Problem installing stacks 1-43

[Sab Le Cam]

Hello,

I am having trouble installing the latest version of stacks (1.43) in Ubuntu 16.04 and I can't find the reason.
I already had warning at the ./configure step (see outcome below)

I still tried sudo make install and I get the following error message

g++: error: ./htslib/libhts.a: No such file or directory
Makefile:1234: recipe for target 'pstacks' failed
make[1]: *** [pstacks] Error 1
make[1]: Leaving directory '/home/slecam/Downloads/stacks-1.43'
Makefile:3417: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1


Thanks in advance for the help
Cheers
Sabrina

./configure

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking whether g++ supports C++11 features by default... no
checking whether g++ supports C++11 features with -std=gnu++11... yes
checking for omp_set_num_threads in -lgomp... yes
checking for gzread in -lz... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for gcc option to support OpenMP... -fopenmp
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether closedir returns void... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for floor... no
checking for memset... yes
checking for pow... no
checking for sqrt... no
checking for gawk... (cached) gawk
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands

[Julian Catchen]

Hi Sabrina,

Run 'make' before you run 'make install'. The 'make install' alone
doesn't trigger the building of the libhts BAM library, but 'make' will.

julian

Sab Le Cam wrote:
> Hello,
>
> I am having trouble installing the latest version of stacks (1.43) in
> Ubuntu 16.04 and I can't find the reason.
> I already had warning at the ./configure step (see outcome below)
>

> I still tried /sudo make install/ and I get the following error message

[Sibelle Vilaça]

Hi Julian,

on the same topic, since I upgraded my linux to 16, the database doens't work anymore. I keep seeing the php code on the browser. This happened to two of our computers, the ones that we didn't upgrade we can still see the normal stacks database page. Do you have any suggestions how to fix this?

Cheers

Sibelle

   \-/  Sibelle Torres Vilaça, PhD

   /\  

  /--|  Postdoctoral Research Fellow

 /---/ 
 |--/   Berlin Center for Genomics in Biodiversity Research

 \-/    Koenigin-Luise-Str. 6-8

 /\     14195 - Berlin, Germany

/--\    +49-(0)30-838-59968
|---\   

 \---\  Leibniz Institute for Zoo and Wildlife Research

  \--|  Department of Evolutionary Genetics

   \-/  Alfred-Kowalke-Str. 17

   /\   10315 - Berlin, Germany

  /--\ 

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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[Julian Catchen]

Hi Sibelle,

If the PHP code is no longer rendering, then my first guess would be
that your PHP installation was not upgraded or it was disabled during
the upgrade. Check that the PHP package is installed and that there is a
configuration file for it in the Apache /etc config directory. Linux
distributions are moving from PHP5 to PHP7 so there may be some
configuration issues that pop up.

Otherwise, check the apache logs (/var/log/apache/error_log,
/var/log/messages or /var/log/syslog) as you try to load the web page in
your browser for errors.

julian

[Sab Le Cam]

many thanks (again!) julian

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