Build / make error with bam-readcount on RHEL 6.6 c++config.h No such file or directory
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6.5 years ago
jnowacki ▴ 100

Installing bam-readcount / bam-readout

I've already installed the dependencies and I've been googling for solutions:

sudo yum groupinstall "Development tools"
sudo yum install zlib-devel ncurses-devel cmake patch

When running "make" I get this error: error: bits/c++config.h: No such file or directory

link.jam: No such file or directory
Performing configuration checks

    - has_icu builds           : no  (cached)

Component configuration:

    - program_options          : building
    - regex                    : building
    - test                     : not building

...patience...
...found 4248 targets...
...updating 34 targets...
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.4.7/release/link-static/threading-multi/cmdline.o
In file included from ./boost/config/select_stdlib_config.hpp:18,
                 from ./boost/config.hpp:40,
                 from ./boost/program_options/config.hpp:10,
                 from libs/program_options/src/cmdline.cpp:7:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:43:28: error: bits/c++config.h: No such file or directory
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string:43,
                 from ./boost/program_options/errors.hpp:12,
                 from ./boost/program_options/detail/cmdline.hpp:11,
                 from libs/program_options/src/cmdline.cpp:11:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h:48:31: error: bits/c++allocator.h: No such file or directory
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string:45,
                 from ./boost/program_options/errors.hpp:12,
                 from ./boost/program_options/detail/cmdline.hpp:11,
                 from libs/program_options/src/cmdline.cpp:11:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h:42:76: error: bits/c++locale.h: No such file or directory
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:41,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string:53,
                 from ./boost/program_options/errors.hpp:12,
                 from ./boost/program_options/detail/cmdline.hpp:11,
                 from libs/program_options/src/cmdline.cpp:11:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h:34:23: error: bits/gthr.h: No such file or directory
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h:35:30: error: bits/atomic_word.h: No such file or directory
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h:39,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios:45,
                 from ./boost/detail/lcast_precision.hpp:12,
                 from ./boost/lexical_cast.hpp:42,
                 from ./boost/program_options/value_semantic.hpp:14,
                 from ./boost/program_options/options_description.hpp:13,
                 from ./boost/program_options/detail/cmdline.hpp:14,
                 from libs/program_options/src/cmdline.cpp:11:
bam-readcount bam-readout make c++config.h • 3.9k views
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Take a look at this. Are you using 32-bit OS?

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I'm on RHEL6 65 bit

  • LSB_VERSION=base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
  • Red Hat Enterprise Linux Server release 6.6 (Santiago)
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Not sure what to do.

I typed this: yum install gcc-c++

and got this:

Loaded plugins: aliases, changelog, downloadonly, presto, product-id, rhnplugin, security, tmprepo, verify, versionlock

This system is receiving updates from RHN Classic or RHN Satellite.
Setting up Install Process
Package matching gcc-c++-4.4.7-11.el6.x86_64 already installed. Checking for update.
Nothing to do
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0
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Do yum install libstdc++-devel and see if that fixes the issue.

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Thank you for the feedback. So that command: yum install libstdc++-devel errors out:

Loaded plugins: aliases, changelog, downloadonly, presto, product-id,

rhnplugin, security, tmprepo, verify, versionlock This system is

receiving updates from RHN Classic or RHN Satellite. Setting up

Install Process Resolving Dependencies

--> Running transaction check

---> Package libstdc++-devel.x86_64 0:4.4.7-11.el6 will be installed

--> Processing Dependency: libstdc++(x86-64) = 4.4.7-11.el6 for package: libstdc++-devel-4.4.7-11.el6.x86_64

--> Finished Dependency Resolution Error: Package: libstdc++-devel-4.4.7-11.el6.x86_64 (prd-lsoe3.1-base)

       Requires: libstdc++(x86-64) = 4.4.7-11.el6
       Installed: libstdc++-4.4.7-17.el6.x86_64 (@res6-x86_64)
           libstdc++(x86-64) = 4.4.7-17.el6
       Available: libstdc++-4.4.6-4.el6.x86_64 (prd-lsoe3.1-base)
           libstdc++(x86-64) = 4.4.6-4.el6
       Available: libstdc++-4.4.7-4.el6.x86_64 (prd-lsoe3.1-base)
           libstdc++(x86-64) = 4.4.7-4.el6
       Available: libstdc++-4.4.7-11.el6.x86_64 (prd-lsoe3.1-base)
           libstdc++(x86-64) = 4.4.7-11.el6  You could try using --skip-broken to work around the problem  You could try running: rpm -Va --nofiles --nodigest
  

so I tried --skip-broken then make and got the same error: bits/c++config.h: No such file or directory

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