Yes, that saw the make move forward, and compiling is running along now. Thanks for the quick reply and fix.
On Tuesday, 9 April 2019 10:32:17 UTC-4, David Shteynberg wrote: > > 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] <javascript:>> > 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
