How do I compile ppflag-fixer?

[lordzappo]

My guess doesn't work...

/opt/common/CentOS_6/gcc/gcc-4.9.3/bin/g++ -std=c++11 -I /opt/common/CentOS_6-dev/htslib/v1.3.2/ ppflag-fixer.cpp -L /opt/common/CentOS_6-dev/htslib/v1.3.2/ -lhts -Wl,-rpath=/opt/common/CentOS_6-dev/htslib/v1.3.2/ -o ppflag-fixer

ppflag-fixer.cpp: In function âint program_main(arguments)â: ppflag-fixer.cpp:115:22: error: expected â)â before âPRIu64â printf("Reading %" PRIu64 "read(s).\n", index_total); ^ ppflag-fixer.cpp:173:13: error: expected â)â before âPRIu64â printf("%" PRIu64 " reads were changed.\n", edited);

[veseshan]

This worked for me in my Ubuntu setup. So I googled "centos PRIu64" and found this link http://stackoverflow.com/questions/14535556/why-doesnt-priu64-work-in-this-code which seems to say you need additional statements in the header file (#define __STDC_FORMAT_MACROS or some such before #inttypes.h).

Let me know if that fixes it and I will add it to ppflag-fixer.h

Thanks, Venkat

[veseshan]

I added #define __STDC_FORMAT_MACROS and it compiled on luna. File updated on GitHub.

Venkat

[lordzappo]

Yes this does indeed fix it thank you

[LisaSikkema]

I'm also having problems compiling, this is the command I'm using:

g++ -std=c++11 -I /Users/sikkemal/Software/htslib-1.6/ ppflag-fixer.cpp -L /Users/sikkemal/Software/htslib-1.6/ -lhts -Wl,-rpath=/Users/sikkemal/Software/htslib-1.6/ -o ppflag-fixer

and it gives me the following error:

ppflag-fixer.cpp:3:10: fatal error: 'argp.h' file not found

The htslib folders do not exactly match up with the ones in the readme file, but I tried different ones and none of them seem to work (htslib-1.6/ or htslib-1.6/htslib/, also tried with and without the /include part.) Am I doing something wrong?

[veseshan]

It seems like you are trying to compile on a Mac. I don't use one and so can't tell if it will work. But on a Linux (Ubuntu Xenial) server I installed htslib locally as follows:

./configure --prefix=$HOME/hts make make install

Then compiled ppflag-fixer using

g++ -std=c++11 -I$HOME/hts/include ppflag-fixer.cpp -L$HOME/hts/lib -lhts -Wl,-rpath=$HOME/hts/lib -o ppflag-fixer

which compiled with no errors. Without the make install step in htslib the files won't be in proper locations which could be the source of your problem.

Venkat

[veseshan]

The message "ppflag-fixer.cpp:3:10: fatal error: 'argp.h' file not found" makes me wonder if there's a more fundamental problem in your setup since argp.h is part of gcc.

[thatoddmailbox]

The compilation problem you are running into here is because on recent versions OS X, gcc is actually an alias to clang. The argp library that I used is only a part of the GNU libc and so is only provided with gcc. However, if you have the Homebrew package manager installed, you should be able to do brew install argp-standalone, which will install a replacement for the argp library that does not require gcc. You will then need to add -largp to the command you run (after the -lhts) so that it knows to link to the argp-standalone library, but it should otherwise be a drop-in replacement, with no code changes needed.

[veseshan]

Thanks Alex. Happy New Year. - Venkat

[LisaSikkema]

Yes, it seems to have worked! Thank you both a lot for your replies and help!

[LisaSikkema]

or actually, it did output a ppflag-fixer executable file, but I still can't seem to run ppflag-fixer:

-bash: ppflag-fixer: command not found

the output of my command ("-v" added)

g++ -std=c++11 ppflag-fixer.cpp -lhts -largp -o ppflag-fixer -v

was this:

Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn) Target: x86_64-apple-darwin13.4.0 Thread model: posix "/Library/Developer/CommandLineTools/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.9.0 -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name ppflag-fixer.cpp -mrelocation-model pic -pic-level 2 -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 241.9 -v -resource-dir /Library/Developer/CommandLineTools/usr/bin/../lib/clang/6.0 -stdlib=libc++ -std=c++11 -fdeprecated-macro -fdebug-compilation-dir /Users/sikkemal/Software/htstools-master -ferror-limit 19 -fmessage-length 110 -stack-protector 1 -mstackrealign -fblocks -fobjc-runtime=macosx-10.9.0 -fencode-extended-block-signature -fcxx-exceptions -fexceptions -fdiagnostics-show-option -fcolor-diagnostics -vectorize-slp -o /var/folders/r2/csyxs9791tvc38wdrrv0d8s109l7vq/T/ppflag-fixer-befdb8.o -x c++ ppflag-fixer.cpp clang -cc1 version 6.0 based upon LLVM 3.5svn default target x86_64-apple-darwin13.4.0 ignoring nonexistent directory "/usr/include/c++/v1"

include "..." search starts here:

include <...> search starts here:

/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1 /usr/local/include /Library/Developer/CommandLineTools/usr/bin/../lib/clang/6.0/include /Library/Developer/CommandLineTools/usr/include /usr/include /System/Library/Frameworks (framework directory) /Library/Frameworks (framework directory) End of search list. "/Library/Developer/CommandLineTools/usr/bin/ld" -demangle -dynamic -arch x86_64 -macosx_version_min 10.9.0 -o ppflag-fixer /var/folders/r2/csyxs9791tvc38wdrrv0d8s109l7vq/T/ppflag-fixer-befdb8.o -lhts -largp -lc++ -lSystem /Library/Developer/CommandLineTools/usr/bin/../lib/clang/6.0/lib/darwin/libclang_rt.osx.a

Not sure if the installation was successful, or how to run ppflag-fixer now. Any ideas?

Thanks!

[veseshan]

Seems like you are doing just ppflag-fixer from the directory where your executable is. You may need to do ./ppflag-fixer Alternately, have you tried using the full path of the ppflag-fixer executable?

[LisaSikkema]

yes, that's it! Thanks! (sorry, I'm kind of new to all of this, which is why my question might be about basic stuff)

[veseshan]

In unix like os current working directory is not in executable path.