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 On Tue, Apr 9, 2019 at 7:27 AM Dean <[email protected]> wrote: > Hello, > > I'm hoping someone can help, the installation instructions > <http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS#Pulling_the_TPP_5.2.0_source_code_from_SourceForge> > 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 > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
