quickbuild.sh failing with missing file

[ijmiller2]

Last line of the error message is:

cp: cannot stat '/home/ijmiller2/Desktop/For_Gary/quandenser/../build/ubuntu64/quandenser/quan*.deb': No such file or directory

Running on Ubuntu 18.04.2 LTS. I've attached the full output from .stdout.

Let me know if you need any other details to help troubleshoot.

Also, have you considered building a Docker image for quandenser?

Thanks in advance for your support, Ian quickbuild.stdout.txt

[percolator]

Hi Ian,

Sorry to hear you have difficulties with the building process.

Here is where your build fails:

Checking packages: CMake Error at /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:106 (find_package): Found package configuration file:

/usr/local/lib/cmake/boost_filesystem-1.71.0/boost_filesystem-config.cmake but it set boost_filesystem_FOUND to FALSE so package "boost_filesystem" is considered to be NOT FOUND. Reason given by package: No suitable build variant has been found. The following variants have been tried and rejected:

• libboost_filesystem.so.1.71.0 (shared, Boost_USE_STATIC_LIBS=ON)

• libboost_filesystem.a (shared runtime, Boost_USE_STATIC_RUNTIME=ON)

  I think you should just get the right versions of the boost libraries.

And yes we are trying to make a (singularity) container out of quandenser: https://github.com/statisticalbiotechnology/quandenser-pipeline

On Wed, May 29, 2019 at 4:53 PM ijmiller2 notifications@github.com wrote:

Last line of the error message is:

cp: cannot stat '/home/ijmiller2/Desktop/For_Gary/quandenser/../build/ubuntu64/quandenser/quan*.deb': No such file or directory```Running on Ubuntu 18.04.2 LTS. I've attached the full output from .stdout.Let me know if you need any other details to help troubleshoot. Also, have you considered building a Docker image for quandenser?Thanks in advance for your support,Ianquickbuild.stdout.txt

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[ijmiller2]

Hi Lukas,

Okay, thanks for the info. I suspected it might be originating from a boost version issue too based on that message. I can try a different/earlier version. Which version are you using?

Thanks, Ian

On May 31, 2019, at 2:42 AM, Lukas Käll notifications@github.com wrote:

Hi Ian,

Sorry to hear you have difficulties with the building process.

Here is where your build fails:

Checking packages: CMake Error at /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:106 (find_package): Found package configuration file:

/usr/local/lib/cmake/boost_filesystem-1.71.0/boost_filesystem-config.cmake but it set boost_filesystem_FOUND to FALSE so package "boost_filesystem" is considered to be NOT FOUND. Reason given by package: No suitable build variant has been found. The following variants have been tried and rejected:

• libboost_filesystem.so.1.71.0 (shared, Boost_USE_STATIC_LIBS=ON)

• libboost_filesystem.a (shared runtime, Boost_USE_STATIC_RUNTIME=ON)

  I think you should just get the right versions of the boost libraries.

And yes we are trying to make a (singularity) container out of quandenser: https://github.com/statisticalbiotechnology/quandenser-pipeline

On Wed, May 29, 2019 at 4:53 PM ijmiller2 notifications@github.com wrote:

Last line of the error message is:

cp: cannot stat '/home/ijmiller2/Desktop/For_Gary/quandenser/../build/ubuntu64/quandenser/quan*.deb': No such file or directory```Running on Ubuntu 18.04.2 LTS. I've attached the full output from .stdout.Let me know if you need any other details to help troubleshoot. Also, have you considered building a Docker image for quandenser?Thanks in advance for your support,Ianquickbuild.stdout.txt

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[MatthewThe]

Hi Ian,

We use version 1.67.0, but this dependency should be fulfilled through the ProteoWizard build. Can you check if ProteoWizard built correctly by looking for the static libraries named "libboost..." and "libpwiz..." in the "~/build/ubuntu64/tools/lib" directory?

[ijmiller2]

Hey Matthew,

Thanks for the info. I assume you mean to represent my home directory path with "~"? If so, I'm not seeing any directory called "build" there. Or within the quandenser directory for that matter (since that's where I'm running sudo ./quickinstall.sh after cloning recursively as specified: git clone --recursive https://github.com/statisticalbiotechnology/quandenser.git.

Let me know if there's any other info I can provide.

Thanks for the help, Ian

[MatthewThe]

Hi Ian,

Sorry, I only realized now you're building from a different directory than the home directory. The folder you should check is /home/ijmiller2/Desktop/For_Gary/quandenser/../build/ubuntu64/tools/lib.

[ijmiller2]

Hey Matthew,

Yes, I do see some relevant looking files/directories in that directory (~/Desktop/For_Gary/build/ubuntu64/tools/lib):

libpwiz_analysis_chromatogram_processing.a libpwiz_analysis_common.a libpwiz_analysis_demux.a libpwiz_analysis_frequency.a libpwiz_analysis_passive.a libpwiz_analysis_passive_core.a libpwiz_analysis_peakdetect.a libpwiz_analysis_peptideid.a libpwiz_analysis_proteome_processing.a libpwiz_analysis_spectrum_processing.a libpwiz_analysis_spectrum_processing_basic.a libpwiz_analysis_version.a libpwiz_data_common.a libpwiz_data_identdata.a libpwiz_data_identdata_examples.a libpwiz_data_identdata_version.a libpwiz_data_misc.a libpwiz_data_msdata.a libpwiz_data_msdata_examples.a libpwiz_data_msdata_version.a libpwiz_data_obo.a libpwiz_data_proteome.a libpwiz_data_proteome_examples.a libpwiz_data_proteome_version.a libpwiz_data_vendor_readers.a libpwiz_reader_abi.a libpwiz_reader_abi_t2d.a libpwiz_reader_agilent.a libpwiz_reader_bruker.a libpwiz_reader_shimadzu.a libpwiz_reader_thermo.a libpwiz_reader_uimf.a libpwiz_reader_unifi.a libpwiz_reader_waters.a libpwiz_utility_chemistry.a libpwiz_utility_image.a libpwiz_utility_math.a libpwiz_utility_minimxml.a libpwiz_utility_misc.a libpwiz_version.a ... libboost_chrono.a libboost_chrono-gcc7-mt-s.a libboost_date_time-gcc7-mt-s.a libboost_filesystem.a libboost_filesystem-gcc7-mt-s.a libboost_iostreams.a libboost_iostreams-gcc7-mt-s.a libboost_nowide-gcc7-mt-s.a libboost_program_options.a libboost_program_options-gcc7-mt-s.a libboost_regex.a libboost_regex-gcc7-mt-s.a libboost_serialization.a libboost_serialization-gcc7-mt-s.a libboost_system.a libboost_system-gcc7-mt-s.a libboost_thread.a libboost_thread-gcc7-mt-s.a

Anything obvious missing?

I'll attach more info on the directory and file metadata for your reference.

Thanks for the help, Ian

build_ubuntu64_tools_lib_dir_contents.txt

[MatthewThe]

Thanks, that actually looks as it is supposed to.

It seems CMake is picking up on another local boost build. I'm not sure why it does not give preference to the CMAKE_PREFIX_PATH that we are setting, but you can try adding -DBoost_NO_BOOST_CMAKE=BOOL:ON to the cmake command in the build file (you might also need to remove the folder /home/ijmiller2/Desktop/For_Gary/quandenser/../build/ubuntu64/quandenser to ensure it does not use cached values).

[ijmiller2]

I'm not familiar enough with cmake to know which file and line to modify with DBoost_NO_BOOST_CMAKE=BOOL:ON. Are you referring to the quick build.sh as the "build file"? I don't see any explicit cmake commands in that file. Or do you mean one of the .cmake files in quandenser/cmake directory? I see currently see four:

FindProteoWizard.cmake FindPthreads.cmake MacroFindPackage.cmake VersionGen.cmake

[ijmiller2]

I think I found that build file:

/home/ijmiller2/Desktop/For_Gary/quandenser/admin/builders/ubuntu64_build.sh and the cmake command in it, which I updated with that flag (after removing the /home/ijmiller2/Desktop/For_Gary/quandenser/../build/ubuntu64/quandenser as suggested): cmake -DTARGET_ARCH=amd64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DBOOST_VARIANT_DO_NOT_USE_VARIADIC_TEMPLATES=ON -DCMAKE_PREFIX_PATH=$build_dir/tools $src_dir/quandenser -DBoost_NO_BOOST_CMAKE=BOOL:ON;

Unfortunately, still getting an error (attached). Though looks like it may be for a different reason? This one for building Dinosaur "Cannot create module Dinosaur, mvn execution failed: 1"

7-Jun-19_quickbuild.stdout.txt

[MatthewThe]

Yes, that was indeed where you should add the flag. The error you get now indicates a problem with Java or Maven, which both should have been installed by the build script.

Could you post the contents of the files: /home/ijmiller2/Desktop/For_Gary/quandenser/../build/ubuntu64/quandenser/dinosaur_maven_stdout.txt /home/ijmiller2/Desktop/For_Gary/quandenser/../build/ubuntu64/quandenser/dinosaur_maven_stderr.txt

One problem I've encountered before is a too new version of Java JDK. The dinosaur build works with JDK 8, but not with JDK 11.

[ijmiller2]

Here are those two files. Looks like it could be something Java version related, as you suggested.

dinosaur_maven_stderr.txt dinosaur_maven_stdout.txt

[MatthewThe]

Yes, that indeed seems to be a Java version error. Could you try to (temporarily) change to JDK 8 with sudo update-alternatives --config java and following the instructions?

[ijmiller2]

The switch to JDK 8 seemed to resolve it. We've got everything compiled and running now.

Thanks for your support! Ian