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Ncbi-Blast+ Version 2.2.23 'Make' Error

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.

repeatmasker blast error
• 6,198 views • link
updated by abhijit.synl abhijit.synl • written by Heidi • Heidi

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

• 0 views • link
written by Ying W Ying W

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.

• 0 views • link
written by SES SES

Hello,

Sorry to be reopening this thread after 7 years! But I am facing issues trying to install rpsblast and rpsproc for interproscan 5. I have followed the instructions around "Compiling Binaries" in the Interproscan handbook for rpsblast and rpsproc. I am able to get to the configure step, but make fails everytime. Here are some details.

I have followed the following instructions:

mkdir cddblast
cd cddblast
wget ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-src.tar.gz
wget ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-src.tar.gz.md5
md5sum -c ncbi-blast-2.9.0+-src.tar.gz.md5
# Above command should return "ncbi-blast-2.9.0+-src.tar.gz: OK" if download successful
tar xvzf ncbi-blast-2.9.0+-src.tar.gz
cd ncbi-blast-2.9.0+-src/c++/src/app/
wget ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/rpsbproc-0.5.0-src.tar.gz
tar xvzf rpsbproc-0.5.0-src.tar.gz
#edit Makefile.in and make sure SUB_PROJ is assigned two applications as follows: SUB_PROJ = blast rpsbproc
cd ../../
./configure
/usr/bin/make
#after compilation is complete
cp ReleaseMT/bin/rpsblast <interproscan_install_dir>/bin/blast/ncbi-blast-2.9.0+/
cp ReleaseMT/bin/rpsbproc <interproscan_install_dir>/bin/blast/ncbi-blast-2.9.0+/

I am using GCC 4.9.4 and running Red Hat Enterprise Linux Server release 6.9 (Santiago)

The installation works fine till the "configure" step. Some of the last lines are as follows

CXXFLAGS =  -Wall -Wno-format-y2k  -pthread -fopenmp -O2 -fPIC
LDFLAGS  =  -Wl,-rpath,/mnt/common/rh6/annotate/GCC/gcc-4.9.4/lib/gcc/x86_64-unknown-linux-gnu/4.9.4/../../../../lib64 -Wl,--enable-new-dtags -Wl,-export-dynamic  -pthread -fopenmp   -O

LIBRARIES:  build as static by default
FEATURES:   GCC MT LFS DLL unix WinMain Linux
PACKAGES:
  enabled:  Iconv Z BZ2 PCRE LocalPCRE MBEDTLS OPENSSL KRB5 CURL MySQL BerkeleyDB BerkeleyDB++ PYTHON PYTHON27 PYTHON3 PERL OpenGL LIBXML JPEG PNG XPM FreeType SASL2 LMDB LocalLMDB
  disabled: UUID FUSE LIBUNWIND LIBDW BACKWARD_CPP LocalZ LocalBZ2 LZO GMP GCRYPT NETTLE GNUTLS Sybase DBLib FreeTDS ODBC PYTHON25 PYTHON26 Boost.Chrono Boost.Filesystem Boost.Iostreams Boost.Program-Options Boost.Regex Boost.Spirit Boost.System Boost.Test Boost.Test.Included Boost.Thread C-Toolkit MESA GLUT GLEW wxWidgets wx2.8 Fast-CGI LocalSSS LocalMSGMAIL2 SSSUTILS LocalNCBILS NCBILS2 SSSDB SP ORBacus ICU EXPAT SABLOT LIBXSLT LIBEXSLT Xerces Xalan Zorba SQLITE3 SQLITE3ASYNC VDB OECHEM SGE MUPARSER HDF5 TIFF GIF UNGIF GL2PS FTGL MAGIC MIMETIC GSOAP AVRO Cereal MONGODB MONGODB3 GMOCK LAPACK LIBUV LIBSSH2 CASSANDRA NGHTTP2 H2O LIBXLSXWRITER PROTOBUF GRPC MSGSL AWS_SDK
PROJECTS:
  enabled:  cgi serial objects dbapi app algo
  disabled: local_lbsm connext ncbi_crypt bdb ctools gui gbench

Tools / flags / paths:  /mnt/common/rh6/annotate/software/cddblast/ncbi-blast-2.9.0+-src/c++/ReleaseMT/build/Makefile.mk
Configuration  header:  /mnt/common/rh6/annotate/software/cddblast/ncbi-blast-2.9.0+-src/c++/ReleaseMT/inc/ncbiconf_unix.h

To build everything:  cd /mnt/common/rh6/annotate/software/cddblast/ncbi-blast-2.9.0+-src/c++/ReleaseMT/build && /usr/bin/make all_r
or simply run /usr/bin/make in the current directory

******* CONFIGURATION SUCCESSFUL *******

However the next "make" step fails. Below is the last lines of the error

/mnt/common/rh6/annotate/software/cddblast/ncbi-blast-2.9.0+-src/c++/ReleaseMT/build/Makefile.app:153: *** multiple target patterns.  Stop.
make[4]: Leaving directory `/mnt/common/rh6/annotate/software/cddblast/ncbi-blast-2.9.0+-src/c++/ReleaseMT/build/build-system/helpers'
make[3]: *** [all.nonusr] Error 2
make[3]: Leaving directory `/mnt/common/rh6/annotate/software/cddblast/ncbi-blast-2.9.0+-src/c++/ReleaseMT/build/build-system/helpers'
make[2]: *** [all_r.real] Error 5
make[2]: Leaving directory `/mnt/common/rh6/annotate/software/cddblast/ncbi-blast-2.9.0+-src/c++/ReleaseMT/build/build-system'
make[1]: *** [all_r.real] Error 5
make[1]: Leaving directory `/mnt/common/rh6/annotate/software/cddblast/ncbi-blast-2.9.0+-src/c++/ReleaseMT/build'
make: *** [all] Error 2

I think this might have something to do with the version of RHEL (6.9) I am using. But I have changed the GCC versions to 4.9.4 and also to 5.5.0. Recommended is any version above 4.7.0. But it fails both times with the same error. I am trying to troubleshoot this for the past 2 weeks, but not getting anywhere. Need help and advice fixing this. I have tried the 

make CXXFLAGS="-fpermissive"

and

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

options as suggested in some blogs. Unsuccessful. I have not tried both together though. In any case I need help

Thanks Abhijit

• 0 views • link
written by abhijit.synl abhijit.synl

As indicated in the compiling binaries page, you probably need to get the old blast (v. 2.2.19) and compile that. Interproscan many not be compatible with the latest blast+.

• 0 views • link
written by GenoMax GenoMax

1 answer

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.

• 0 views • link
written by Michael Schubert Michael Schubert

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

• 0 views • link
written by Heidi • Heidi

Hey,

Newblet question; Where can I find walkthrough instructions about how to edit CXXFLAGS? I'm new to linux and still educating myself.

• 0 views • link
written by Seth Munholland • Seth Munholland

@weebo.m55/Seth Munholland: This is a bioinformatics Q&A, your comment is actually a new question, and is best suited for stackexchange.com. So, I'm deleting it.

• 0 views • link
written by Leonor Palmeira Leonor Palmeira

I know this is about bioinformatics. I'm having the same problem in trying to get NCBI Blast set up for RepeatMasker and trying to follow this solution, however don't understand the profered isntructions well enough so I am asking for clarification. If you delete my post how am I supposed to get help with this same issue?

For the sake of clarity, I'm asking how to add -fpermissive to CXXFLAGS?

• 0 views • link
written by Seth Munholland • Seth Munholland

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