# Building GMT. CMake warning. Conflict with Anaconda3? **URL:** \ **Category:** Q&A\ **Created:** [May 7, 2022, 12:04pm UTC](https://forum.generic-mapping-tools.org/t/building-gmt-cmake-warning-conflict-with-anaconda3/2891 "2022-05-07T12:04:04Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Esteban82](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/esteban82/32/54_2.png) [@Esteban82](https://forum.generic-mapping-tools.org/u/Esteban82)\ **Post date:** [May 7, 2022, 12:04pm UTC](https://forum.generic-mapping-tools.org/t/building-gmt-cmake-warning-conflict-with-anaconda3/2891/1 "2022-05-07T12:04:04Z")
## Intro I try to build GMT from scratch (as indicated [here](https://github.com/GenericMappingTools/gmt/blob/master/BUILDING.md#configuring)) on Ubuntu 20.04. ## Warning When I run `cmake ..` I got this message (I copy the final of it): ``` ... * GMT_DOCDIR : /usr/local/share/doc * GMT_MANDIR : /usr/local/share/man -- Configuring done CMake Warning at src/CMakeLists.txt:510 (add_library): Cannot generate a safe runtime search path for target gmtlib because files in some directories may conflict with libraries in implicit directories: runtime library [libz.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/federico/anaconda3/lib Some of these libraries may not be found correctly. CMake Warning at src/CMakeLists.txt:770 (add_library): Cannot generate a safe runtime search path for target supplements because files in some directories may conflict with libraries in implicit directories: runtime library [libz.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/federico/anaconda3/lib Some of these libraries may not be found correctly. CMake Warning at src/CMakeLists.txt:561 (add_executable): Cannot generate a safe runtime search path for target gmt because files in some directories may conflict with libraries in implicit directories: runtime library [libz.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/federico/anaconda3/lib Some of these libraries may not be found correctly. -- Generating done -- Build files have been written to: /home/federico/Software/gmt/build ``` ## Error: Then, when I run `cmake --build . --target install` I get an error. ``` ... /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib/libgdal.so: referencia a `TIFFReadScanline@LIBTIFF_4.0' sin definir /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib/libgdal.so: referencia a `TIFFNumberOfTiles@LIBTIFF_4.0' sin definir collect2: error: ld returned 1 exit status make[2]: *** [src/CMakeFiles/gmt.dir/build.make:96: src/gmt] Error 1 make[1]: *** [CMakeFiles/Makefile2:833: src/CMakeFiles/gmt.dir/all] Error 2 make: *** [Makefile:152: all] Error 2 ``` ---
**Author:** ![seisman](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/seisman/32/4_2.png) [@seisman](https://forum.generic-mapping-tools.org/u/seisman)\ **Post date:** [May 7, 2022, 12:15pm UTC](https://forum.generic-mapping-tools.org/t/building-gmt-cmake-warning-conflict-with-anaconda3/2891/2 "2022-05-07T12:15:36Z")
That’s because your system have two copies of some library (e.g., `libz.so`), one from Anaconda and another one from the system. I don’t have a final solution, but there are two workarounds: 1. You can temporarily uncomment conda init settings from shell init script, restart a terminal, and build GMT again. Before building GMT, remember to remove the old build directory completely. After building GMT, you need to restore the conda init settings. 2. You can specify the path to look for the libraries in your `ConfigUser.cmake` file. The folllowing works well for me on macOS. I think changing `/usr/local` to `/usr/lib` or `/usr/lib/x86_64-linux-gnu` for work for you. ```auto set (GDAL_ROOT "/usr/local/") set (GEOS_ROOT "/usr/local/") set (PCRE_ROOT "/usr/local/") set (NETCDF_ROOT "/usr/local/") ``` ---
**Author:** ![rmm-san](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/rmm-san/32/3080_2.png) [@rmm-san](https://forum.generic-mapping-tools.org/u/rmm-san)\ **Post date:** [May 4, 2023, 6:20pm UTC](https://forum.generic-mapping-tools.org/t/building-gmt-cmake-warning-conflict-with-anaconda3/2891/3 "2023-05-04T18:20:28Z")
@seisman and @Esteban82 kindly, did you find a solution for this issue? I am using Ubuntu 22.04, and getting the same error when building GMT 6.4 from source. Here is part of the output I am getting: CMake Warning at src/CMakeLists.txt:510 (add\_library): Cannot generate a safe runtime search path for target gmtlib because files in some directories may conflict with libraries in implicit directories: ``` runtime library [libz.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/robin/anaconda3/lib ``` Some of these libraries may not be found correctly. CMake Warning at src/CMakeLists.txt:561 (add\_executable): Cannot generate a safe runtime search path for target gmt because files in some directories may conflict with libraries in implicit directories: ``` runtime library [libz.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/robin/anaconda3/lib ``` Some of these libraries may not be found correctly. CMake Warning at src/CMakeLists.txt:770 (add\_library): Cannot generate a safe runtime search path for target supplements because files in some directories may conflict with libraries in implicit directories: ``` runtime library [libz.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/robin/anaconda3/lib ``` Some of these libraries may not be found correctly. ---
**Author:** ![rmm-san](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/rmm-san/32/3080_2.png) [@rmm-san](https://forum.generic-mapping-tools.org/u/rmm-san)\ **Post date:** [May 4, 2023, 6:25pm UTC](https://forum.generic-mapping-tools.org/t/building-gmt-cmake-warning-conflict-with-anaconda3/2891/4 "2023-05-04T18:25:18Z")
@pwessel and team, kindly help … ---
**Author:** ![Joaquim](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/joaquim/32/16_2.png) [@Joaquim](https://forum.generic-mapping-tools.org/u/Joaquim)\ **Post date:** [May 4, 2023, 10:01pm UTC](https://forum.generic-mapping-tools.org/t/building-gmt-cmake-warning-conflict-with-anaconda3/2891/5 "2023-05-04T22:01:34Z")
Well, you have an advice in the post before yours. Did you try it? ---
**Author:** ![rmm-san](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/rmm-san/32/3080_2.png) [@rmm-san](https://forum.generic-mapping-tools.org/u/rmm-san)\ **Post date:** [May 5, 2023, 6:28am UTC](https://forum.generic-mapping-tools.org/t/building-gmt-cmake-warning-conflict-with-anaconda3/2891/6 "2023-05-05T06:28:13Z")
Yes I tried that, still does not work \*\*\*\* After upgrading to Ubuntu 22.10, I was able to install from source seamlessly. The upgrade may have resolved the references to Anaconda3. Thank you ---
**Author:** ![pwessel](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/pwessel/32/30_2.png) [@pwessel](https://forum.generic-mapping-tools.org/u/pwessel)\ **Post date:** [May 5, 2023, 7:37am UTC](https://forum.generic-mapping-tools.org/t/building-gmt-cmake-warning-conflict-with-anaconda3/2891/7 "2023-05-05T07:37:17Z")
I am neither using conda nor Linux so have nothing to add beyond what was stated t ---
**Author:** ![Joaquim](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/joaquim/32/16_2.png) [@Joaquim](https://forum.generic-mapping-tools.org/u/Joaquim)\ **Post date:** [May 5, 2023, 12:38pm UTC](https://forum.generic-mapping-tools.org/t/building-gmt-cmake-warning-conflict-with-anaconda3/2891/8 "2023-05-05T12:38:32Z")
If you move anaconda out of the path (how, I don’t know since I don’t use too and I’m a Win guy), the problem will disappear for sure.