Two error occur when I use "make" in the dictionary "CESAR2.0/kent/src"

[chemy-cm]

Two errors as below:
#######
hmac.c:11:10: fatal error: openssl/hmac.h: No such file or directory
11 | #include "openssl/hmac.h"
| ^~~~~~~~~~~~~~~~
compilation terminated.
make[1]: *** [../inc/common.mk:420: hmac.o] Error 1
make[1]: Leaving directory '/root/software/CESAR2.0/kent/src/lib'
make: *** [makefile:9: topLibs] Error 2
#######
WHat should I do?

[MichaelHiller]

Pls check the gcc version. We have
gcc version 8.3.1 20191121 (Red Hat 8.3.1-5) (GCC)

But the error looks like openssl is not installed. Pls try
sudo apt-get install libssl-dev

[chemy-cm]

Thanks！
After I tried sometimes，except "gcc",I found that we need some lib:
1.libssl-dev
2.libpng-dev
3.uuid-dev
sudo apt-get install *
and then make success.
then, I still have problems.

When I run the cmd:

annotateGenesViaCESAR.pl POLR3K hg38_oryAfe1.bb twoGenes.gp.forCESAR hg38 oryAfe1 CESARoutput 2bitDir $profilePath -maxMemory 1

This software told me:

Can't locate Scalar/Util/Numeric.pm in @inc (you may need to install the Scalar::Util::Numeric module) (@inc contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /root/CESAR2.0/tools/annotateGenesViaCESAR.pl line 8.
BEGIN failed--compilation aborted at /root/CESAR2.0/tools/annotateGenesViaCESAR.pl line 8.

So I install the module Scalar::Util::Numeric by "cpan",It seems work.

And then I run the cmd:

bed2GenePred.pl oryAfe1 CESARoutput oryAfe1.gp

a new error is:

executing 'find CESARoutput -type f -path '/oryAfe1/' -exec cat {} ;' ...
gives 8 exons
overlapSelect: error while loading shared libraries: libssl.so.10: cannot open shared object file: No such file or directory
ERROR!! 'overlapSelect /dev/shm/P2MvR.bed /dev/shm/P2MvR.bed stdout -mergeOutput' failed in filterOverlappingExons function

I don't know what's wrong with libssl.so.10,could U plz tell me what to do now?
sincerely

[MichaelHiller]

I see. The issue is that overlapSelect is provided as a precompiled binary in tools/ and this doesn't work for you.

I tried to add the code to our slimmed down UCSC kent src directory, but it doesn't compile because it requires so many linked libs.

Can you pls try to install the entire kent code base from https://github.com/ucscGenomeBrowser/kent
This includes overlapSelect, which will be installed in the binDir that you specify.
If you have this binDir in your $PATH variable, then the perl script (which calls overlapSelect) should work.

[chemy-cm]

I attempt to install the entire kent code,seems install.
And I tried again.

executing  'find CESARoutput -type f -path '*/oryAfe1/*' -exec cat {} \;'  ...

The software told me：

gives 8 exons
overlapSelect: error while loading shared libraries: libssl.so.10: cannot open shared object file: No such file or directory
ERROR!! 'overlapSelect /dev/shm/pIddH.bed /dev/shm/pIddH.bed stdout -mergeOutput' failed in filterOverlappingExons function

the ERROR!! 'overlapSelect /dev/shm/P2MvR.bed /dev/shm/P2MvR.bed
become ERROR!! 'overlapSelect /dev/shm/pIddH.bed /dev/shm/pIddH.bed
Things very interesting.

It is difficult for me to probably resolve one by one errors,because I am not a computer coder,just a normal researcher or a user without some simple knowledge about linux and related knowledge.
I'm sure these errors could be solved. As the same time, It will take a lot of time to identify and solve these problems.

So,

I hope this software could use conda to install convenient or maybe you can release a Docker Container version to make sure everyone could install this software easily.

I think this is a good way.This is a very helpful for me and other users!
Thank you to answer my question!
Thanks a lot!
sincerely

[MichaelHiller]

Looks like overlapSelect is still not properly installed (pls test it by calling the UCSC version you installed with the full path to it).
Also, pls delete or rename the overlapSelect in CESAR's tools/ directory. It could be the script is still calling that, which would explain the same error message (except the temp file with different names).

Wrt Docker: Sorry for your trouble. And yes, a good idea. Our tool was developed in 2016 and unfortunately I don't have the manpower at the moment.

Also, CESAR2.0 is integrated in TOGA https://github.com/hillerlab/TOGA which is much more powerful and provides a docker container.