Bio++ Installation MAC

[Lee SangJin]

Hello guys! 

I am trying to install Bio++ to use maffilter and I am receiving this error message.

CMake Error at CMakeLists.txt:152 (MESSAGE):

  bpp-phyl-omics required but not found.

Call Stack (most recent call first):

  CMakeLists.txt:168 (IMPROVED_FIND_LIBRARY)

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:

bpp-phyl-omics_INCLUDE_DIR

   used as include directory in directory /Users/jin/Desktop/maffilter-1.1.0

   used as include directory in directory /Users/jin/Desktop/maffilter-1.1.0

   used as include directory in directory /Users/jin/Desktop/maffilter-1.1.0

   used as include directory in directory /Users/jin/Desktop/maffilter-1.1.0

It seems though bpp-phyl-omics is not available as a dmg file for Mac. Do you recommend that I just use the source to install it? I have installed all other dependencies with the provided dmg file.

Cheers,

Jin

[Lee SangJin]

I have also tried the auto-installation by changing the directory to my wget, tar, cmake, etc, as following, 

PATH_GET=/usr/local/bin/wget

PATH_TAR=/usr/bin/tar

PATH_CMK=/usr/local/bin/cmake

PATH_MAK=/usr/bin/make 

PATH_INSTALL=/usr/local

BPP_DOWNLOAD_URL=http://biopp.univ-montp2.fr/repos/sources

but I receive the following errors, for example. 

error: use of undeclared identifier 'MultiRange'

 error: unexpected type name 'size_t': expected expression

[Julien Yann Dutheil]

Dear Jin,

I am afraid dmg files are not up-to-date, I will try to fix that asap.
For maffilter, it looks like there are version compatibilities issues. If
you are ready to compile from sources, please be sure to install bio++
version 2.2.0 and MafFilter 1.1.0. Alternatively, you can use the latest
development version of the libraries and of maffilter, using git (see Wiki
for instructions).

Hope this helps,

Julien.

PS: looks like I managed to create a decent dmg file, will generate for all
libs and update the repository.

[Lee SangJin]

Dear Julien,

Thank you for the prompt answer.

I will try to compile the development version of the libraries and of MafFilter.

"Note: a bug was found when extracting annotation. In case the alignment is not projected on the reference sequence, some blocks may include the negative strand of the reference sequence. This leads to a segfault during program execution. The bug was fixed on the source repository and in 1.1.1 release. Statically linked executables are provided which include the bug fix, but other packages are not been updated and still provided as version 1.1.0. New packages will be generated for the next release. Do not hesitate to contact us if you are facing this issue and need help.

Note2: another bug was found, leading to a segfault. The bug is linked to the use of block statistics, when written to files. A fix release for MafFilter? 1.1.2 has been issued, only as linux executables. The version can also be compiled from the source code, but will require the latest development version of bpp-seq-omics."

On the MafFilter website, it says that the the bug fixes are only available as linux executables. Does this mean that the a fix release for MafFilter 1.12 is not available as Unix executables? 

PS: Would it be possible to get a notice when the repository is updated? 

Cheers,

Jin

[Julien Yann Dutheil]

Dear Jin,

The bugs are of course also fixed on the repository source code. I just did not redo all packages. I will let you know for the dmg, went into a small pb in the last minute, but I'll hopefully figure it out.

Best,

J.

[Julien Yann Dutheil]

Dear Jin,

I've looked a bit more into dmg and pkg files. I must say, I do not find that very convenient for distributing libraries :s

I think it would be much better to have a port repository so that the libs could be installed via macport (and/or homebrew). I will investigate that. In the mean time, I would recommend that you install from git (this works relatively well to my experience, but please do not hesitate to report any issue).

Cheers,

Julien.

[Lee SangJin]

Hey Julien,

Thanks for all the updates! I will wait for the poor to be established :)

Best,

Jin

[Lee SangJin]

Hey Julien,

I was wondering if there were any updates to MafFilter for Mac. 

Best,

Jin

[Julien Yann Dutheil]

Dear Lee,

Are you referring to the availability of Bio++ in macport? If so, I did not have time to look more into that, and I cannot promise any time schedule given the current status of my agenda :D I recommend that you compile from the git code. I did it on my macbook and I did not face any issue. If mac would support statically linked executables, I could send you one, but well, for some reason Mac seems to be against all kind of easy and convenient thing (I stop here otherwise I'll get off topic :p). Talking about off-topic, for MafFilter specific questions, please consider posting on the MafFilter forum.

Best,

Julien.

[Julien Yann Dutheil]

Just one note: looks like it is easier to write a Homebrew's formula than a Portfile, so I'm looking at the moment in the possibilities of having Bio++ & co there.

J.

[Lee SangJin]

Cheers :)

[Julien Yann Dutheil]

Dear Lee (and others)

I have made a first attempt to get bio++ into homebrew. So far, I have my own repository, with the libs and maffilter. If everything works fine, I will make a pull request to have that into homebrew-science. After installing homebrew, you can add my repository by typing:

brew tap jydu/homebrew-biopp

then, you can install maffilter using

brew install maffilter

This should install all dependencies as well.
I had to create a 1.1.1 version, which is identical to 1.1.0 but with slightly different include files. Note that version 1.2.0 will only be provided with the next release of Bio++. In between, you do need to compile manually from git.

Hope this helps,

J.

[mto...@asu.edu]

Did the homebrew install work for anybody? I am having issues with it, I keep getting this error:

brew install maffilter
==> Installing maffilter from jydu/homebrew-biopp
Error: compile error
/usr/local/Library/Taps/jydu/homebrew-biopp/libbpp-phyl-omics.rb:11: syntax error, unexpected tSTRING_BEG, expecting tAMPER
    system "cmake", ".", *std_cmake_args, "-DBUILD_TESTING=no"

Thanks,
Marc

[Lee SangJin]

brew install maffilter worked after brew tap jydu/homebrew-biopp, but I got the following error:

-- Configuring incomplete, errors occurred!

See also "/tmp/libbpp-seq-omics20150416-22497-1wo0gzp/bpp-seq-omics-2.2.0/CMakeFiles/CMakeOutput.log".

Warning: It appears you have MacPorts or Fink installed.

Software installed with other package managers causes known problems for

Homebrew. If a formula fails to build, uninstall MacPorts/Fink and try again.

READ THIS: https://git.io/brew-troubleshooting

If reporting this issue please do so at (not Homebrew/homebrew):

  https://github.com/jydu/homebrew-biopp/issues

so i am uninstalling macports and trying it again

[Lee SangJin]

I uninstalled macports and tried it agin, but it didn't work.

I must be doing something wrong.... I will update!

[Lee SangJin]

okay, so I got maffilter installed and working.

-- Configuring incomplete, errors occurred!

See also "/tmp/maffilter20150416-27546-1pwpqad/maffilter-1.1.0-1/CMakeFiles/CMakeOutput.log".

Warning: It appears you have MacPorts or Fink installed.

Software installed with other package managers causes known problems for

Homebrew. If a formula fails to build, uninstall MacPorts/Fink and try again.

READ THIS: https://git.io/brew-troubleshooting

If reporting this issue please do so at (not Homebrew/homebrew):

  https://github.com/jydu/homebrew-biopp/issues

after that error comes up I did, brew install maffilter again.

and then it will give me:

Error: You must `brew link libbpp-phyl-omics' before maffilter can be installed

  brew link --overwrite libbpp-phyl-omics

and i did brew link --overwrite "formula" each error that came up like this and it worked like a charm. I don't know why though.

Jin

[Julien Yann Dutheil]

Hi there,

One can really have macport and homebrew together, if one pay a bit care... the problem is that they might end installing things in the same directory, which complicates the dependency scheme. But as biopp has very few dependencies, and very standard ones, having it work with macport installed should be no pb. There should be a --force option in the brew command to safely bypass the warning.

For the link thing, is a version of the libs is already present in the destination directory (either from a previous install or from a manual install), homebrew will not create the links and one has to manually run the link command (with --overwrite option).

As for the first error (reported by Marc), I have not seen that before. I would need more details on the system version and log files...

Cheers,

Julien.

[Kevin Gori]

Dear Julien,

I have just got a bio++ formula accepted into homebrew (homebrew/science/biopp). I didn't realise you were working on your own formula, sorry if I have stepped on anyone's toes.

Best,

Kevin

[Julien Yann Dutheil]

Dear Kevin,

No pb ! And your formula looks much more advanced than mine. Would be
cool to include bpp-phyl-omics and bpp-qt though (maybe my code would
be helpful for that?). Is that possible?

Best,

Julien.

[Kevin Gori]

Dear Julien,

Thanks. I'll take a look at bpp-qt. I had a problem getting it to install, but I don't remember what it was, so I'll try again. bpp-phyl-omics is in there already (it's in the final block, separate from the other libs, because of a homebrew quirk).

Best,

Kevin

[Kevin Gori]

Dear All,

My updated formula is in homebrew: run 

'brew tap homebrew/science

'brew install biopp'

to install all the libraries, or

'brew install biopp --without-qt'

if you want to avoid building Qt. (This leaves out bpp-qt).

Cheers,

Kevin

[Julien Yann Dutheil]

Dear Kevin,

That's wonderful! Will you maintain this formula in the future? If so, I think I will migrate the other formulas (comap, maffilter etc) to homebrew-science and make them depend on yours.

Cheers,

Julien.

[Kevin Gori]

Hi Julien,

I can commit to maintaining the formula for the foreseeable future. I'll post back here if that changes.

Kevin

[Julien Yann Dutheil]

Dear Kevin,

I am wondering if you would still be keen on maintaining the formula for Bio++ on Homebrew?

If so, we have now released a new version, with tag 2.3.1. Everything is now on github: https://github.com/BioPP, as well as releases for each library: https://github.com/BioPP/bpp-core/releases .

All the best,

Julien.

[Will]

I'm tried Kevin's formula and received an error. Terminal output is as follows:

$ brew install biopp

Updating Homebrew...

==> Installing biopp from homebrew/science

==> Downloading http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-omics-2.2.0.tar.gz

######################################################################## 100.0%

==> Downloading http://biopp.univ-montp2.fr/repos/sources/bpp-core-2.2.0.tar.gz

######################################################################## 100.0%

==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/biop

==> make bppcore-shared bppcore-static

==> make install

==> Downloading http://biopp.univ-montp2.fr/repos/sources/bpp-seq-2.2.0.tar.gz

######################################################################## 100.0%

==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/biop

==> make bppseq-shared bppseq-static

==> make install

==> Downloading http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-2.2.0.tar.gz

######################################################################## 100.0%

==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/biop

==> make bppphyl-shared bppphyl-static

==> make install

Last 15 lines from /Users/kjsdhjasv/Library/Logs/Homebrew/biopp/09.make:

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

make[1]: *** Waiting for unfinished jobs....

[ 92%] Linking CXX executable test_likelihood_clock

cd /tmp/biopp--bppphyl-20171218-87191-1srv94k/bpp-phyl-2.2.0/build/test && /usr/local/Cellar/cmake/3.10.1/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood_clock.dir/link.txt --verbose=1

/usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -Wall -Wshadow -Weffc++ -Wconversion -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names  CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o  -o test_likelihood_clock /usr/local/Cellar/biopp/2.2.0/lib/libbpp-seq.dylib /usr/local/Cellar/biopp/2.2.0/lib/libbpp-core.dylib /usr/local/lib/libbpp-phyl.dylib 

[ 92%] Built target test_likelihood_clock

[ 92%] Linking CXX executable test_mapping_codon

cd /tmp/biopp--bppphyl-20171218-87191-1srv94k/bpp-phyl-2.2.0/build/test && /usr/local/Cellar/cmake/3.10.1/bin/cmake -E cmake_link_script CMakeFiles/test_mapping_codon.dir/link.txt --verbose=1

/usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -Wall -Wshadow -Weffc++ -Wconversion -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names  CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o  -o test_mapping_codon /usr/local/Cellar/biopp/2.2.0/lib/libbpp-seq.dylib /usr/local/Cellar/biopp/2.2.0/lib/libbpp-core.dylib /usr/local/lib/libbpp-phyl.dylib 

[ 92%] Built target test_mapping_codon

[ 93%] Linking CXX executable test_mapping

cd /tmp/biopp--bppphyl-20171218-87191-1srv94k/bpp-phyl-2.2.0/build/test && /usr/local/Cellar/cmake/3.10.1/bin/cmake -E cmake_link_script CMakeFiles/test_mapping.dir/link.txt --verbose=1

/usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -Wall -Wshadow -Weffc++ -Wconversion -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names  CMakeFiles/test_mapping.dir/test_mapping.cpp.o  -o test_mapping /usr/local/Cellar/biopp/2.2.0/lib/libbpp-seq.dylib /usr/local/Cellar/biopp/2.2.0/lib/libbpp-core.dylib /usr/local/lib/libbpp-phyl.dylib 

[ 93%] Built target test_mapping

make: *** [all] Error 2

Let me know if more information is required.

[Julien Yann Dutheil]

Dear Will,

This formula is outdated. I have create a separate homebrew tap for Bio++, available at jydu/homebrew-biopp. Can you give it a try and tell me if it works for you?

Julien.

[Will]

Julien,

Yes, that worked.

Thanks.