'lzma.h' file not found, please help!

The program you are trying to compile needs to include the lzma.h header file which it cannot find.

Either the source code that you downloaded was incomplete, or it was expecting to find something installed by default and it is not where it expected it to be.

ssabu1234 wrote:

Furthermore, I do have lzma file in bin, I even try to rewrite it in lzma.h. However, it does not work...

This does not make sense.

A .h file is a "header" file that contains definitions of stuff so other parts of the program know how to use them.

Either the xz package was not correctly installed, or the lzma.h file is there but the compiler can't find it.

Probably because it is an folder that includes a version number in the path.

You should find where xz is installed.

Try this command in Terminal:

sudo find /usr -name lzma.h -print

enter your password when asked (nothing will display), and press enter. In a few seconds it should show you something. Let us know.

/usr/local/Cellar/xz/5.2.3/include/lzma.h

/usr/local/include/lzma.h

was the print

Have tried installing a few packages and also get

fatal error: 'lzma.h' file not found

#include <lzma.h>

Thoughts?

astroperson08 wrote:

/usr/local/Cellar/xz/5.2.3/include/lzma.h

/usr/local/include/lzma.h

was the print

Have tried installing a few packages and also get

fatal error: 'lzma.h' file not found

#include <lzma.h>

Thoughts?

Try adding the path to the appropriate include folders to the command line, with the -I option (that is a capital vowel "eye", not a lowercase "ell")

It could be something like:

gcc -g -Wall -O2 -I. -I/usr/local/include -c -o cram/cram_io.o cram/cram_io.c

I had the same not found issue and ended up downloading the xz-5.2.3 source from (https://tukaani.org/xz/) and building it from source.This solved my problem.

Note that I first downloaded the OS package installer (same page) which did not add the libraries, you apparently really need to build the whole thing from source to get the right files put in /usr/local/include and alikes ....

Hope this will help others!

I would like to say that I am still facing the issue. I am trying to install a tool known as samtools and it has the problem with this lzma.h, so going through the forums, I downloaded the xz utils from this link (https://tukaani.org/xz/) , downloaded source *.tar.gz and build it , compiled. It ran smoothly but then again when am trying to complile the samtools it shows the same error below

samtools-1.5 vdas$ make

cd htslib-1.5 && /Applications/Xcode.app/Contents/Developer/usr/bin/make lib-static

gcc -g -Wall -O2 -I.
-c -o cram/cram_io.o cram/cram_io.c

cram/cram_io.c:60:10: fatal error: 'lzma.h' file not found

#include <lzma.h>

^

1 error generated.

make[1]: *** [cram/cram_io.o] Error 1

make: *** [htslib-1.5/libhts.a] Error 2

Now having tried to see where the lzma files are I tried

sudo find /usr -name lzma.h -print

Password:

/usr/local/Cellar/xz/5.2.3/include/lzma.h

/usr/local/include/lzma.h

/usr/local/octave/3.8.0/include/lzma/lzma.h

/usr/local/octave/3.8.0/include/lzma.h

I also tried the below command:

host009:samtools-1.5 vdas$ gcc -g -Wall -O2 -I. -I/usr/local/include -c -o cram/cram_io.o cram/cram_io.c

clang: error: no such file or directory: 'cram/cram_io.c'

clang: error: no input files

Now am not sure how to get rid of this error. It would be nice to have some pointers.

When you run the gcc command, it is not finding the .h file.

You need to help it find it, by adding the appropriate path to look for includes.

Change the line:

gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c

to

gcc -g -Wall -O2 -I. -I/usr/local/include -c -o cram/cram_io.o cram/cram_io.c

Hello:

I had this same problem as well and tried various iterations of installing xz. I finally managed to fix it by including a flag --disable-lzma in the configure step.

So, from start to finish:

cd bcftools-1.5

./configure --disable-lzma --prefix=

/where/to/install

make

make install

export PATH=

/where/to/install

Best of luck!

chmod 777 /usr/local/share/doc/xz

brew link --overwrite xz

Thanks! That was helpful. It worked for me.