31630bc-1
mingw-w64-x86_64-xz 5.8.1-2
mingw-w64-x86_64-zlib 1.3.1-1
mingw-w64-x86_64-zstd 1.5.7-1
mintty 1~3.8.0-1
mpdecimal 4.0.1-1
mpfr 4.2.2-1
msys2-keyring 1~20250619-1
msys2-launcher 1.5-3
msys2-runtime 3.6.4-1
nano 8.6-1
ncurses 6.5.20240831-2
nettle 3.10.2-1
openssh 10.0p1-2
openssl 3.5.2-1
p11-kit 0.25.7-1
pacman 6.1.0-19
pacman-contrib 1.10.6-1
pacman-mirrors 20250607-1
perl 5.40.3-1
perl-Authen-SASL 2.1900-1
perl-Clone 0.47-2
perl-Convert-BinHex 1.125-2
perl-Encode-Locale 1.05-2
perl-Error 0.17030-1
perl-File-Listing 6.16-1
perl-HTML-Parser 3.83-2
perl-HTML-Tagset 3.24-1
perl-HTTP-Cookies 6.11-1
perl-HTTP-Daemon 6.16-1
perl-HTTP-Date 6.06-1
perl-HTTP-Message 7.00-1
perl-HTTP-Negotiate 6.01-3
perl-IO-HTML 1.004-2
perl-IO-Socket-SSL 2.094-1
perl-IO-Stringy 2.113-2
perl-LWP-MediaTypes 6.04-2
perl-MIME-tools 5.515-1
perl-MailTools 2.22-1
perl-Net-HTTP 6.23-1
perl-Net-SMTP-SSL 1.04-2
perl-Net-SSLeay 1.94-3
perl-TermReadKey 2.38-7
perl-TimeDate 2.33-2
perl-Try-Tiny 0.32-1
perl-URI 5.32-1
perl-WWW-RobotRules 6.02-3
perl-http-cookiejar 0.014-1
perl-libwww 6.80-1
pinentry 1.3.2-1
pkgconf 2.5.1-1
python 3.12.11-1
rebase 4.5.0-5
sed 4.9-1
tar 1.35-2
time 1.9-3
tzcode 2025b-1
util-linux 2.40.2-2
wget 1.25.0-1
which 2.23-4
xz 5.8.1-1
zlib 1.3.1-1
zstd 1.5.7-1

Any assistance would be greatly appreciated.

[rsmith]

Hi Sue,

The shortcuts ultimately just pass command-line flags to the shell command. So if for whatever reason you do not have the corresponding shortcut, you could try just making one.

On my Windows 11 system:

• The “MSYS2 MSYS” shortcut, which is not the one to use, invokes:
  msys2_shell.cmd -msys
• The “MSYS2 MinGW 64-bit” shortcut, which is the one to use, invokes:
  msys2_shell.cmd -mingw64

The information that should otherwise be visible within the configure script’s log file can probably be generated at the terminal by using the -verbose flag. I suspect the error won’t actually be anything esoteric about C++11 compliance as suggested by its output, but will be some more fundamental clash between libraries.

Regards
Rob

[SueKim]

Hi Rob, I’m not sure if I quite follow.

I believe I’m using the right shortcut (in administrator). This is the only one that pops up if I search for “mingw64”. All the others ones do not have the mingw64 name.

I ran ./configure -verbose and this was the output:

# ./configure -verbose

MRtrix build type requested: release version


PATH set to: /mingw64/bin:/usr/local/bin:/usr/bin:/usr/bin:/c/Windows/System32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl
Detecting OS: windows
Looking for compiler [g++]: EXEC <<
CMD: g++ --version
EXIT: 0
STDOUT:
g++.exe (Rev8, Built by MSYS2 project) 15.2.0
Copyright (C) 2025 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>>

g++.exe (Rev8, Built by MSYS2 project) 15.2.0
Checking for C++11 compliance:
COMPILE /tmp/tmpvo2rt5wu.cpp:
---

#include <cstddef>
struct Base {
    Base (int);
};
struct Derived : Base {
    using Base::Base;
};

int main() {
  Derived D (int); // check for contructor inheritance
  return 0;
}

---
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -DMRTRIX_WINDOWS -mms-bitfields -Wa,-mbig-obj -D_FILE_OFFSET_BITS=64 /tmp/tmpvo2rt5wu.cpp -o /tmp/tmpvo2rt5wu.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpvo2rt5wu.o -Wl,--sort-common,--as-needed -pthread -Wl,--allow-multiple-definition -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
error invoking command "./a.out": Permission denied
>>

test failed (see configure.log for details)

Looking for compiler [clang++]: EXEC <<
CMD: clang++ --version
error invoking command "clang++": No such file or directory
>>

not found

ERROR: no suitable compiler found!



  Set the CXX environment variable to inform 'configure' of the path to the
  compiler on your system, as follows:
    $ export CXX=/usr/bin/g++-5.5
    $./configure
  (amend with the actual path to the compiler on your system)

  If you are using a compiler other than gcc or clang, you can also set the CXX_ARGS
  environment variable to specify how your compiler expects different arguments
  to be presented on the command line, for instance as follows:
    $ export CXX_ARGS="-c CFLAGS SRC -o OBJECT"
    $ ./configure


  See the file 'configure.log' for details. If this doesn't help and you need
  further assistance, please post on the MRtrix3 community forum
  (http://community.mrtrix.org/), and make sure to include the full contents of
  the 'configure.log' file.

Still no ‘configure.log’ file to be seen, but hopefully this is enough information.

[SueKim]

Sorry for the double post, but I believe a.out was being blocked due to my institution’s IT system. I’ve gotten in touch with them to get the appropriate permissions.

I will update this post if that solves my installation issues. Many thanks for your help, Rob!

[SueKim]

Hello, I’m back to share that it was indeed my institution’s firewall that was causing the error. I have since finished up the installation.

I did come across another issue while running ./build, but my problem was solved with the solution outlined in this forum post: Installation error at build stage - #3 by daljit46