Build fails due to fmt

[robertzeibich]

CMake Error at CMakeLists.txt:23 (find_package): By not providing "Findfmt.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "fmt", but CMake did not find one.

Could not find a package configuration file provided by "fmt" with any of the following names:

fmtConfig.cmake
fmt-config.cmake

Add the installation prefix of "fmt" to CMAKE_PREFIX_PATH or set "fmt_DIR" to a directory containing one of the above files. If "fmt" provides a separate development package or SDK, be sure it has been installed.

[egor-dolzhenko]

Apologies about the error. Are you on macOS? If yes, could you please check if brew install fmt solves the problem?

If you are using Linux, you can download the latest binary from here. (The binary is located under "Assets".)

[robertzeibich]

Thank you for getting back to me. I am working on a cluster, but I also have Ubuntu on my windows machine.

I installed fmt on my local machine (sudo apt-get install -y libfmt-dev), but I am still receiving an error.

In file included from /home/robert/REViewer/reviewer/metrics/Workflow.hh:25:0,

             from /home/robert/REViewer/reviewer/metrics/Workflow.cpp:21:

/home/robert/REViewer/reviewer/core/Aligns.hh: In constructor ‘FragPathAlign::FragPathAlign(ReadPathAlign, ReadPathAlign)’:

/home/robert/REViewer/reviewer/core/Aligns.hh:88:9: error: ‘assert’ was not declared in this scope

     assert(this->readAlign.pathIndex == this->mateAlign.pathIndex);

     ^~~~~~

/home/robert/REViewer/reviewer/core/Aligns.hh:88:9: note: suggested alternative: ‘qsort’

     assert(this->readAlign.pathIndex == this->mateAlign.pathIndex);

     ^~~~~~

     qsort

CMakeFiles/Metrics.dir/build.make:62: recipe for target 'CMakeFiles/Metrics.dir/metrics/Workflow.cpp.o' failed

make[5]: *** [CMakeFiles/Metrics.dir/metrics/Workflow.cpp.o] Error 1

CMakeFiles/Makefile2:105: recipe for target 'CMakeFiles/Metrics.dir/all' failed

make[4]: *** [CMakeFiles/Metrics.dir/all] Error 2

Makefile:129: recipe for target 'all' failed

make[3]: *** [all] Error 2

CMakeFiles/reviewer.dir/build.make:110: recipe for target 'reviewer-prefix/src/reviewer-stamp/reviewer-build' failed

make[2]: *** [reviewer-prefix/src/reviewer-stamp/reviewer-build] Error 2

CMakeFiles/Makefile2:218: recipe for target 'CMakeFiles/reviewer.dir/all' failed

make[1]: *** [CMakeFiles/reviewer.dir/all] Error 2

Makefile:83: recipe for target 'all' failed

make: *** [all] Error 2

I would also appreciate some help to install the software on a cluster because at the end of the day, I need to use it there. Do you have any suggestions?

I am looking forward to hearing back from you.

Kind regards,

Robert

From: Egor Dolzhenko @.> Sent: Thursday, 2 December 2021 2:20 PM To: Illumina/REViewer @.> Cc: robertzeibich @.>; Author @.> Subject: Re: [Illumina/REViewer] Build fails due to fmt (Issue #34)

Apologies about the error. Are you on macOS? If yes, could you please check if brew install fmt solves the problem?

If you are using Linux, you can download the latest binary from here https://github.com/Illumina/REViewer/releases/tag/v0.2.4 . (The binary is located under "Assets".)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Illumina/REViewer/issues/34#issuecomment-984256428 , or unsubscribe https://github.com/notifications/unsubscribe-auth/ARSVAPXHQ5RLZIHGTXOLMHDUO3QXLANCNFSM5JGA7A5A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub . https://github.com/notifications/beacon/ARSVAPVD2YKSQ32QFJHGDSTUO3QXLA5CNFSM5JGA7A5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOHKVI7LA.gif

[egor-dolzhenko]

Thank you for letting me know, Robert. We'll work on fixing the issue first thing tomorrow. Meanwhile, would you be open to using the pre-built binary on your cluster? If yes, this might be the simplest way to resolve the issue.

Best wishes, Egor

[robertzeibich]

Hi Egor,

Where can I find your pre-built binary and how can I install it?

Regards,

Robert

From: Egor Dolzhenko @.> Sent: Thursday, 2 December 2021 3:09 PM To: Illumina/REViewer @.> Cc: robertzeibich @.>; Author @.> Subject: Re: [Illumina/REViewer] Build fails due to fmt (Issue #34)

Thank you for letting me know, Robert. We'll work on fixing the issue first thing tomorrow. Meanwhile, would you be open to using the pre-built binary on your cluster? If yes, this might be the simplest way to resolve the issue.

Best wishes, Egor

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Illumina/REViewer/issues/34#issuecomment-984274517 , or unsubscribe https://github.com/notifications/unsubscribe-auth/ARSVAPTA67KMNZ6ZXAGN7G3UO3WMNANCNFSM5JGA7A5A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub . https://github.com/notifications/beacon/ARSVAPWVDS5P4OWHZJFAXL3UO3WMNA5CNFSM5JGA7A5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOHKVNMVI.gif

[egor-dolzhenko]

Hi Robert,

The binary can be downloaded from this page:

https://github.com/Illumina/REViewer/releases/tag/v0.2.4

The file REViewer-v0.2.4-linux_x86_64.gz is located in the "Assets" section of that page.

Once you download the file to your cluster, you can just uncompress it and then run it.

Best wishes, Egor

[egor-dolzhenko]

Hi Robert,

I just wanted to let you know that we have resolved the "fmt" library issue you reported. You should now be able to build REViewer from source on your cluster. Of course, you can also just continue using the provided binaries. Also, we will soon release binaries for a new version of REViewer that will output per-repeat quality metrics.

Best wishes, Egor