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alekseyzimin / masurca

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configure:error: cannot find boost/icl/interval_set.hpp #36

Open ashaneev opened 6 years ago

ashaneev commented 6 years ago

home@home-Lenovo-H30-50:~/Documents/Chloroplast_Assembly/MaSuRCA-3.2.7$ sudo ./install.sh

LarsDu commented 6 years ago

I'm having this error as well.

sguizard commented 6 years ago

Hi, In my case the installer was not able to found the boost libraries. My solution have been to ask to the installer to download and install boost itself : BOOST_ROOT=install ./install.sh

I hope it help.

LarsDu commented 6 years ago

I actually get the interval_set.hpp error when running 

BOOST_ROOT=install ./install.sh
sguizard commented 6 years ago

Try to install the dev pakage of boost (apt install libboost-dev or dnf install boost-devel), and run the installation without BOOST_ROOT=install.

alekseyzimin commented 6 years ago

Hi, you can also get the BOOST libraries and set BOOST_ROOT to where they are located.

LarsDu commented 6 years ago

If we use conda to install boost, how do we retrieve the appropriate BOOST_ROOT location in build.sh?

alekseyzimin commented 5 years ago

Hi,

You can set the BOOST_ROOT variable to the location of your boost headers. Example:

export BOOST_ROOT=/path

where path is the location of your boost headers

/path/boost/icl/interval_set.hpp

Alternatively, you can download the distribution tarball and run ./install.sh, it will give you an informative message on how to solve this problem.

--Aleksey

On Wed, May 29, 2019 at 3:00 AM Kadoi Takemaru notifications@github.com wrote:

@alekseyzimin https://github.com/alekseyzimin Hello.

I am having the same issue here. How can we solve this problem with Boost? spec

  • CentOS6 via SSH
  • Boost 1.6.8
  • MaSuRCA's version is up to date

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-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

abskumar commented 3 years ago

Installation is broken.

I have tried to install it on Mac Big Sur. I installed boost by "brew install boost" as well as "conda install brew" I set export BOOST_ROOT=/path/to/include/boost/icl/interval_set.hpp or export BOOST_ROOT=/path/to/include.
where /path/to was replaced by actual location. Then I ran install.sh I get the error: configure: error: cannot find Boost

I also tried BOOST_ROOT=install ./install.sh configure: error: cannot find boost/icl/interval_set.hpp Although I can see that file in global-1/include

alekseyzimin commented 3 years ago

Hello, The MaSuRCA distribution is being successfully installed on many systems. What operating system and hardware are you using? I recall BOOST_ROOT must point to path to boost libraries, "include must" be a subfolder in that path. If you are using MAC OS, unfortunately it is not supported. Aleksey

On Tue, May 4, 2021 at 6:49 PM Abhinav Kumar @.***> wrote:

Installation is broken.

I have tried to install it on Mac Big Sur. I installed boost by "brew install boost" as well as "conda install brew" I set export BOOST_ROOT=/path/to/include/boost/icl/interval_set.hpp or export BOOST_ROOT=/path/to/include. where /path/to was replaced by actual location. Then I ran install.sh I get the error: configure: error: cannot find Boost

I also tried BOOST_ROOT=install ./install.sh configure: error: cannot find boost/icl/interval_set.hpp Although I can see that file in global-1/include

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-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

abskumar commented 3 years ago

Thanks for getting back. I was trying to install it on Mac Big Sur. I didn’t know that it does not install on macs. I will try it on some linux system.

Abhinav

On May 4, 2021, at 4:17 PM, Aleksey Zimin @.**@.>> wrote:

Hello, The MaSuRCA distribution is being successfully installed on many systems. What operating system and hardware are you using? I recall BOOST_ROOT must point to path to boost libraries, "include must" be a subfolder in that path. If you are using MAC OS, unfortunately it is not supported. Aleksey

On Tue, May 4, 2021 at 6:49 PM Abhinav Kumar @.***> wrote:

Installation is broken.

I have tried to install it on Mac Big Sur. I installed boost by "brew install boost" as well as "conda install brew" I set export BOOST_ROOT=/path/to/include/boost/icl/interval_set.hpp or export BOOST_ROOT=/path/to/include. where /path/to was replaced by actual location. Then I ran install.sh I get the error: configure: error: cannot find Boost

I also tried BOOST_ROOT=install ./install.sh configure: error: cannot find boost/icl/interval_set.hpp Although I can see that file in global-1/include

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-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

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abskumar commented 3 years ago

I tried it on Linux (Amazon EC2): Now I get this error: swig/perl5/swig_wrap.cpp:322:10: fatal error: string.h: No such file or directory

include 

      ^~~~~~~~~~

compilation terminated. make[2]: [swig/perl5/swig_perl5_mummer_la-swig_wrap.lo] Error 1 make[2]: Waiting for unfinished jobs.... make[2]: Leaving directory /home/ec2-user/soft/MaSuRCA-4.0.3/global-1/MUMmer' make[1]: *** [install] Error 2 make[1]: Leaving directory/home/ec2-user/soft/MaSuRCA-4.0.3/global-1/MUMmer' make: *** [install-special] Error 2

valery-shap commented 3 years ago

Hello,

I have the same issue. Firstly I had problems with Boost: cannot find Boost headers version >= 1.46.0, configure: error: cannot find Boost Then I tried BOOST_ROOT=install ./install.sh and had the error: swig/perl5/swig_wrap.cpp:322:10: fatal error: string.h: No such file or directory Also I tried to install boost via conda and BOOST_ROOT=/home/miniconda3/pkgs/libboost-dev-1.68.0-2749 and the error was the same : configure: error: cannot find Boost I don't have root permissions and docker. Masurca-4.0.4 CentOS Linux

Valery

alekseyzimin commented 3 years ago

Hi,

BOOST_ROOT=install ./install.sh is the correct way to automatically download the Boost headers. The swig error is separate, it means that your perl installation is missing swig headers.

Best, Aleksey

On Thu, Aug 19, 2021 at 3:29 AM valery-shap @.***> wrote:

Hello,

I have the same issue. Firstly I had problems with Boost: cannot find Boost headers version >= 1.46.0, configure: error: cannot find Boost Then I tried BOOST_ROOT=install ./install.sh and had the error: swig/perl5/swig_wrap.cpp:322:10: fatal error: string.h: No such file or directory Also I tried to install boost via conda and BOOST_ROOT=/home/miniconda3/pkgs/libboost-dev-1.68.0-2749 and the error was the same : configure: error: cannot find Boost I don't have root permissions and docker. Masurca-4.0.4

Valery

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-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

valery-shap commented 3 years ago

Thank you for reply. I created new conda env and install

conda install -c anaconda perl conda install -c conda-forge swig

And I have the same error after: cd MaSuRCA-4.0.4 BOOST_ROOT=install ./install.sh

wig/perl5/swig_wrap.cpp:322:10: fatal error: string.h: No such file or directory

include 

      ^~~~~~~~~~

compilation terminated. make[2]: [Makefile:1830: swig/perl5/swig_perl5_mummer_la-swig_wrap.lo] Error 1 make[2]: Waiting for unfinished jobs.... make[2]: Leaving directory '/home/MaSuRCA-4.0.4/global-1/MUMmer' make[1]: [Makefile:2418: install] Error 2 make[1]: Leaving directory '/home/MaSuRCA-4.0.4/global-1/MUMmer' make: [Makefile:847: install-special] Error 2

gcc (GCC) 8.3.1 20191121 (Red Hat 8.3.1-5)

Maybe there is a way to point the path of perl and swig conda?

Valery

alekseyzimin commented 3 years ago

Can you add the perl headers installed by condat to the $PATH?

On Thu, Aug 19, 2021 at 11:22 AM valery-shap @.***> wrote:

Thank you for reply. I created new conda env and install

conda install -c anaconda perl conda install -c conda-forge swig

And I have the same error after: cd MaSuRCA-4.0.4 BOOST_ROOT=install ./install.sh

wig/perl5/swig_wrap.cpp:322:10: fatal error: string.h: No such file or directory

include

^~~~~~ compilation terminated. make[2]: [Makefile:1830: swig/perl5/swig_perl5_mummer_la-swig_wrap.lo] Error 1 make[2]: Waiting for unfinished jobs.... make[2]: Leaving directory '/home/MaSuRCA-4.0.4/global-1/MUMmer' make[1]: [Makefile:2418: install] Error 2 make[1]: Leaving directory '/home/MaSuRCA-4.0.4/global-1/MUMmer' make: [Makefile:847: install-special] Error 2

gcc (GCC) 8.3.1 20191121 (Red Hat 8.3.1-5)

Maybe there is a way to point the path of perl and swig conda?

Valery

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-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

valery-shap commented 3 years ago

Do you mean this path?

export PATH=$PATH:/home/miniconda3/lib/5.32.0/x86_64-linux-thread-multi/CORE/ it contains the following files and many others:

opnames.h op_reg_common.h overload.h pad.h parser.h patchlevel.h perlapi.h perl.h perl_inc_macro.h perlio.h perliol.h perl_langinfo.h perlsdio.h perlvars.h

Error is still present. Should perl be built in specific way?

Valery

alekseyzimin commented 3 years ago

Sorry for the earlier confusion, SWIG is unable to find , which is actually not a perl header it is a standard C header used by SWIG. Are standard C libraries and headers available on your system?

On Thu, Aug 19, 2021 at 2:01 PM valery-shap @.***> wrote:

Do you mean this path?

export PATH=$PATH:/home/miniconda3/lib/5.32.0/x86_64-linux-thread-multi/CORE/ it contains the following files and many others: -rw-rw-r-- 3 vshapovalova vshapovalova 8927 Nov 8 2020 opnames.h -rw-rw-r-- 3 vshapovalova vshapovalova 5911 Nov 8 2020 op_reg_common.h -rw-rw-r-- 3 vshapovalova vshapovalova 3276 Nov 8 2020 overload.h -rw-rw-r-- 3 vshapovalova vshapovalova 17232 Nov 8 2020 pad.h -rw-rw-r-- 3 vshapovalova vshapovalova 6993 Nov 8 2020 parser.h -rw-rw-r-- 3 vshapovalova vshapovalova 5321 Nov 8 2020 patchlevel.h -rw-rw-r-- 3 vshapovalova vshapovalova 7680 Nov 8 2020 perlapi.h -rw-rw-r-- 3 vshapovalova vshapovalova 283516 Nov 8 2020 perl.h -rw-rw-r-- 3 vshapovalova vshapovalova 6223 Nov 8 2020 perl_inc_macro.h -rw-rw-r-- 3 vshapovalova vshapovalova 9555 Nov 8 2020 perlio.h -rw-rw-r-- 3 vshapovalova vshapovalova 13761 Nov 8 2020 perliol.h -rw-rw-r-- 3 vshapovalova vshapovalova 2914 Nov 8 2020 perl_langinfo.h -rw-rw-r-- 3 vshapovalova vshapovalova 527 Nov 8 2020 perlsdio.h -rw-rw-r-- 3 vshapovalova vshapovalova 12934 Nov 8 2020 perlvars.h

Error is still present. Should perl be built in specific way?

Valery

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-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

valery-shap commented 3 years ago

Yes, I can build a "hello world" application with gcc/g++ and including string.h doesn't make an error

alekseyzimin commented 3 years ago

This is still definitely a problem with C headers, or build environment configuration. Can you start a clean terminal without conda, etc on the PATH (comment it out in ~/.bashrc), untar/unzip maSuRCA and re-run install.sh. It looks like configure is setting up the wrong path to the C headers. You can do

export CPPFLAGS="-I/path_to_C headers/include"

On Thu, Aug 19, 2021 at 3:01 PM valery-shap @.***> wrote:

Yes, I can build a "hello world" application with gcc/g++ and including string.h doesn't make an error

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-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

valery-shap commented 3 years ago

After cleaning changes in ~/.bashrc and setting CPPFLAGS=-I/usr/include the error with string.h is gone, but the other one appeared: fatal error: xlocale.h: No such file or directory I have no write permissions for /usr/include, so I copied /usr/include to /tmp/include and made a link there: ln -s /usr/include/locale.h /tmp/include/xlocale.h and changed CPPFLAGS to -I/tmp/include/ Now xlocale.h error is gone too, but it fails like this now: `In file included from /usr/include/c++/8/ext/string_conversions.h:41, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from /usr/include/c++/8/stdexcept:39, from swig/perl5/swig_wrap.cpp:1541: /usr/include/c++/8/cstdlib:75:15: fatal error: stdlib.h: No such file or directory

include_next `

stdlib.h is definitely exists in /tmp/include

The version of CentOS is 8, could this be a reason?

Upd. Success installation on Ubuntu 18, but there is another error with #239

alekseyzimin commented 3 years ago

Hi, Thank you for troubleshooting this, MaSuRCA compiles fine under standard Redhat 8 so CentOS should not be a problem. Can you delete the MaSuRCA folder, do fresh untar/unzip and rerun ./install.sh 1>install.log 2>&1 and post install.log

On Fri, Aug 20, 2021 at 1:20 AM valery-shap @.***> wrote:

After cleaning changes in ~/.bashrc and setting CPPFLAGS=-I/usr/include the error with string.h is gone, but the other one appeared: fatal error: xlocale.h: No such file or directory I have no write permissions for /usr/include, so I copied /usr/include to /tmp/include and made a link there: ln -s /usr/include/locale.h /tmp/include/xlocale.h and changed CPPFLAGS to -I/tmp/include/ Now xlocale.h error is gone too, but it fails like this now: In file included from /usr/include/c++/8/ext/string_conversions.h:41, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from /usr/include/c++/8/stdexcept:39, from swig/perl5/swig_wrap.cpp:1541: /usr/include/c++/8/cstdlib:75:15: fatal error: stdlib.h: No such file or directory #include_next stdlib.h is definitely exists in /tmp/include

The version of CentOS is 8, could this be a reason?

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-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

valery-shap commented 3 years ago

Hello,

I've found the server with another operation system: #246 But now I have problems during working. Too fast assembly with default assembler and no final fasta. Or assembling with Flye but the assembly.fasta doesn't have very important plasmid. This plasmid was lost by hybrid Unicycler too. But it is present in short only and long only assemblies. And in mega fast hybrid .primary assembly of masurca.

A lot of thanks, Valery