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DionLab / RepeatDetector

Algorithm to count repeat size
GNU General Public License v2.0
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Unsuccesful installation #1

Open alanmejiamaza opened 2 years ago

alanmejiamaza commented 2 years ago

Hi, Thank you for adding this package for repeat analysis. I tried to install this on Centos6, in a conda environment (python=3.6.3). I got the following error: /user/ RepeatDetector/cmake/tests/TestSuite.cmake

Then, I tried the same on Mac OS X, Big Sur I got the following error: /user/ RepeatDetector/cmake/tests/TestSuite.cmake

I tried to install this on Centos7, in a conda environment (python=3.6.3). I got the following error: -- +--------------------------------------------------------------------+ -- RepeatDetecter -- +--------------------------------------------------------------------+ -- (C) Copyright SIB Swiss Institute of Bioinformatics -- Thierry Schuepbach (thierry.schuepbach@sib.swiss)

-- +--------------------------------------------------------------------+ -- Found Git: /usr/bin/git (found version "1.8.3.1") fatal: Needed a single revision -- This is patch version -- Compilation on architecture x86_64. -- testing flag -msse4.1... -- Add -std=c99 to C compiler options -- Add SSE2 to C compiler options -- Perl found - full test suite usable -- Found data directory in /data/wheeler_lab/2022/RepeatDetector/data -- Found utils directory in /data/wheeler_lab/2022/RepeatDetector/utils -- libprf found in /data/wheeler_lab/2022/libprf -- GIT version a2b1923 -- Gtest is in /data/wheeler_lab/2022/RepeatDetector/build/external/gtest/src/gtest -- Compilation on architecture x86_64. -- testing flag -msse4.1... -- Add -std=c99 to C compiler options -- Add SSE2 to C compiler options -- Perl found - full test suite usable -- This is the install RPATH : /usr/local/lib -- Unable to determine HDF5 C flags from HDF5 wrapper. -- Unable to determine HDF5 C version from HDF5 wrapper. -- Found HDF5: /usr/lib64/libhdf5.so
-- HDF5 library found -- HTS lib is required to compile PBBAM, trying downloading -- htslib downloaded into /data/wheeler_lab/2022/RepeatDetector/build/external/htslib/src/htslib CMake Error at /data/wheeler_lab/ALAN/SMRTLINK3/share/cmake-3.9/Modules/FindBoost.cmake:1253 (file): file STRINGS file "/usr/include/boost/version.hpp" cannot be read. Call Stack (most recent call first): /data/wheeler_lab/2022/libprf/cmake/build_internal_pbbam.cmake:51 (FIND_PACKAGE) /data/wheeler_lab/2022/libprf/CMakeLists.txt:318 (INCLUDE)

-- Boost version: 0.0.0 -- Boost 1.6 or higher is required to compile PBBAM, trying downloading -- Boost downloaded into /data/wheeler_lab/2022/RepeatDetector/build/external/Boost/src/Boost -- PBBam not found on the system, downloading from GitHub... -- PBBam built in /data/wheeler_lab/2022/RepeatDetector/build/external/pbbam -- Found data directory in /data/wheeler_lab/2022/libprf/data -- Found utils directory in /data/wheeler_lab/2022/libprf/utils CMake Error at src/CMakeLists.txt:50 (INCLUDE): INCLUDE could not find load file:

**/RepeatDetector/cmake/tests/TestSuite.cmake**

-- Configuring incomplete, errors occurred! See also "/data/wheeler_lab/2022/RepeatDetector/build/CMakeFiles/CMakeOutput.log". See also "/data/wheeler_lab/2022/RepeatDetector/build/CMakeFiles/CMakeError.log".

Could you let me know how to fix this please? Thanks Alan

schoopy commented 2 years ago

Hi Alan I ran into this as well as I clean too many files, I thought I fixed it though! As a quick fix I would just create a dummy TestSuite.txt in the correct location so that cmake will not complain any more. Tests will be implemented in the future but I need to import them all from the pftools and perform the necessary changes to match libprf.

Hopefully you will be able to get further with this.

Cheers,

Thierry

Sent from Mail for Windows

From: alanmejiamaza Sent: Monday, 14 March 2022 23:18 To: DionLab/RepeatDetector Cc: Subscribed Subject: [DionLab/RepeatDetector] Unsuccesful installation (Issue #1)

Hi, Thank you for adding this package for repeat analysis. I tried to install this on Centos6, in a conda environment (python=3.6.3). I got the following error: /user/ RepeatDetector/cmake/tests/TestSuite.cmake Then, I tried the same on Mac OS X, Big Sur I got the following error: /user/ RepeatDetector/cmake/tests/TestSuite.cmake I tried to install this on Centos7, in a conda environment (python=3.6.3). I got the following error: -- +--------------------------------------------------------------------+ -- RepeatDetecter -- +--------------------------------------------------------------------+ -- (C) Copyright SIB Swiss Institute of Bioinformatics -- Thierry Schuepbach @.***)

-- +--------------------------------------------------------------------+ -- Found Git: /usr/bin/git (found version "1.8.3.1") fatal: Needed a single revision -- This is patch version -- Compilation on architecture x86_64. -- testing flag -msse4.1... -- Add -std=c99 to C compiler options -- Add SSE2 to C compiler options -- Perl found - full test suite usable -- Found data directory in /data/wheeler_lab/2022/RepeatDetector/data -- Found utils directory in /data/wheeler_lab/2022/RepeatDetector/utils -- libprf found in /data/wheeler_lab/2022/libprf -- GIT version a2b1923 -- Gtest is in /data/wheeler_lab/2022/RepeatDetector/build/external/gtest/src/gtest -- Compilation on architecture x86_64. -- testing flag -msse4.1... -- Add -std=c99 to C compiler options -- Add SSE2 to C compiler options -- Perl found - full test suite usable -- This is the install RPATH : /usr/local/lib -- Unable to determine HDF5 C flags from HDF5 wrapper. -- Unable to determine HDF5 C version from HDF5 wrapper. -- Found HDF5: /usr/lib64/libhdf5.so -- HDF5 library found -- HTS lib is required to compile PBBAM, trying downloading -- htslib downloaded into /data/wheeler_lab/2022/RepeatDetector/build/external/htslib/src/htslib CMake Error at /data/wheeler_lab/ALAN/SMRTLINK3/share/cmake-3.9/Modules/FindBoost.cmake:1253 (file): file STRINGS file "/usr/include/boost/version.hpp" cannot be read. Call Stack (most recent call first): /data/wheeler_lab/2022/libprf/cmake/build_internal_pbbam.cmake:51 (FIND_PACKAGE) /data/wheeler_lab/2022/libprf/CMakeLists.txt:318 (INCLUDE) -- Boost version: 0.0.0 -- Boost 1.6 or higher is required to compile PBBAM, trying downloading -- Boost downloaded into /data/wheeler_lab/2022/RepeatDetector/build/external/Boost/src/Boost -- PBBam not found on the system, downloading from GitHub... -- PBBam built in /data/wheeler_lab/2022/RepeatDetector/build/external/pbbam -- Found data directory in /data/wheeler_lab/2022/libprf/data -- Found utils directory in /data/wheeler_lab/2022/libprf/utils CMake Error at src/CMakeLists.txt:50 (INCLUDE): INCLUDE could not find load file: /RepeatDetector/cmake/tests/TestSuite.cmake -- Configuring incomplete, errors occurred! See also "/data/wheeler_lab/2022/RepeatDetector/build/CMakeFiles/CMakeOutput.log". See also "/data/wheeler_lab/2022/RepeatDetector/build/CMakeFiles/CMakeError.log". Could you let me know how to fix this please? Thanks Alan — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you are subscribed to this thread.Message ID: @.***>

DionLab commented 2 years ago

Merci Thierry! Vincent

On 14 Mar 2022, at 22:23, schoopy @.***> wrote:

 External email to Cardiff University - Take care when replying/opening attachments or links. Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni.

Hi Alan I ran into this as well as I clean too many files, I thought I fixed it though! As a quick fix I would just create a dummy TestSuite.txt in the correct location so that cmake will not complain any more. Tests will be implemented in the future but I need to import them all from the pftools and perform the necessary changes to match libprf.

Hopefully you will be able to get further with this.

Cheers,

Thierry

Sent from Mail for Windows

From: alanmejiamaza Sent: Monday, 14 March 2022 23:18 To: DionLab/RepeatDetector Cc: Subscribed Subject: [DionLab/RepeatDetector] Unsuccesful installation (Issue #1)

Hi, Thank you for adding this package for repeat analysis. I tried to install this on Centos6, in a conda environment (python=3.6.3). I got the following error: /user/ RepeatDetector/cmake/tests/TestSuite.cmake Then, I tried the same on Mac OS X, Big Sur I got the following error: /user/ RepeatDetector/cmake/tests/TestSuite.cmake I tried to install this on Centos7, in a conda environment (python=3.6.3). I got the following error: -- +--------------------------------------------------------------------+ -- RepeatDetecter -- +--------------------------------------------------------------------+ -- (C) Copyright SIB Swiss Institute of Bioinformatics -- Thierry Schuepbach @.***)

-- +--------------------------------------------------------------------+ -- Found Git: /usr/bin/git (found version "1.8.3.1") fatal: Needed a single revision -- This is patch version -- Compilation on architecture x86_64. -- testing flag -msse4.1... -- Add -std=c99 to C compiler options -- Add SSE2 to C compiler options -- Perl found - full test suite usable -- Found data directory in /data/wheeler_lab/2022/RepeatDetector/data -- Found utils directory in /data/wheeler_lab/2022/RepeatDetector/utils -- libprf found in /data/wheeler_lab/2022/libprf -- GIT version a2b1923 -- Gtest is in /data/wheeler_lab/2022/RepeatDetector/build/external/gtest/src/gtest -- Compilation on architecture x86_64. -- testing flag -msse4.1... -- Add -std=c99 to C compiler options -- Add SSE2 to C compiler options -- Perl found - full test suite usable -- This is the install RPATH : /usr/local/lib -- Unable to determine HDF5 C flags from HDF5 wrapper. -- Unable to determine HDF5 C version from HDF5 wrapper. -- Found HDF5: /usr/lib64/libhdf5.so -- HDF5 library found -- HTS lib is required to compile PBBAM, trying downloading -- htslib downloaded into /data/wheeler_lab/2022/RepeatDetector/build/external/htslib/src/htslib CMake Error at /data/wheeler_lab/ALAN/SMRTLINK3/share/cmake-3.9/Modules/FindBoost.cmake:1253 (file): file STRINGS file "/usr/include/boost/version.hpp" cannot be read. Call Stack (most recent call first): /data/wheeler_lab/2022/libprf/cmake/build_internal_pbbam.cmake:51 (FIND_PACKAGE) /data/wheeler_lab/2022/libprf/CMakeLists.txt:318 (INCLUDE) -- Boost version: 0.0.0 -- Boost 1.6 or higher is required to compile PBBAM, trying downloading -- Boost downloaded into /data/wheeler_lab/2022/RepeatDetector/build/external/Boost/src/Boost -- PBBam not found on the system, downloading from GitHub... -- PBBam built in /data/wheeler_lab/2022/RepeatDetector/build/external/pbbam -- Found data directory in /data/wheeler_lab/2022/libprf/data -- Found utils directory in /data/wheeler_lab/2022/libprf/utils CMake Error at src/CMakeLists.txt:50 (INCLUDE): INCLUDE could not find load file: /RepeatDetector/cmake/tests/TestSuite.cmake -- Configuring incomplete, errors occurred! See also "/data/wheeler_lab/2022/RepeatDetector/build/CMakeFiles/CMakeOutput.log". See also "/data/wheeler_lab/2022/RepeatDetector/build/CMakeFiles/CMakeError.log". Could you let me know how to fix this please? Thanks Alan — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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Alenap26 commented 5 months ago

I have the same problem `CMake Error at CMakeLists.txt:298 (MESSAGE): Unable to locate libprf source directory

-- Configuring incomplete, errors occurred! See also "/data3/softwares/RepeatDetector/RepeatDetector/CMakeFiles/CMakeOutput.log". See also "/data3/softwares/RepeatDetector/RepeatDetector/CMakeFiles/CMakeError.log". ` news to solve it ?

rubanrex commented 5 months ago

I have the same problem `CMake Error at CMakeLists.txt:298 (MESSAGE): Unable to locate libprf source directory

-- Configuring incomplete, errors occurred! See also "/data3/softwares/RepeatDetector/RepeatDetector/CMakeFiles/CMakeOutput.log". See also "/data3/softwares/RepeatDetector/RepeatDetector/CMakeFiles/CMakeError.log". ` news to solve it ?

Hi

Is your libprf installed within the Repeat Detector folder?

Looking at your error message, that might be the issue.

Alenap26 commented 5 months ago

[ 18%] Performing download step (download, verify and extract) for 'Boost' -- Downloading... dst='/data3/softwares/RepeatDetector/RepeatDetector/build/external/Boost/src/boost_1_65_1.tar.bz2' timeout='60 seconds' inactivity timeout='none' -- Using src='https://dl.bintray.com/boostorg/release/1.65.1/source/boost_1_65_1.tar.bz2' CMake Error at Boost-stamp/download-Boost.cmake:170 (message): Each download failed!

error: downloading 'https://dl.bintray.com/boostorg/release/1.65.1/source/boost_1_65_1.tar.bz2' failed
      status_code: 22
      status_string: "HTTP response code said error"
      log:
      --- LOG BEGIN ---
        Trying 18.232.172.199...

``

rubanrex commented 5 months ago

Could you try downloading boost manually using this link and exporting to path?

https://boostorg.jfrog.io/artifactory/main/release/1.65.1/source/boost_1_65_1.tar.bz2

Keep us updated how the installation goes. We could arrange a virtual meeting if you still have issue installing.

rubanrex commented 1 week ago

Hi, we have executable version of repeat detector available now

To use on Windows: https://github.com/DionLab/RepeatDetector/tree/main/Windows To use on macOS: https://github.com/DionLab/RepeatDetector/tree/main/macOS