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urgi-anagen / TE_finder

A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.
https://urgi.versailles.inra.fr/Tools/REPET
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CMake Error CPPUNIT_INCLUDE_DIR-NOTFOUND #5

Closed EmilieSmeets22 closed 6 months ago

EmilieSmeets22 commented 7 months ago

Hi,

I cloned the repository, went into the directory but I am unable to run cmake successfully:


TE_finder $ cmake .
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done (1.1s)
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
CPPUNIT_INCLUDE_DIR
   used as include directory in directory /home/workspace/git/TE_finder
   used as include directory in directory /home/workspace/git/TE_finder
   used as include directory in directory /home/workspace/git/TE_finder
   used as include directory in directory /home/workspace/git/TE_finder
   used as include directory in directory /home/workspace/git/TE_finder
   used as include directory in directory /home/workspace/git/TE_finder
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/SDGlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/DGElib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/BLRlib/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/blaster
   used as include directory in directory /home/workspace/git/TE_finder/src/blaster
   used as include directory in directory /home/workspace/git/TE_finder/src/blaster
   used as include directory in directory /home/workspace/git/TE_finder/src/blaster
   used as include directory in directory /home/workspace/git/TE_finder/src/blaster
   used as include directory in directory /home/workspace/git/TE_finder/src/blaster
   used as include directory in directory /home/workspace/git/TE_finder/src/blaster
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/matcher.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/grouper.threads/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/duster
   used as include directory in directory /home/workspace/git/TE_finder/src/duster
   used as include directory in directory /home/workspace/git/TE_finder/src/duster
   used as include directory in directory /home/workspace/git/TE_finder/src/duster
   used as include directory in directory /home/workspace/git/TE_finder/src/duster
   used as include directory in directory /home/workspace/git/TE_finder/src/duster
   used as include directory in directory /home/workspace/git/TE_finder/src/duster
   used as include directory in directory /home/workspace/git/TE_finder/src/duster/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/duster/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/duster/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/duster/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/duster/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/duster/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/duster/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools
   used as include directory in directory /home/workspace/git/TE_finder/src/tools/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/tools/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/tools/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/tools/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/tools/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/tools/testfiles
   used as include directory in directory /home/workspace/git/TE_finder/src/tools/testfiles
CPPUNIT_LIBRARY
    linked by target "test_SDG" in directory /home/workspace/git/TE_finder/src/SDGlib/testfiles
    linked by target "test_DGE" in directory /home/workspace/git/TE_finder/src/DGElib/testfiles
    linked by target "test_BLR" in directory /home/workspace/git/TE_finder/src/BLRlib/testfiles
    linked by target "test_matcherThreads2.31" in directory /home/workspace/git/TE_finder/src/matcher.threads/testfiles
    linked by target "test_grouperThreads2.31" in directory /home/workspace/git/TE_finder/src/grouper.threads/testfiles
    linked by target "test_duster2.31" in directory /home/workspace/git/TE_finder/src/duster/testfiles
    linked by target "test_Tools" in directory /home/workspace/git/TE_finder/src/tools/testfiles

CMake Error in src/SDGlib/CMakeLists.txt:
  Found relative path while evaluating include directories of "SDGlib":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/SDGlib/testfiles/CMakeLists.txt:
  Found relative path while evaluating include directories of "test_SDG":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/DGElib/CMakeLists.txt:
  Found relative path while evaluating include directories of "DGElib":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/DGElib/testfiles/CMakeLists.txt:
  Found relative path while evaluating include directories of "test_DGE":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/BLRlib/CMakeLists.txt:
  Found relative path while evaluating include directories of "BLRlib":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/BLRlib/testfiles/CMakeLists.txt:
  Found relative path while evaluating include directories of "test_BLR":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/blaster/CMakeLists.txt:
  Found relative path while evaluating include directories of "blaster2.31":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/matcher.threads/CMakeLists.txt:
  Found relative path while evaluating include directories of
  "matcherThreads2.31":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/matcher.threads/testfiles/CMakeLists.txt:
  Found relative path while evaluating include directories of
  "test_matcherThreads2.31":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/grouper.threads/CMakeLists.txt:
  Found relative path while evaluating include directories of
  "grouperThreads2.31":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/grouper.threads/testfiles/CMakeLists.txt:
  Found relative path while evaluating include directories of
  "test_grouperThreads2.31":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/duster/CMakeLists.txt:
  Found relative path while evaluating include directories of "duster2.31":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/duster/testfiles/CMakeLists.txt:
  Found relative path while evaluating include directories of
  "test_duster2.31":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "cutterDB":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "itrsearch":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "ltrsearch":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "TRsearch":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "polyAtail":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "TSDsearch":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "map2db":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "mapdist":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "mapsize":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "map2flank53":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "map2flank5":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "map2flank3":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "mapview":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "mapOp":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "refalign":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "statalign":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "fastlalign":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "hrepeat":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "halign":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "hsearch":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "SWalign":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "NWalign":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "orienter":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "setnum2id":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "pathnum2id":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "align2piler":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "align2recon":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "filterAlign":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "tabnum2id":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/CMakeLists.txt:
  Found relative path while evaluating include directories of "rpt_map":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

CMake Error in src/tools/testfiles/CMakeLists.txt:
  Found relative path while evaluating include directories of "test_Tools":

    "CPPUNIT_INCLUDE_DIR-NOTFOUND"

-- Generating done (0.2s)
CMake Generate step failed.  Build files cannot be regenerated correctly.
hquesneville commented 6 months ago

Dear Emilie,

It seems that you have not installed the cppunit library as explained in the INSTALL.md file.

For example for Debian: sudo apt -y install libcppunit-dev.

I hope it will help.

Best,

Hadi

EmilieSmeets22 commented 6 months ago

Hey, My bad it is very clear cppunit is not installed. thanks!