pacoxph

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jk20
Posts: 3
Joined: Sun Nov 15, 2015 10:58 pm

pacoxph

Postby jk20 » Mon Nov 16, 2015 12:06 am

Hi,

I installed ProbABEL(probabel-0.4.5.tar.gz) in unix with Eigen following installation instructions. Everything works well, except for "pacoxph". I have no idea why only pacoxph was not installed properly. Could you help me to fix it?

There was no error message during installation. After installation, pacoxph, palinear, and palogist were in the bin folder of "ProbABEL".
When running each of them, palinear and palogist run well but pacoxph does not.

Code: Select all

@:~/ProbABEL/bin> palinear
ProbABEL v. 0.2.0 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
Usage: palinear options

Code: Select all

@:~/ProbABEL/bin> palogist
ProbABEL v. 0.2.0 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
Usage: palogist options

Code: Select all

@:~/ProbABEL/bin> pacoxph
If 'pacoxph' is not a typo you can run the following command to lookup the package that contains the binary:
    command-not-found pacoxph
-bash: pacoxph: command not found

Would you give any suggestions to figure it out?

Thanks,
Joey
Last edited by lckarssen on Mon Nov 16, 2015 9:13 am, edited 1 time in total.
Reason: Reformatted output with the [code] tag

lckarssen
Site Admin
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Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: pacoxph

Postby lckarssen » Mon Nov 16, 2015 9:41 am

That's strange! I just double checked and if I simply run

Code: Select all

./configure
make
make install

the pacoxph binary gets installed properly.

Can you run the following grep command in the ProbABEL source directory? In my case it shows that building of pacoxph is enabled. Maybe it's somehow different in your case.

Code: Select all

$ grep cox config.log
configure:5861: building of pacoxph is enabled
BUILD_pacoxph_FALSE='#'
BUILD_pacoxph_TRUE=''


And can you run these commands as well and post the output:

Code: Select all

which palinear
which pacoxph
-------
Lennart Karssen
PolyOmica
The Netherlands
-------

jk20
Posts: 3
Joined: Sun Nov 15, 2015 10:58 pm

Re: pacoxph

Postby jk20 » Tue Nov 17, 2015 2:56 am

I ran the grep command in the ProbABEL source directory. It showed that pacoxph was enabled.

Code: Select all

@:~/bin/probabel-0.4.5> grep cox config.log
configure:5861: building of pacoxph is enabled
BUILD_pacoxph_FALSE='#'
BUILD_pacoxph_TRUE=''

But when I run which command, only pacoxph was not found. It's very weird.

Code: Select all

@:~/bin/probabel-0.4.5> which palinear
/usr/local/bin/palinear
@:~/bin/probabel-0.4.5> which palogist
/usr/local/bin/palogist
@:~/bin/probabel-0.4.5> which pacoxph
which: no pacoxph in (/home/bin/EIG5.0.2/bin:/usr/local/lib:/home/bin:/usr/local/bin)

Would you give any more advices or suggestions? Do you think it would be resolved if I re-install ProbABEL?

Thanks for all help.
Joey

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: pacoxph

Postby lckarssen » Tue Nov 17, 2015 10:57 am

jk20 wrote:Would you give any more advices or suggestions? Do you think it would be resolved if I re-install ProbABEL?

That may indeed be a good idea. Trying it won't hurt in any case. It would be great if you could then post the screen output of the make install command so we can try to track what went wrong.


As a side note: when posting command output or programming code you can encapsulate it in between [code] tags for proper formatting like I did with your posts above.
-------
Lennart Karssen
PolyOmica
The Netherlands
-------

jk20
Posts: 3
Joined: Sun Nov 15, 2015 10:58 pm

Re: pacoxph

Postby jk20 » Sat Nov 21, 2015 8:01 pm

Hi Lennart, I re-installed ProbABEL and pacoxph is still not working with the same error message above. The below is the screen output of the make install command. Can you help me to know if you find anything wrong below?
Thanks for your time and help.

Code: Select all

@:~/bin/probabel-0.4.5> make install
Making install in src
make[1]: Entering directory `/home/bin/probabel-0.4.5/src'
make[2]: Entering directory `/home/bin/probabel-0.4.5/src'
 /bin/mkdir -p '/home/bin/ProbABEL/bin'
  /usr/bin/install -c palinear palogist pacoxph '/home/bin/ProbABEL/bin'
 /bin/mkdir -p '/home/bin/ProbABEL/bin'
 /usr/bin/install -c probabel '/home/bin/ProbABEL/bin'
 /bin/mkdir -p '/home/bin/ProbABEL/etc'
 /usr/bin/install -c -m 644 probabel_config.cfg.example '/home/bin/ProbABEL/etc'
make  install-exec-hook
make[3]: Entering directory `/home/bin/probabel-0.4.5/src'
/usr/bin/sed -i -e "s;probabel_config.cfg;/home/bin/ProbABEL/etc/probabel_config.cfg;" \
      /home/bin/ProbABEL/bin/probabel
/usr/bin/sed -i -e "s;\./;/home/bin/ProbABEL/bin/;" /home/bin/ProbABEL/bin/probabel
/usr/bin/sed -i -e "s;PROBABEL_VERSION;0.4.5;" /home/bin/ProbABEL/bin/probabel
ln -s /home/bin/ProbABEL/bin/probabel /home/bin/ProbABEL/bin/probabel.pl
make[3]: Leaving directory `/home/bin/probabel-0.4.5/src'
 /bin/mkdir -p '/home/bin/ProbABEL/share/probabel/scripts'
 /usr/bin/install -c -m 644 prepare_data.R extIDS.pl '/home/bin/ProbABEL/share/probabel/scripts'
make  install-data-hook
make[3]: Entering directory `/home/bin/probabel-0.4.5/src'
chmod a+rx //home/bin/ProbABEL/share/probabel/scripts/extIDS.pl
make[3]: Leaving directory `/home/bin/probabel-0.4.5/src'
make[2]: Leaving directory `/home/bin/probabel-0.4.5/src'
make[1]: Leaving directory `/home/bin/probabel-0.4.5/src'
Making install in doc
make[1]: Entering directory `/home/bin/probabel-0.4.5/doc'
make[2]: Entering directory `/home/bin/probabel-0.4.5/doc'
make[2]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/home/bin/ProbABEL/share/doc/probabel'
 /usr/bin/install -c -m 644 ProbABEL_manual.tex QuickStart.txt short_coxph_data.txt short_height_base_add.out.txt.save short_height.txt short_logist_data.txt short_test.mldose test.map test.mlinfo test_regression.R COPYING LICENSE INSTALL ChangeLog TODO '/home//bin/ProbABEL/share/doc/probabel'
 /bin/mkdir -p '/home/bin/ProbABEL/share/man/man1'
 /usr/bin/install -c -m 644 probabel.1 probabel.pl.1 palinear.1 palogist.1 pacoxph.1 '/home/bin/ProbABEL/share/man/man1'
make[2]: Leaving directory `/home/bin/probabel-0.4.5/doc'
make[1]: Leaving directory `/home/bin/probabel-0.4.5/doc'
Making install in checks
make[1]: Entering directory `/home/bin/probabel-0.4.5/checks'
make[2]: Entering directory `/home/bin/probabel-0.4.5/checks'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/bin/probabel-0.4.5/checks'
make[1]: Leaving directory `/home/bin/probabel-0.4.5/checks'
Making install in examples
make[1]: Entering directory `/home/bin/probabel-0.4.5/examples'
make[2]: Entering directory `/home/bin/probabel-0.4.5/examples'
make[2]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/home/bin/ProbABEL/share/probabel/examples'
 /usr/bin/install -c -m 644 height.txt logist_data.txt mmscore_pheno.PHE coxph_data.txt mmscore.R mmscore_InvSigma_aj.sex.age.dat README '/home//bin/ProbABEL/share/probabel/examples'
 /bin/mkdir -p '/home/bin/ProbABEL/share/probabel/examples'
 /usr/bin/install -c example_qt.sh example_bt.sh example_cox.sh example_mmscore.sh '/home/bin/ProbABEL/share/probabel/examples'
 /bin/mkdir -p '/home/bin/ProbABEL/share/probabel/examples/gtdata'
 /usr/bin/install -c -m 644 gtdata/test.mldose gtdata/test.mlprob gtdata/test.mlinfo gtdata/test.map gtdata/test.dose.fvi gtdata/test.dose.fvd gtdata/test.prob.fvi gtdata/test.prob.fvd gtdata/mmscore_gen.mlinfo gtdata/mmscore_gen.mldose gtdata/mmscore_gen.mlprob gtdata/mmscore_gen.dose.fvi gtdata/mmscore_gen.dose.fvd gtdata/mmscore_gen.prob.fvi gtdata/mmscore_gen.prob.fvd '/home//bin/ProbABEL/share/probabel/examples/gtdata'
make[2]: Leaving directory `/home/bin/probabel-0.4.5/examples'
make[1]: Leaving directory `/home/bin/probabel-0.4.5/examples'
Making install in checks/R-tests
make[1]: Entering directory `/home/bin/probabel-0.4.5/checks/R-tests'
make[2]: Entering directory `/home/bin/probabel-0.4.5/checks/R-tests'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/bin/probabel-0.4.5/checks/R-tests'
make[1]: Leaving directory `/home/bin/probabel-0.4.5/checks/R-tests'
make[1]: Entering directory `/home/bin/probabel-0.4.5'
make[2]: Entering directory `/home/bin/probabel-0.4.5'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/bin/probabel-0.4.5'
make[1]: Leaving directory `/home/bin/probabel-0.4.5'

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: pacoxph

Postby lckarssen » Sat Nov 21, 2015 9:04 pm

Ah, I think I overlooked something, I must have been sleeping. I
n your first post, you wrote that you were in the directory ~/ProbABEL/bin/ and then you ran palinear. But as the which command showed, you already have palinear and palogist installed in /usr/local/bin/. I should have noticed this, and as you can see in your first post these are the ones that are selected when you type palinear, they are version 0.2.0 (very old!).

Please double check that the three tools are indeed installed in ~/ProbABEL/bin, then instead of typing e.g. pacoxph, type ~/ProbABEL/bin/pacoxph[/i] (so the full path to the executable). This is because Unix/Linux doesn't look in the current directory when searching executable files.


By the way, which options did you specify when you ran ./configure? Looking at the output you posted above, I guess you (at least) used the --prefix=/home/bin/ProbABEL option. This means that the binaries end up in /home/bin/ProbABEL/bin, not in /usr/local/bin/.

One strange thing to note: the output says /home/bin/ProbABEL/bin, but in your first post you wrote ~/ProbABEL/bin/, is your home directory indeed just /home instead of /home/username?
-------
Lennart Karssen
PolyOmica
The Netherlands
-------


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