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one line matlab installer on Ubuntu 20.04 does not work out of the box #1159

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traversaro opened this issue Jun 10, 2022 · 3 comments
Open

one line matlab installer on Ubuntu 20.04 does not work out of the box #1159

traversaro opened this issue Jun 10, 2022 · 3 comments

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@traversaro
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After 20 hours it was merged, the test of one line matlab installer failed.

Last Successful Build: https://github.com/robotology/robotology-superbuild/runs/6810705069
First CI Fail: https://github.com/robotology/robotology-superbuild/actions/runs/2473119223
@traversaro
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The error is:

  {�Error using yarp.Vector
  Invalid MEX-file
  '/home/runner/work/robotology-superbuild/robotology-superbuild/scripts/robotology-matlab/mex/yarpMEX.mexa64':
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.30' not found
  (required by
  /home/runner/work/robotology-superbuild/robotology-superbuild/scripts/robotology-matlab/mex/../lib/libYARP_os.so.3)
  
  Error in command_751a7662_794c_4a02_ae5c_0042c0fd82b9 (line 4)
  vec = yarp.Vector()
  }�

Difference between before and after:

--- <unnamed>
+++ <unnamed>
@@ -1,28 +1,30 @@
-    Package                              Version  Build                Channel                   Size
+   Package                              Version  Build                Channel                   Size
   ─────────────────────────────────────────────────────────────────────────────────────────────────────
     Install:
   ─────────────────────────────────────────────────────────────────────────────────────────────────────
   
-    + ace                                  7.0.6  h9c3ff4c_0           conda-forge/linux-64       8MB
+    + ace                                  7.0.7  h27087fc_0           conda-forge/linux-64       7MB
     + alsa-lib                           1.2.6.1  h7f98852_0           conda-forge/linux-64     592kB
     + ampl-mp                              3.1.0  h2cc385e_1006        conda-forge/linux-64       1MB
     + aom                                  3.3.0  h27087fc_1           conda-forge/linux-64       3MB
-    + assimp                               5.2.3  h4c92fa2_1           conda-forge/linux-64       4MB
+    + assimp                               5.2.4  h4c92fa2_0           conda-forge/linux-64       4MB
     + asttokens                            2.0.5  pyhd8ed1ab_0         conda-forge/noarch        22kB
+    + attr                                 2.5.1  h166bdaf_0           conda-forge/linux-64      71kB
     + backcall                             0.2.0  pyh9f0ad1d_0         conda-forge/noarch        14kB
     + backports                              1.0  py_2                 conda-forge/noarch         4kB
     + backports.functools_lru_cache        1.6.4  pyhd8ed1ab_0         conda-forge/noarch         9kB
-    + blockfactory                         0.8.3  h27087fc_53          robotology/linux-64      209kB
-    + boost-cpp                           1.74.0  h6cacc03_7           conda-forge/linux-64      17MB
-    + cairo                               1.16.0  ha12eb4b_1010        conda-forge/linux-64       2MB
+    + blockfactory                         0.8.3  h27087fc_54          robotology/linux-64      209kB
+    + boost-cpp                           1.74.0  h75c5d50_8           conda-forge/linux-64      17MB
+    + cairo                               1.16.0  ha61ee94_1011        conda-forge/linux-64       2MB
     + casadi                               3.5.5  py39h8234669_9       conda-forge/linux-64       5MB
-    + casadi-matlab-bindings             3.5.5.2  h27087fc_53          robotology/linux-64        1MB
+    + casadi-matlab-bindings             3.5.5.2  h27087fc_54          robotology/linux-64        1MB
     + dbus                                1.13.6  h5008d03_3           conda-forge/linux-64     619kB
     + decorator                            5.1.1  pyhd8ed1ab_0         conda-forge/noarch        12kB
     + eigen                                3.4.0  h4bd325d_0           conda-forge/linux-64       1MB
     + executing                            0.8.3  pyhd8ed1ab_0         conda-forge/noarch        19kB
     + expat                                2.4.8  h27087fc_0           conda-forge/linux-64     192kB
-    + ffmpeg                               4.4.1  hd7ab26d_2           conda-forge/linux-64      10MB
+    + ffmpeg                               4.4.1  habc3f16_5           conda-forge/linux-64      10MB
+    + fftw                                3.3.10  nompi_h77c792f_102   conda-forge/linux-64       7MB
     + font-ttf-dejavu-sans-mono             2.37  hab24e00_0           conda-forge/noarch       397kB
     + font-ttf-inconsolata                 3.000  h77eed37_0           conda-forge/noarch        97kB
     + font-ttf-source-code-pro             2.038  h77eed37_0           conda-forge/noarch       701kB
@@ -35,21 +37,22 @@
     + gettext                           0.19.8.1  h73d1719_1008        conda-forge/linux-64       4MB
     + giflib                               5.2.1  h36c2ea0_2           conda-forge/linux-64      79kB
     + gmp                                  6.2.1  h58526e2_0           conda-forge/linux-64     826kB
-    + gnutls                              3.6.13  h85f3911_1           conda-forge/linux-64       2MB
+    + gnutls                               3.7.6  hbf5b4be_4           conda-forge/linux-64       2MB
     + graphite2                           1.3.13  h58526e2_1001        conda-forge/linux-64     105kB
     + gsl                                    2.7  he838d99_0           conda-forge/linux-64       3MB
     + gst-plugins-base                    1.20.2  hf6a322e_1           conda-forge/linux-64       3MB
     + gstreamer                           1.20.2  hd4edc92_1           conda-forge/linux-64       2MB
-    + harfbuzz                             4.2.0  h40b6f09_0           conda-forge/linux-64       2MB
+    + harfbuzz                             4.3.0  hf9f4e7c_0           conda-forge/linux-64       2MB
     + hdf5                                1.12.1  nompi_h2386368_104   conda-forge/linux-64       4MB
-    + icub-firmware-shared                1.24.0  h27087fc_53          robotology/linux-64      253kB
-    + icub-main                           1.24.1  py39he6d5064_53      robotology/linux-64       13MB
+    + icub-firmware-shared                1.25.0  h27087fc_54          robotology/linux-64      250kB
+    + icub-main                           1.25.0  py39ha65b035_54      robotology/linux-64       14MB
     + icub-models                         1.24.0  py39h5a03fae_0       conda-forge/linux-64      25MB
-    + idyntree                             5.1.0  py39h1aa75c2_2       conda-forge/linux-64       3MB
-    + idyntree-matlab-bindings             5.1.0  h27087fc_53          robotology/linux-64      736kB
+    + idyntree                             5.2.1  py39hf4e83cc_1       conda-forge/linux-64       3MB
+    + idyntree-matlab-bindings             5.2.1  h27087fc_54          robotology/linux-64      758kB
     + ipopt                               3.14.6  h630875f_0           conda-forge/linux-64       1MB
     + ipython                              8.4.0  py39hf3d152e_0       conda-forge/linux-64       1MB
     + irrlicht                             1.8.5  h80a045a_2           conda-forge/linux-64       2MB
+    + jack                                1.9.18  h8c3723f_1002        conda-forge/linux-64     658kB
     + jasper                              2.0.33  ha77e612_0           conda-forge/linux-64       1MB
     + jedi                                0.18.1  py39hf3d152e_1       conda-forge/linux-64       1MB
     + jpeg                                    9e  h166bdaf_1           conda-forge/linux-64     274kB
@@ -57,34 +60,44 @@
     + lcms2                                 2.12  hddcbb42_0           conda-forge/linux-64     453kB
     + lerc                                   3.0  h9c3ff4c_0           conda-forge/linux-64     222kB
     + libblas                              3.9.0  15_linux64_openblas  conda-forge/linux-64      13kB
+    + libcap                                2.64  ha37c62d_0           conda-forge/linux-64      99kB
     + libcblas                             3.9.0  15_linux64_openblas  conda-forge/linux-64      13kB
-    + libclang                            13.0.1  default_hc23dcda_0   conda-forge/linux-64      12MB
+    + libclang                            14.0.4  default_h2e3cab8_0   conda-forge/linux-64     130kB
+    + libclang13                          14.0.4  default_h3a83d3e_0   conda-forge/linux-64      11MB
+    + libcups                              2.3.3  hf5a7f15_1           conda-forge/linux-64       5MB
+    + libdb                               6.2.32  h9c3ff4c_0           conda-forge/linux-64      24MB
     + libdc1394                            2.2.6  he1b5a44_0           conda-forge/linux-64     248kB
     + libdeflate                            1.10  h7f98852_0           conda-forge/linux-64      79kB
     + libdrm                             2.4.111  h166bdaf_0           conda-forge/linux-64     288kB
     + libevent                            2.1.10  h9b69904_4           conda-forge/linux-64       1MB
+    + libflac                              1.3.4  h27087fc_0           conda-forge/linux-64     485kB
     + libgfortran-ng                      12.1.0  h69a702a_16          conda-forge/linux-64      23kB
     + libgfortran5                        12.1.0  hdcd56e2_16          conda-forge/linux-64       2MB
     + libglib                             2.70.2  h174f98d_4           conda-forge/linux-64       3MB
     + libglu                               9.0.0  he1b5a44_1001        conda-forge/linux-64     423kB
     + libi2c                                 4.3  h9c3ff4c_0           conda-forge/linux-64      17kB
+    + libidn2                              2.3.2  h7f98852_0           conda-forge/linux-64     100kB
     + libjpeg-turbo                        2.1.1  h7f98852_0           conda-forge/linux-64       1MB
     + liblapack                            3.9.0  15_linux64_openblas  conda-forge/linux-64      13kB
     + liblapacke                           3.9.0  15_linux64_openblas  conda-forge/linux-64      13kB
-    + libllvm13                           13.0.1  hf817b99_2           conda-forge/linux-64      35MB
+    + libllvm14                           14.0.4  he0ac6c6_0           conda-forge/linux-64      37MB
     + libode                              0.16.2  h5a03fae_10          conda-forge/linux-64     546kB
     + libogg                               1.3.4  h7f98852_1           conda-forge/linux-64     211kB
     + libopenblas                         0.3.20  pthreads_h78a6416_0  conda-forge/linux-64      11MB
-    + libopencv                            4.5.5  py38hdaef270_10      conda-forge/linux-64      37MB
+    + libopencv                            4.5.5  py38hcc5f2f6_11      conda-forge/linux-64      37MB
     + libopus                              1.3.1  h7f98852_1           conda-forge/linux-64     261kB
     + libosqp                              0.6.2  h9c3ff4c_3           conda-forge/linux-64      80kB
     + libpciaccess                          0.16  h516909a_0           conda-forge/linux-64      38kB
     + libpng                              1.6.37  h21135ba_2           conda-forge/linux-64     314kB
     + libpq                                 14.3  hd77ab85_0           conda-forge/linux-64       3MB
     + libprotobuf                         3.20.1  h6239696_0           conda-forge/linux-64       3MB
+    + libsndfile                          1.0.31  h9c3ff4c_1           conda-forge/linux-64     616kB
     + libsodium                           1.0.18  h36c2ea0_1           conda-forge/linux-64     375kB
+    + libtasn1                            4.18.0  h166bdaf_1           conda-forge/linux-64     116kB
     + libtiff                              4.4.0  h0fcbabc_0           conda-forge/linux-64     621kB
+    + libtool                              2.4.6  h9c3ff4c_1008        conda-forge/linux-64     523kB
     + libudev1                               249  h166bdaf_3           conda-forge/linux-64     111kB
+    + libunistring                        0.9.10  h7f98852_0           conda-forge/linux-64       1MB
     + libusb                              1.0.26  h0b4f0b6_100         conda-forge/linux-64      84kB
     + libva                               2.14.0  h7f98852_0           conda-forge/linux-64     187kB
     + libvorbis                            1.3.7  h9c3ff4c_0           conda-forge/linux-64     286kB
@@ -93,7 +106,7 @@
     + libwebp-base                         1.2.2  h7f98852_1           conda-forge/linux-64     844kB
     + libxcb                                1.13  h7f98852_1004        conda-forge/linux-64     400kB
     + libxkbcommon                         1.0.3  he3ba5ed_0           conda-forge/linux-64     595kB
-    + matlab-whole-body-simulator          3.0.0  h27087fc_53          robotology/linux-64      201kB
+    + matlab-whole-body-simulator          3.0.0  h27087fc_54          robotology/linux-64      200kB
     + matplotlib-inline                    0.1.3  pyhd8ed1ab_0         conda-forge/noarch        11kB
     + meshcat-python                       0.3.2  pyhd8ed1ab_0         conda-forge/noarch       573kB
     + metis                                5.1.0  h58526e2_1006        conda-forge/linux-64       4MB
@@ -101,44 +114,47 @@
     + mumps-seq                            5.2.1  h2104b81_11          conda-forge/linux-64       3MB
     + mysql-common                        8.0.29  haf5c9bc_1           conda-forge/linux-64       2MB
     + mysql-libs                          8.0.29  h28c427c_1           conda-forge/linux-64       2MB
-    + nettle                                 3.6  he412f7d_0           conda-forge/linux-64       7MB
+    + nettle                                 3.8  hc379101_0           conda-forge/linux-64       1MB
     + nspr                                  4.32  h9c3ff4c_1           conda-forge/linux-64     239kB
     + nss                                   3.78  h2350873_0           conda-forge/linux-64       2MB
     + numpy                               1.22.4  py39hc58783e_0       conda-forge/linux-64       7MB
     + openh264                             2.1.1  h780b84a_0           conda-forge/linux-64       2MB
     + openjpeg                             2.4.0  hb52868f_1           conda-forge/linux-64     455kB
     + osqp-eigen                           0.7.0  h9c3ff4c_0           conda-forge/linux-64      35kB
-    + osqp-matlab                        0.6.2.3  h27087fc_53          robotology/linux-64       29kB
+    + osqp-matlab                        0.6.2.3  h27087fc_54          robotology/linux-64       29kB
+    + p11-kit                            0.23.21  hc5aa10d_4           conda-forge/linux-64       5MB
     + parso                                0.8.3  pyhd8ed1ab_0         conda-forge/noarch        71kB
     + pcre                                  8.45  h9c3ff4c_0           conda-forge/linux-64     259kB
     + pexpect                              4.8.0  pyh9f0ad1d_2         conda-forge/noarch        48kB
     + pickleshare                          0.7.5  py_1003              conda-forge/noarch         9kB
     + pillow                               9.1.1  py39hae2aec6_1       conda-forge/linux-64      47MB
     + pixman                              0.40.0  h36c2ea0_0           conda-forge/linux-64     643kB
+    + portaudio                           19.6.0  h57a0ea0_5           conda-forge/linux-64     134kB
     + prompt-toolkit                      3.0.29  pyha770c72_0         conda-forge/noarch       258kB
     + pthread-stubs                          0.4  h36c2ea0_1001        conda-forge/linux-64       6kB
     + ptyprocess                           0.7.0  pyhd3deb0d_0         conda-forge/noarch        17kB
+    + pulseaudio                            14.0  h7f54b18_8           conda-forge/linux-64       2MB
     + pure_eval                            0.2.2  pyhd8ed1ab_0         conda-forge/noarch        15kB
     + pygments                            2.12.0  pyhd8ed1ab_0         conda-forge/noarch       837kB
     + pyngrok                              5.1.0  pyhd8ed1ab_0         conda-forge/noarch        19kB
     + pyyaml                                 6.0  py39hb9d737c_4       conda-forge/linux-64     183kB
     + pyzmq                               23.1.0  py39headdf64_0       conda-forge/linux-64     503kB
     + qpoases                              3.2.1  h27087fc_0           conda-forge/linux-64     782kB
-    + qt                                  5.12.9  h1304e3e_6           conda-forge/linux-64     103MB
+    + qt-main                             5.15.4  ha5833f6_1           conda-forge/linux-64      64MB
     + robot-testing-framework              2.0.1  h9c3ff4c_0           conda-forge/linux-64     199kB
     + scotch                               6.0.9  hb2e6521_2           conda-forge/linux-64       1MB
     + sdl                                 1.2.52  h27087fc_1           conda-forge/linux-64     164kB
     + sdl2                                2.0.22  h27087fc_1           conda-forge/linux-64       2MB
     + stack_data                           0.2.0  pyhd8ed1ab_0         conda-forge/noarch        22kB
-    + svt-av1                              0.9.1  h27087fc_0           conda-forge/linux-64       3MB
+    + svt-av1                              1.1.0  h27087fc_1           conda-forge/linux-64       3MB
     + tinyxml                              2.6.2  h4bd325d_2           conda-forge/linux-64      57kB
     + tornado                                6.1  py39hb9d737c_3       conda-forge/linux-64     665kB
     + traitlets                      5.2.2.post1  pyhd8ed1ab_0         conda-forge/noarch        87kB
     + u-msgpack-python                     2.7.1  pyh9f0ad1d_0         conda-forge/noarch        13kB
     + unixodbc                            2.3.10  h583eb01_0           conda-forge/linux-64     303kB
-    + wb-toolbox                           5.5.0  h27087fc_53          robotology/linux-64        1MB
+    + wb-toolbox                           5.5.0  h27087fc_54          robotology/linux-64        1MB
     + wcwidth                              0.2.5  pyh9f0ad1d_2         conda-forge/noarch        34kB
-    + whole-body-controllers               2.5.6  h27087fc_53          robotology/linux-64      289kB
+    + whole-body-controllers               2.5.6  h27087fc_54          robotology/linux-64      292kB
     + x264                            1!161.3030  h7f98852_1           conda-forge/linux-64       3MB
     + x265                                   3.5  h924138e_3           conda-forge/linux-64       3MB
     + xorg-fixesproto                        5.0  h7f98852_1002        conda-forge/linux-64       9kB
@@ -156,29 +172,13 @@
     + xorg-renderproto                    0.11.1  h7f98852_1002        conda-forge/linux-64      10kB
     + xorg-xextproto                       7.3.0  h7f98852_1002        conda-forge/linux-64      28kB
     + xorg-xproto                         7.0.31  h7f98852_1007        conda-forge/linux-64      75kB
-    + yarp                                 3.6.0  py39hd74ac5e_53      robotology/linux-64       14MB
-    + yarp-matlab-bindings                 3.6.1  h27087fc_53          robotology/linux-64        2MB
+    + yarp                                 3.7.0  py39h5fa39a5_54      robotology/linux-64       14MB
+    + yarp-matlab-bindings                 3.7.0  h27087fc_54          robotology/linux-64        2MB
     + ycm-cmake-modules                   0.14.1  h27087fc_0           conda-forge/linux-64     136kB
     + zeromq                               4.3.4  h9c3ff4c_1           conda-forge/linux-64     360kB
   
-    Change:
-  ─────────────────────────────────────────────────────────────────────────────────────────────────────
-  
-    - libarchive                           3.5.2  hb890918_2           installed                     
-    + libarchive                           3.5.2  hccf745f_1           conda-forge/linux-64       2MB
-  
-    Downgrade:
-  ─────────────────────────────────────────────────────────────────────────────────────────────────────
-  
-    - icu                                   70.1  h27087fc_0           installed                     
-    + icu                                   69.1  h9c3ff4c_0           conda-forge/linux-64      14MB
-    - libxml2                             2.9.14  h22db469_0           installed                     
-    + libxml2                             2.9.12  h885dcf4_1           conda-forge/linux-64     778kB
-  
     Summary:
   
-    Install: 157 packages
-    Change: 1 packages
-    Downgrade: 2 packages
+    Install: 173 packages
   
-    Total download: 479MB
+    Total download: 466MB

The change is that now YARP 3.7.0 package is used instead of the old 3.6.0 package. Probably the GCC/libstdcxx version used to compile this package changed, and the version of stdcxx available in 20.04 is not new enough. This problem is similar to ami-iit/mystica#6, we just did not encounter it here as we were using an old YARP version.

@traversaro
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The tricky thing here is that we do not know a-priori the location of the CONDA_PREFIX, so it is trycky to use the LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6 trick.

@traversaro
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w.r.t. to https://github.com/gcc-mirror/gcc/blob/master/libstdc%2B%2B-v3/ChangeLog-2021#L102, the symbol looked for is from version GLIBCXX_3.4.30, that I think is libstdcxx from GCC 12.1, so quite recent.

@traversaro traversaro mentioned this issue Jun 10, 2022
Merged
@traversaro traversaro changed the title Failure in one line matlab installer on Linux one line matlab installer on Ubuntu 20.04 does not work out of the box Apr 26, 2023
@traversaro traversaro mentioned this issue Jun 30, 2023
Open
@traversaro traversaro mentioned this issue Dec 17, 2024
Open
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