not found in Ubuntu Lunar Lobster 23.04

Ubuntu 23.04 ships with and doesn’t seem to be available. I’ve installed MRtrix3 throught anaconda and have used a workaround to make it work by creating a symbolic link to version 6 with the following commands:

cd /usr/lib/x86_64-linux-gnu/
sudo ln -s

However, this is risky and not clean. Do you have antoher suggestion to fix this issue? Will this be fixed in the future?

Hi @Alexandre,

I’ve also seen similar issues, and resorted to a similar fix, which I agree is an ugly hack. Thinking about this more, I am surprised that this would be an issue on anaconda, given that it’s supposed to provide a uniform platform. On my (outdated) anaconda installation, everything was fine, and I could see that the MRtrix executables were using the anaconda-supplied version of libtiff. But having just updated my anaconda installation, it now fails to find, as you mention. Clearly, anaconda now also ships with…

In short, the problem is with anaconda, not Ubuntu. The fix is probably just to update the version of the dependency in the anaconda recipe and regenerate the package. I’ll try to do that this afternoon…

All the best,

Quick update: I’ve had a go at re-running our recipe for building MRtrix on anaconda, and I can’t get things to work at all at the moment… I won’t have time to look into this for the foreseeable future, and truth be told, I’m struggling to understand Anaconda’s obscure inner workings and figure out what to try next…

For reference, the error I end up with is at the configure stage:

Checking for Qt moc: moc (version 5.15.8)
Checking for Qt qmake: qmake (version 5.15.8)
Checking for Qt rcc: rcc (version 5.15.8)
Checking for Qt: 
ERROR: error linking Qt application!

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

which turns out to be due to this weird error during linking a test Qt application (from configure.log):

CMD: /home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/bin/x86_64-conda-linux-gnu-c++ -Wl,--sort-common,--as-needed -pthread -L/home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/lib -Wl,-rpath,/home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/lib -lz -ltiff -lpng -lfftw3 qt_moc.o qt.o -o qt /home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/lib/ /home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/lib/ /home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/lib/ /home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/lib/ /home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/lib/ /home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/lib/ -L$(CONDA_BUILD_SYSROOT)/usr/lib64 -lGL -lpthread
/home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/lib/ undefined reference to `memcpy@GLIBC_2.14'
/home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/lib/ undefined reference to `clock_gettime@GLIBC_2.17'
/home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.1.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env/lib/ undefined reference to `getauxval@GLIBC_2.16'
collect2: error: ld returned 1 exit status

I don’t understand how or why this happens… It looks like the version of libc is too old for Qt5, but I’ve no idea how to get around that. For reference, here is the full listing of packages in the build environment. If anyone has a clue how to fix this, I’m all ears!

$ conda list
# packages in environment at /home/donald/miniconda3/conda-bld/mrtrix3_1691598950271/_build_env:
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
alsa-lib                  1.2.8                h166bdaf_0    conda-forge
attr                      2.5.1                h166bdaf_1    conda-forge
binutils_impl_linux-64    2.40                 hf600244_0    conda-forge
binutils_linux-64         2.40                 hbdbef99_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.19.1               hd590300_0    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
cairo                     1.16.0            hbbf8b49_1016    conda-forge
curl                      8.1.2                h409715c_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
eigen                     3.4.0                h00ab1b0_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
fftw                      3.3.10          nompi_hc118613_108    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
gcc_impl_linux-64         13.1.0               hc4be1a9_0    conda-forge
gcc_linux-64              13.1.0               hd2d1137_1    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
giflib                    5.2.1                h0b41bf4_3    conda-forge
git                       2.41.0          pl5321h86e50cf_0    conda-forge
glib                      2.76.4               hfc55251_0    conda-forge
glib-tools                2.76.4               hfc55251_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
gst-plugins-base          1.22.3               h938bd60_1    conda-forge
gstreamer                 1.22.3               h977cf35_1    conda-forge
gxx_impl_linux-64         13.1.0               hc4be1a9_0    conda-forge
gxx_linux-64              13.1.0               h5006d2a_1    conda-forge
harfbuzz                  7.3.0                hdb3a94d_0    conda-forge
icu                       72.1                 hcb278e6_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_16    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.20.1               h81ceb04_0    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libcap                    2.69                 h0f662aa_0    conda-forge
libclang                  16.0.6          default_h1cdf331_1    conda-forge
libclang13                16.0.6          default_h4d60ac6_1    conda-forge
libcups                   2.3.3                h36d4200_3    conda-forge
libcurl                   8.1.2                h409715c_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libdrm-cos6-x86_64        2.4.65            h9b0a68f_1105    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.4.3                h59595ed_0    conda-forge
libgcc-devel_linux-64     13.1.0               he3cc6c4_0    conda-forge
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgcrypt                 1.10.1               h166bdaf_0    conda-forge
libgfortran-ng            13.1.0               h69a702a_0    conda-forge
libgfortran5              13.1.0               h15d22d2_0    conda-forge
libglib                   2.76.4               hebfc3b9_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
libgpg-error              1.47                 h71f35ed_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libjpeg-turbo                 h0b41bf4_0    conda-forge
libllvm16                 16.0.6               h5cf9203_2    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libpq                     15.3                 hbcd7760_1    conda-forge
libsanitizer              13.1.0               hfd8a6a1_0    conda-forge
libselinux-cos6-x86_64    2.0.94            h9b0a68f_1105    conda-forge
libselinux-devel-cos6-x86_64 2.0.94            h9b0a68f_1105    conda-forge
libsepol-cos6-x86_64      2.0.41            h9b0a68f_1105    conda-forge
libsepol-devel-cos6-x86_64 2.0.41            h9b0a68f_1105    conda-forge
libsndfile                1.2.0                hb75c966_0    conda-forge
libsqlite                 3.42.0               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-devel_linux-64  13.1.0               he3cc6c4_0    conda-forge
libstdcxx-ng              13.1.0               hfd8a6a1_0    conda-forge
libsystemd0               254                  h3516f8a_0    conda-forge
libtiff                   4.5.1                h8b53f26_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp                   1.3.1                hbf2b3c1_0    conda-forge
libwebp-base              1.3.1                hd590300_0    conda-forge
libx11-common-cos6-x86_64 1.6.4             h9b0a68f_1105    conda-forge
libx11-cos6-x86_64        1.6.4             h9b0a68f_1105    conda-forge
libx11-devel-cos6-x86_64  1.6.4             h9b0a68f_1105    conda-forge
libxau-cos6-x86_64        1.0.6             h9b0a68f_1105    conda-forge
libxau-devel-cos6-x86_64  1.0.6             h9b0a68f_1105    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxdamage-cos6-x86_64    1.1.3             h9b0a68f_1105    conda-forge
libxdamage-devel-cos6-x86_64 1.1.3             h9b0a68f_1105    conda-forge
libxext-cos6-x86_64       1.3.3             h9b0a68f_1105    conda-forge
libxext-devel-cos6-x86_64 1.3.3             h9b0a68f_1105    conda-forge
libxfixes-cos6-x86_64     5.0.3             h9b0a68f_1105    conda-forge
libxfixes-devel-cos6-x86_64 5.0.3             h9b0a68f_1105    conda-forge
libxkbcommon              1.5.0                h5d7e998_3    conda-forge
libxml2                   2.11.5               h0d562d8_0    conda-forge
libxrender-cos6-x86_64    0.9.10            h9b0a68f_1105    conda-forge
libxrender-devel-cos6-x86_64 0.9.10            h9b0a68f_1105    conda-forge
libxxf86vm-cos6-x86_64    1.1.3             h9b0a68f_1105    conda-forge
libxxf86vm-devel-cos6-x86_64 1.1.3             h9b0a68f_1105    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
mesa-dri-drivers-cos6-x86_64 11.0.7            h9b0a68f_1105    conda-forge
mesa-dri1-drivers-cos6-x86_64 7.11              h9b0a68f_1105    conda-forge
mesa-libegl-cos6-x86_64   11.0.7            h9b0a68f_1105    conda-forge
mesa-libegl-devel-cos6-x86_64 11.0.7            h9b0a68f_1105    conda-forge
mesa-libgl-cos6-x86_64    11.0.7            h9b0a68f_1105    conda-forge
mesa-libgl-devel-cos6-x86_64 11.0.7            h9b0a68f_1105    conda-forge
mpg123                    1.31.3               hcb278e6_0    conda-forge
mysql-common              8.0.33               hf1915f5_2    conda-forge
mysql-libs                8.0.33               hca2cd23_2    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
nspr                      4.35                 h27087fc_0    conda-forge
nss                       3.89                 he45b914_0    conda-forge
openssl                   3.1.2                hd590300_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
perl                      5.32.1          4_hd590300_perl5    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkg-config                0.29.2            h36c2ea0_1008    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pulseaudio-client         16.1                 hb77b528_4    conda-forge
python                    3.11.4          hab00c5b_0_cpython    conda-forge
qt                        5.15.8               hf11cfaa_0    conda-forge
qt-main                   5.15.8              h01ceb2d_12    conda-forge
qt-webengine              5.15.8               h27f4a20_2    conda-forge
readline                  8.2                  h8228510_1    conda-forge
setuptools                68.0.0             pyhd8ed1ab_0    conda-forge
sysroot_linux-64          2.12                he073ed8_16    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
wheel                     0.41.1             pyhd8ed1ab_0    conda-forge
xcb-util                  0.4.0                hd590300_1    conda-forge
xcb-util-image            0.4.0                h8ee46fc_1    conda-forge
xcb-util-keysyms          0.4.0                h8ee46fc_1    conda-forge
xcb-util-renderutil       0.3.9                hd590300_1    conda-forge
xcb-util-wm               0.4.1                h8ee46fc_1    conda-forge
xkeyboard-config          2.39                 hd590300_0    conda-forge
xorg-compositeproto       0.4.2             h7f98852_1001    conda-forge
xorg-damageproto          1.2.1             h7f98852_1002    conda-forge
xorg-fixesproto           5.0               h7f98852_1002    conda-forge
xorg-inputproto           2.3.2             h7f98852_1002    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.6                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxcomposite        0.4.6                h0b41bf4_1    conda-forge
xorg-libxdamage           1.1.5                h7f98852_1    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxi                1.7.10               h7f98852_0    conda-forge
xorg-libxrandr            1.5.2                h7f98852_1    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-libxtst              1.2.3             h7f98852_1002    conda-forge
xorg-randrproto           1.5.0             h7f98852_1001    conda-forge
xorg-recordproto          1.14.2            h7f98852_1002    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-util-macros          1.19.3               h7f98852_0    conda-forge
xorg-x11-proto-devel-cos6-x86_64 7.7               h9b0a68f_1105    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xf86vidmodeproto     2.3.1             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.2                hfc55251_7    conda-forge