No download info given for 'dssp' and its source directory

[lewisbb]

No download info given for 'dssp' and its source directory

[mhekkel]

Curious error. Could you please try to move your code to a directory where there is no space in the path?

[lewisbb]

Curious error. Could you please try to move your code to a directory where there is no space in the path?

I've tried to do so, and nothing changed :(
The error remained the same as explained in my previous comment, with different source directory path given.

[mhekkel]

Could you please remove the build directory and run the command again but now with --debug-output appended? And share the result here?

[lewisbb]

Done. The output was just as following (with commands provided):

$ rm -r build
$ cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HOME/.local --debug-output
Running with debug output on.
-- The CXX compiler identification is AppleClang 15.0.0.15000100
   Called from: [3]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/CMakeDetermineCompilerId.cmake
                [2]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/CMakeDetermineCXXCompiler.cmake
                [1]	/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/CMakeLists.txt
-- Detecting CXX compiler ABI info
   Called from: [3]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/CMakeDetermineCompilerABI.cmake
                [2]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/CMakeTestCXXCompiler.cmake
                [1]	/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/CMakeLists.txt
-- Detecting CXX compiler ABI info - done
   Called from: [3]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/CMakeDetermineCompilerABI.cmake
                [2]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/CMakeTestCXXCompiler.cmake
                [1]	/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/CMakeLists.txt
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
   Called from: [2]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/CMakeTestCXXCompiler.cmake
                [1]	/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/CMakeLists.txt
-- Detecting CXX compile features
   Called from: [3]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/CMakeDetermineCompileFeatures.cmake
                [2]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/CMakeTestCXXCompiler.cmake
                [1]	/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/CMakeLists.txt
-- Detecting CXX compile features - done
   Called from: [3]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/CMakeDetermineCompileFeatures.cmake
                [2]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/CMakeTestCXXCompiler.cmake
                [1]	/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/CMakeLists.txt
CMake Warning (dev) at /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:3091 (message):
  The DOWNLOAD_EXTRACT_TIMESTAMP option was not given and policy CMP0135 is
  not set.  The policy's OLD behavior will be used.  When using a URL
  download, the timestamps of extracted files should preferably be that of
  the time of extraction, otherwise code that depends on the extracted
  contents might not be rebuilt if the URL changes.  The OLD behavior
  preserves the timestamps from the archive instead, but this is usually not
  what you want.  Update your project to the NEW behavior or specify the
  DOWNLOAD_EXTRACT_TIMESTAMP option with a value of true to avoid this
  robustness issue.
Call Stack (most recent call first):
  /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:4208 (_ep_add_download_command)
  CMakeLists.txt:58 (ExternalProject_Add)
This warning is for project developers.  Use -Wno-dev to suppress it.

   Called from: [3]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake
                [2]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake
                [1]	/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/CMakeLists.txt
-- Found Git: /usr/bin/git (found version "2.39.3 (Apple Git-145)")
   Called from: [4]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/FindPackageMessage.cmake
                [3]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/FindPackageHandleStandardArgs.cmake
                [2]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/FindGit.cmake
                [1]	/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/CMakeLists.txt
'/opt/homebrew/Cellar/cmake/3.26.3/bin/cmake' '-E' 'env' '/usr/bin/git' 'clone' 'file:///Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/' '/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/build/dssp' '-b' 'trunk'
Cloning into '/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/build/dssp'...
fatal: Remote branch trunk not found in upstream origin
CMake Error at /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:3131 (message):
  No download info given for 'dssp' and its source directory:

   /Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/build/dssp

  is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:4208 (_ep_add_download_command)
  CMakeLists.txt:99 (ExternalProject_Add)


   Called from: [3]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake
                [2]	/opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake
                [1]	/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/CMakeLists.txt
-- Configuring incomplete, errors occurred!

[mhekkel]

OK, found it. And I must apologise, I made the classic error of typing in some instructions without testing them myself.

Apparently the git checkout step does not fetch all info required. You will have to run git fetch first before running cmake.

I'll update the readme for this.

Thanks for reporting this problem

[lewisbb]

Thank you very much!

[lewisbb]

I'm sorry, I've had a moment to check your solution just now. Adding git fetch command doesn't literally changed anything, the error keeps the same, as in my first message. Could you help me? My commands:

$ git clone https://github.com/PDB-REDO/dssp.git -b dssp-builder
Cloning into 'dssp'...
remote: Enumerating objects: 1398, done.
remote: Counting objects: 100% (143/143), done.
remote: Compressing objects: 100% (84/84), done.
remote: Total 1398 (delta 89), reused 100 (delta 59), pack-reused 1255
Receiving objects: 100% (1398/1398), 1.34 MiB | 1.12 MiB/s, done.
Resolving deltas: 100% (872/872), done.
$ cd dssp
$ git fetch
$ cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HOME/.local
-- The CXX compiler identification is AppleClang 15.0.0.15000100
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning (dev) at /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:3091 (message):
  The DOWNLOAD_EXTRACT_TIMESTAMP option was not given and policy CMP0135 is
  not set.  The policy's OLD behavior will be used.  When using a URL
  download, the timestamps of extracted files should preferably be that of
  the time of extraction, otherwise code that depends on the extracted
  contents might not be rebuilt if the URL changes.  The OLD behavior
  preserves the timestamps from the archive instead, but this is usually not
  what you want.  Update your project to the NEW behavior or specify the
  DOWNLOAD_EXTRACT_TIMESTAMP option with a value of true to avoid this
  robustness issue.
Call Stack (most recent call first):
  /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:4208 (_ep_add_download_command)
  CMakeLists.txt:58 (ExternalProject_Add)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found Git: /usr/bin/git (found version "2.39.3 (Apple Git-145)")
'/opt/homebrew/Cellar/cmake/3.26.3/bin/cmake' '-E' 'env' '/usr/bin/git' 'clone' 'file:///Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/' '/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/build/dssp' '-b' 'trunk'
Cloning into '/Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/build/dssp'...
fatal: Remote branch trunk not found in upstream origin
CMake Error at /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:3131 (message):
  No download info given for 'dssp' and its source directory:

   /Users/lewis/Documents/Информация/Мое/Учеба/Университет/Курсовая 4-й курс/server/dssp/build/dssp

  is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:4208 (_ep_add_download_command)
  CMakeLists.txt:99 (ExternalProject_Add)


-- Configuring incomplete, errors occurred!

./dssp/build/dssp directory remains empty.

[drlemmus]

Did you try working in a directory without spaces and Cyrillic characters?

[lewisbb]

Sure. It ended likewise:

$ git clone https://github.com/PDB-REDO/dssp.git -b dssp-builder
Cloning into 'dssp'...
remote: Enumerating objects: 1398, done.
remote: Counting objects: 100% (143/143), done.
remote: Compressing objects: 100% (84/84), done.
remote: Total 1398 (delta 89), reused 100 (delta 59), pack-reused 1255
Receiving objects: 100% (1398/1398), 1.34 MiB | 509.00 KiB/s, done.
Resolving deltas: 100% (872/872), done.
$ cd dssp
$ git fetch
$ cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HOME/.local
-- The CXX compiler identification is AppleClang 15.0.0.15000100
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning (dev) at /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:3091 (message):
  The DOWNLOAD_EXTRACT_TIMESTAMP option was not given and policy CMP0135 is
  not set.  The policy's OLD behavior will be used.  When using a URL
  download, the timestamps of extracted files should preferably be that of
  the time of extraction, otherwise code that depends on the extracted
  contents might not be rebuilt if the URL changes.  The OLD behavior
  preserves the timestamps from the archive instead, but this is usually not
  what you want.  Update your project to the NEW behavior or specify the
  DOWNLOAD_EXTRACT_TIMESTAMP option with a value of true to avoid this
  robustness issue.
Call Stack (most recent call first):
  /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:4208 (_ep_add_download_command)
  CMakeLists.txt:58 (ExternalProject_Add)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found Git: /usr/bin/git (found version "2.39.3 (Apple Git-145)")
'/opt/homebrew/Cellar/cmake/3.26.3/bin/cmake' '-E' 'env' '/usr/bin/git' 'clone' 'file:///Users/lewis/Desktop/dssp/' '/Users/lewis/Desktop/dssp/build/dssp' '-b' 'trunk'
Cloning into '/Users/lewis/Desktop/dssp/build/dssp'...
fatal: Remote branch trunk not found in upstream origin
CMake Error at /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:3131 (message):
  No download info given for 'dssp' and its source directory:

   /Users/lewis/Desktop/dssp/build/dssp

  is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /opt/homebrew/Cellar/cmake/3.26.3/share/cmake/Modules/ExternalProject.cmake:4208 (_ep_add_download_command)
  CMakeLists.txt:99 (ExternalProject_Add)


-- Configuring incomplete, errors occurred!

[mhekkel]

That's strange, I tried it and it worked for me.

OK, then there is only one solution: replace

git fetch

with

git checkout trunk
git checkout dssp-builder

[lewisbb]

On a git checkout step it started to work fine. But a new error occurred on a cmake --build build step. See attached files.
stderr.txt
stdout.txt
How can I handle it?

[mhekkel]

If you have an hour, I'll fix the make process. This is not going to work.

(problem is that the download of zlib failed since the file no longer exists at the remote site)

[lewisbb]

Thank you very much for your help. I'll be awaiting.

[mhekkel]

I'm very sorry, but I had to give up trying to get dssp-builder up and running again. It's too much work for now.

So you will have to fall back to installing the requirements first, i.e. you have to install zilb, libmcfp and libcifpp by hand first. See the updated readme.

[lewisbb]

Hello! Are there any progressions? I had no luck to install requirements for DSSP successfully. I need your algorithm implementation in my work :(

[mhekkel]

Like I commented last week, the dssp-builder trick no longer works. You will have to build and install the requirements manually as stated in the new README. Or you can download a pre built executable from the release page:

https://github.com/PDB-REDO/dssp/releases/tag/v4.4.0

[lewisbb]

Understood. Have you any, maybe, docker things with executable version of DSSP?

[mhekkel]

There is a tool called pdb-redo-builder that uses docker to create linux executables that can run on older Linux versions. You can find it here: https://github.com/PDB-REDO/pdb-redo-builder

The executable we have for download at the release page, is that really not working for you?

[lewisbb]

I'm using Mac with M1, and I don't really know how to use these executables :(

[drlemmus]

Could you reach out to us by email to explain for what you need DSSP and how often? Perhaps we can help you with a different DSSP solution that doesn't require local software.