TPP 5.2 Compile Error

[Dean]

Hello,

I'm hoping someone can help, the installation instructions mention I should post the error message here.  Below is the error message I'm getting stuck at when attempting to compile comet.

[~/TPP/release_5-2-0]$ make all

cd /root/TPP/release_5-2-0/build/gnu-x86_64/artifacts/comet_source_2018014; make

make[1]: Entering directory '/root/TPP/release_5-2-0/build/gnu-x86_64/artifacts/comet_source_2018014'

g++ -O3 -Wall -Wextra -static -Wno-char-subscripts -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -IMSToolkit/include -ICometSearch Comet.cpp -c

In file included from CometSearch/Common.h:40,

                 from Comet.cpp:18:

MSToolkit/include/MSReader.h:96:80: error: invalid conversion from âcharâ to âchar*â [-fpermissive]

   void writeFile(const char* c, MSFileFormat ff, MSObject& m, char* sha1Report='\0');

                                                                                ^~~~

Comet.cpp: In function âvoid LoadParameters(char*, CometInterfaces::ICometSearchManager*)â:

Comet.cpp:235:24: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]

                sprintf(szVersion, "%s %s %s", szVersion, szRev1, szRev2);

                        ^~~~~~~~~              ~~~~~~~~~

Makefile:20: recipe for target 'Comet.o' failed

make[1]: *** [Comet.o] Error 1

make[1]: Leaving directory '/root/TPP/release_5-2-0/build/gnu-x86_64/artifacts/comet_source_2018014'

extern/Makefile:353: recipe for target '/root/TPP/release_5-2-0/build/gnu-x86_64/artifacts/comet_source_2018014/comet' failed

make: *** [/root/TPP/release_5-2-0/build/gnu-x86_64/artifacts/comet_source_2018014/comet] Error 2

[~/TPP/release_5-2-0 ]$ g++ -v

Using built-in specs.

COLLECT_GCC=g++

COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/8/lto-wrapper

OFFLOAD_TARGET_NAMES=nvptx-none

OFFLOAD_TARGET_DEFAULT=1

Target: x86_64-linux-gnu

Configured with: ../src/configure -v --with-pkgversion='Debian 8.3.0-6' --with-bugurl=file:///usr/share/doc/gcc-8/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-8 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu

Thread model: posix

gcc version 8.3.0 (Debian 8.3.0-6)

[~/TPP/release_5-2-0 ]$ lsb_release -a

No LSB modules are available.

Distributor ID: Debian

Description:    Debian GNU/Linux unstable (sid)

Release:        unstable

Codename:       sid

[~/TPP/release_5-2-0 ]$

Any assistance would be greatly appreciated.

Thanks,

-Dean

[David Shteynberg]

Hello Dean,

There is a bug in the comet zip file that causes some newer (stricter) compiler error out.  If you replace the version you have:

/root/TPP/release_5-2-0/extern/comet_source_2018014.zip

with

https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/extern/comet_source_2018014.zip

It should solve this problem.

Cheers,

-David

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[Dean]

Yes, that saw the make move forward, and compiling is running along now.

Thanks for the quick reply and fix.

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