Question: Ncbi-Blast+ Version 2.2.23 'Make' Error
1
gravatar for Heidi
7.1 years ago by
Heidi10
Heidi10 wrote:

I'm getting errors when I run 'make' for rmblast-1.2-ncbi-blast-2.2.23+-src. This is the version of RMBlast modified for use with RepeatMasker from their site. I had no problem installing it in Ubuntu on my laptop (64-bit), but am now struggling with it on my Desktop (32-bit, Ubuntu 11.10). The configure runs successfully, but here are the errors I get after running 'make':

/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp:234:32: error: reference ‘m_Conn’ cannot be declared ‘mutable’ [-fpermissive]
make[8]: *** [public.o] Error 1
make[8]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver'
make[8]: Entering directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver'
rm -f libdbapi_driver.a .dbapi_driver.dep .libdbapi_driver.a.stamp
if [ '/bin/bash /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/scripts/common/impl/if_diff.sh "ln -f"' != '@:' -a -d /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/status -a -w /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/status -a /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/src/dbapi/driver != . ]; then \
        rm -f /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/lib/libdbapi_driver.a /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/status/.dbapi_driver.dep \
            /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/lib/libdbapi_driver-static.a /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/status/.dbapi_driver-static.dep; \
    fi
rm -f libdbapi_driver-dll.so .dbapi_driver-dll.dep .libdbapi_driver-dll.so.stamp
if [ '/bin/bash /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/scripts/common/impl/if_diff.sh "ln -f"' != '@:' -a -d /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/status -a -w /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/status -a /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/src/dbapi/driver != . ]; then \
        rm -f /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/lib/libdbapi_driver-dll.so /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/lib/libdbapi_driver-dll.so \
           /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/status/.dbapi_driver-dll.dep /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/status/.dbapi_driver-dll.dep; \
        [ '@# ' = '@# ' ]  ||  \
         rm -f /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/lib/libdbapi_driver-dll.so /usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/lib/libdbapi_driver-dll.so; \
    fi
make[8]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver'
make[7]: *** [all.nonusr] Error 2
make[7]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver'
make[6]: *** [all.real] Error 2
make[6]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver'
make[5]: *** [all_r.needs-reqs] Error 2
make[5]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver'
make[4]: *** [all_r.real] Error 5
make[4]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi'
make[3]: *** [all_r.needs-reqs] Error 2
make[3]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi'
make[2]: *** [all_r.real] Error 5
make[2]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build'
make[1]: *** [all_r.needs-reqs] Error 2
make[1]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build'
make: *** [all] Error 2

Another site suggested the following fix:

make LDFLAGS="-Wl,--no-as-needed"

I tried that with the same results. Any further help would be greatly appreciated.

blast error repeatmasker • 3.0k views
ADD COMMENTlink modified 7.1 years ago by Michael Schubert6.9k • written 7.1 years ago by Heidi10

this is probably not the right place to be asking this type of question but I would make sure that the version of gcc is the same for laptop and desktop and to wrap the error output in code tags so it is easier to read

ADD REPLYlink written 7.1 years ago by Ying W3.9k

From the documentation: "Please visit www.repeatmasker.org to submit questions or feedback for us." Probably best to provide a step by step account of your errors to the authors.

ADD REPLYlink written 7.1 years ago by SES8.2k
1
gravatar for Michael Schubert
7.1 years ago by
Cambridge, UK
Michael Schubert6.9k wrote:

The error is related to a change in behaviour between gcc 4.5 and 4.6. I assume your laptop had 4.5 and your desktop 4.6.

Try adding -fpermissive to your CXXFLAGS.

ADD COMMENTlink written 7.1 years ago by Michael Schubert6.9k

I apologize if this was the wrong place to post my question, but I appreciate the responses. Adding -fpermissive solved the errors, thank you!

ADD REPLYlink written 7.1 years ago by Heidi10
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