Error with installation

[sigven]

Hi,

I have used your nice tool for a long time, downloading and installing within a Dockerfile. It has worked perfect for my purposes (multiallelic variant decomposition). However, I am now unable to compile with make for some reason, not really sure why it's now complaining:

cd lib/libdeflate; make || exit 1;
make[1]: Entering directory '/data/sigven/software/vt/lib/libdeflate'
CC lib/deflate_decompress.o
make[1]: *** No rule to make target 'lib/utils.c', needed by 'lib/utils.o'. Stop.
make[1]: Leaving directory '/data/sigven/software/vt/lib/libdeflate'
make: *** [Makefile:151: lib/libdeflate/libdeflate.a] Error 1

Make version:
GNU Make 4.3

Any idea what's the problem?

thanks,
Sigve

[evatosco]

I was just about to post the same issue. I'm installing Vt first time (Ubuntu 20.04) because I need it to decompose vcf files as input for another software I'm trying. My error logs are the exact same when I try make test, but in spanish though -just ignore that-:

$make test
cd lib/libdeflate; make || exit 1; 
make[1]: se entra en el directorio '/home/nebulosa/Software/Vt/vt/lib/libdeflate'
make[1]: *** No hay ninguna regla para construir el objetivo 'lib/utils.c', necesario para 'lib/utils.o'.  Alto.
make[1]: se sale del directorio '/home/nebulosa/Software/Vt/vt/lib/libdeflate'
make: *** [Makefile:151: lib/libdeflate/libdeflate.a] Error 1

My Make version:

GNU Make 4.2.1

I hope there's a way to solve this!

Thanks in advance!
Eva

[sigven]

Eva,

You may try a workaround using Conda, that worked for me, i.e.

wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
chmod 0755 miniconda.sh
./miniconda.sh
conda update conda
conda install -c bioconda vt

regards,
Sigve

[evatosco]

I installed it using miniconda, and it works for now. I just guess I have to get to the folder where the vt executable is saved to run it and then add file paths and so on to the commands. It seems to work. Thank you so much!!

[kkapuria3]

same issue with installation in dockerfile. Miniconda can only be used if you are using a centos based container. I was running vt in alpine container, and with this, its totally unusable

[webhash]

hey @atks ... I'm also seeing the same issue and can't use Conda ... there is no lib/utils.c file and thus the compilation fails ... any workaround please ?

[thedam]

yep, same error too :)

[marchoeppner]

For those with this particular issue, you can clone the repo and then:
cd vt
git checkout 0.577
make

I.e. you go back to the previous "working" release 0.577 and then it should compile. Still, this issue should be adressed with a proper fix.

[clarek20]

Going back to release 0.577 results in a different error for me:

In file included from bgzf.c:39:
htslib/bgzf.h:34:10: fatal error: zlib.h: No such file or directory
34 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.

[ayamgupta]

I got past this error by manually pulling the libdeflate from git. But there is an issue with the hts_utils.cpp file
got this error

hts_utils.cpp: In function 'void bam_get_base_and_qual_and_read_and_qual(bam1_t*, uint32_t, char&, char&, int32_t&, kstring_t*, kstring_t*)':
hts_utils.cpp:310:24: error: 'assert' was not declared in this scope
assert(stop);
^
Makefile:174: recipe for target 'hts_utils.o' failed
make: *** [hts_utils.o] Error 1

A workaround this is to add header --> #include "assert.h" in the "hts_utils.cpp" file.

now i am stuck here.

ahmm.o: In function AHMM::track2string[abi:cxx11](int)': ahmm.cpp:(.text+0x2446): undefined reference to ks_resize2(kstring_t*, unsigned long)'
ahmm.cpp:(.text+0x25a0): undefined reference to ks_resize2(kstring_t*, unsigned long)' ahmm.cpp:(.text+0x25e6): undefined reference to ks_resize2(kstring_t*, unsigned long)'
ahmm.cpp:(.text+0x266e): undefined reference to ks_resize2(kstring_t*, unsigned long)' ahmm.cpp:(.text+0x268e): undefined reference to ks_resize2(kstring_t*, unsigned long)'
ahmm.o:ahmm.cpp:(.text+0x26ae): more undefined references to `ks_resize2(kstring_t*, unsigned long)' follow
collect2: error: ld returned 1 exit status
Makefile:169: recipe for target 'vt' failed
make: *** [vt] Error 1

[aydemiro]

@clarek20: marchoeppner's suggestion should work. See if installing libz-dev (or the corresponding package for your OS) solves your issue.

[addievereijken]

I got similar experiences with compiling vt after cloning it from github. Now, instead of compiling vt-master,
I have downloaded the source file vt-0.57721. After giving permission to some *.sh file I could compile VT without errors.