Dear all, I am trying to install demeter on my debian 7 computer and I cannot reach the end of the compilation. I followed the instructions from the https://gist.github.com/3959252 page. First, the "perl ./Build.PL" still requires "PDL::stats" even after several "./Build installdeps". I have the following message: """""""""""""""""""""""""""""""""""""""""""""""""""" letard@pcikieffer:~/demeter$ perl ./Build.PL Checking prerequisites... requires: ! PDL::Stats is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Demeter' version 'v0.9.21' If all dependencies are met, build and install Demeter by doing: ./Build ./Build test ./Build install # (or sudo ./Build install) If you are reinstalling Demeter after updating your operating system (or updating perl), you may find that none of the programs will run successfully. You may need to do: ./Build touch_wrapper ./Build test ./Build install # (or sudo ./Build install) """""""""""""""""""""""""""""""""""""""""""""""""""" Then, I decided to continue despite this missing prerequisite and the "./Build" ends with the folowing error: ##### Building Artemis User's Guide Building Athena User's Guide ! plugin error - Can't locate Clone.pm in @INC (@INC contains: /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/letard/perl5/lib/perl5 /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /usr/local/share/perl/5.14.2/PPI/Element.pm line 25. BEGIN failed--compilation aborted at /usr/local/share/perl/5.14.2/PPI/Element.pm line 25. Compilation failed in require at /usr/local/share/perl/5.14.2/PPI.pm line 19. BEGIN failed--compilation aborted at /usr/local/share/perl/5.14.2/PPI.pm line 19. Compilation failed in require at Template/Plugin/PerlSyntaxHtml.pm line 5. BEGIN failed--compilation aborted at Template/Plugin/PerlSyntaxHtml.pm line 5. Compilation failed in require at /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Template/Plugins.pm line 206. ##### So I don't know if something is missing on my computer or if one of you encountered similar problems. If one of you has some ideas to help me going further, I would really appreciate! Thanks a lot in advance. Isabelle -- Isabelle KIEFFER, Ingénieur de Recherche CNRS, Ligne CRG FAME (BM30B) ESRF - The European Synchrotron CS 40220 - 38043 Grenoble Cedex 9 - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50
Isabelle, Problem 1: I don't know why PDL::Stats is not installing correctly on your computer. That would be an issue to take up with its maintainer. Perhaps the easiest solution for you would be to install the debian package, which, in debian, is called libpdl-stats-perl. Problem 2: The error about Clone.pm not being installed suggests that another dependency, called PPI, did not install correctly. I would recommend installing the debian package for that one as well. Doing so should resolve all of PPI's own dependencies. In debian, that one is called libppi-perl. Try installing those two debian packages and trying the ".\Build" step again. Let us know if that does the trick. Cheers, B PS: I suppose I should mention that Demeter does not really care how you resolve its dependencies. The Build script makes no assumption about what kind of computer it is running on and so tries to resolve all of the dependencies by downloading and build the individual perl packages. However, resolving Demeter's dependencies by installing system specific packages (in this case, the debian packages) is functionally equivalent. So that is a good strategy for getting past a hurdle like this. On 07/13/2015 11:54 AM, Isabelle Kieffer wrote:
Dear all,
I am trying to install demeter on my debian 7 computer and I cannot reach the end of the compilation.
I followed the instructions from the https://gist.github.com/3959252 page.
First, the "perl ./Build.PL" still requires "PDL::stats" even after several "./Build installdeps". I have the following message: """""""""""""""""""""""""""""""""""""""""""""""""""" letard@pcikieffer:~/demeter$ perl ./Build.PL Checking prerequisites... requires: ! PDL::Stats is not installed
ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation
Run 'Build installdeps' to install missing prerequisites.
Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Demeter' version 'v0.9.21'
If all dependencies are met, build and install Demeter by doing:
./Build ./Build test ./Build install # (or sudo ./Build install)
If you are reinstalling Demeter after updating your operating system (or updating perl), you may find that none of the programs will run successfully. You may need to do:
./Build touch_wrapper ./Build test ./Build install # (or sudo ./Build install) """"""""""""""""""""""""""""""""""""""""""""""""""""
Then, I decided to continue despite this missing prerequisite and the "./Build" ends with the folowing error: ##### Building Artemis User's Guide Building Athena User's Guide ! plugin error - Can't locate Clone.pm in @INC (@INC contains: /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/letard/perl5/lib/perl5 /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /usr/local/share/perl/5.14.2/PPI/Element.pm line 25. BEGIN failed--compilation aborted at /usr/local/share/perl/5.14.2/PPI/Element.pm line 25. Compilation failed in require at /usr/local/share/perl/5.14.2/PPI.pm line 19. BEGIN failed--compilation aborted at /usr/local/share/perl/5.14.2/PPI.pm line 19. Compilation failed in require at Template/Plugin/PerlSyntaxHtml.pm line 5. BEGIN failed--compilation aborted at Template/Plugin/PerlSyntaxHtml.pm line 5. Compilation failed in require at /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Template/Plugins.pm line 206. #####
So I don't know if something is missing on my computer or if one of you encountered similar problems. If one of you has some ideas to help me going further, I would really appreciate!
Thanks a lot in advance. Isabelle
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
On 07/14/2015 09:41 AM, Bruce Ravel wrote:
The error about Clone.pm not being installed suggests that another dependency, called PPI, did not install correctly. I would recommend installing the debian package for that one as well. Doing so should resolve all of PPI's own dependencies. In debian, that one is called libppi-perl.
Doing "apt-cache depends libppi-perl" on my ubuntu machine shows that libclone-perl will be installed when you install libppi-perl. So that should resolve your second problem. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Dear Bruce, Thank you very much for your prompt answer. Indeed, I could complete the compilation. I have now a new dependency problem. The error concerns PerlIO/utf8_strict.pm. I found that I need the libperlio-utf8-strict-perl package, but my computer is running under wheezy and this package exists only in jessie or sid. Is there a solution to install only this package and its dependencies from jessie and preserve my wheezy installation? -- Did you manage to install demeter on Debian 7 or should I really consider to upgrade my computer? -- Thanks again, Isabelle On 14/07/2015 15:41, Bruce Ravel wrote:
Isabelle,
Problem 1:
I don't know why PDL::Stats is not installing correctly on your computer. That would be an issue to take up with its maintainer.
Perhaps the easiest solution for you would be to install the debian package, which, in debian, is called libpdl-stats-perl.
Problem 2:
The error about Clone.pm not being installed suggests that another dependency, called PPI, did not install correctly. I would recommend installing the debian package for that one as well. Doing so should resolve all of PPI's own dependencies. In debian, that one is called libppi-perl.
Try installing those two debian packages and trying the ".\Build" step again. Let us know if that does the trick.
Cheers, B
PS: I suppose I should mention that Demeter does not really care how you resolve its dependencies. The Build script makes no assumption about what kind of computer it is running on and so tries to resolve all of the dependencies by downloading and build the individual perl packages. However, resolving Demeter's dependencies by installing system specific packages (in this case, the debian packages) is functionally equivalent. So that is a good strategy for getting past a hurdle like this.
On 07/13/2015 11:54 AM, Isabelle Kieffer wrote:
Dear all,
I am trying to install demeter on my debian 7 computer and I cannot reach the end of the compilation.
I followed the instructions from the https://gist.github.com/3959252 page.
First, the "perl ./Build.PL" still requires "PDL::stats" even after several "./Build installdeps". I have the following message: """""""""""""""""""""""""""""""""""""""""""""""""""" letard@pcikieffer:~/demeter$ perl ./Build.PL Checking prerequisites... requires: ! PDL::Stats is not installed
ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation
Run 'Build installdeps' to install missing prerequisites.
Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Demeter' version 'v0.9.21'
If all dependencies are met, build and install Demeter by doing:
./Build ./Build test ./Build install # (or sudo ./Build install)
If you are reinstalling Demeter after updating your operating system (or updating perl), you may find that none of the programs will run successfully. You may need to do:
./Build touch_wrapper ./Build test ./Build install # (or sudo ./Build install) """"""""""""""""""""""""""""""""""""""""""""""""""""
Then, I decided to continue despite this missing prerequisite and the "./Build" ends with the folowing error: ##### Building Artemis User's Guide Building Athena User's Guide ! plugin error - Can't locate Clone.pm in @INC (@INC contains: /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/letard/perl5/lib/perl5 /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /usr/local/share/perl/5.14.2/PPI/Element.pm line 25. BEGIN failed--compilation aborted at /usr/local/share/perl/5.14.2/PPI/Element.pm line 25. Compilation failed in require at /usr/local/share/perl/5.14.2/PPI.pm line 19. BEGIN failed--compilation aborted at /usr/local/share/perl/5.14.2/PPI.pm line 19. Compilation failed in require at Template/Plugin/PerlSyntaxHtml.pm line 5. BEGIN failed--compilation aborted at Template/Plugin/PerlSyntaxHtml.pm line 5. Compilation failed in require at /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Template/Plugins.pm
line 206. #####
So I don't know if something is missing on my computer or if one of you encountered similar problems. If one of you has some ideas to help me going further, I would really appreciate!
Thanks a lot in advance. Isabelle
-- Isabelle KIEFFER, Ingénieur de Recherche CNRS, Ligne CRG FAME (BM30B) ESRF - The European Synchrotron CS 40220 - 38043 Grenoble Cedex 9 - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50
Just to follow up on this thread, after a lengthy and detailed-filled off-line conversation with Isabelle, we managed to clear up several issues related to Demeter's build scripts. Isabelle was very patient and helpful. Several improvements have been checked into the github repository. Isabelle's initial question was about a failed installation somewhere deep in Demeter's tree of dependencies when installing on a Debian linux computer. In its build script, Demeter identifies a list of packages that it uses. Each of those packages has its own list of dependencies. One of Demeter's installation steps attempts to retrieve the entire tree of dependencies from the repository of Perl packages and build each one. In Isabelle's case, a couple of items deep in the dependency tree failed to install correctly. Demeter does not much care how these dependencies get resolved. In the case of Isabelle's Debian linux computer, she was able to use the Debian packaging system to meet the dependencies that, for some reason, did not install correctly using Demeter's build script. For example, one of the problems she ran into gave an error message that read, in part: Can't locate PerlIO/utf8_strict.pm in @INC It turns out that this package: https://metacpan.org/pod/PerlIO::utf8_strict was deep in the dependency tree. (Something called Config::INI is an immediate dependency of Demeter, PerlIO::utf8_strict is one of its dependencies.) In Debian, this package is called "libperlio-utf8-strict-perl". By installing the Debian package, she met Demeter's requirement. Many of the packages that Demeter's build script attempts to download and build could be installed in this way. The reason I am explaining all this is because this is a common sort of problem for those installing Demeter from source code. I wanted to leave this explanation in the m ailing list archives for the benefit of anyone in the future who runs into a similar snag. Cheers, B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Dear Bruce, dear all, After installing demeter on my computer, I am now trying to install it on our beamline: a Ubuntu 12.04 machine. I followed https://gist.github.com/waveform80/3959252 instructions and I have a problem with PDL::Stats that persists as "not installed" dependency (see depsPDL_errors_2015-08-13.txt). I can find the corresponding package (libpdl-stats-perl) only for later Ubuntu versions thus I tried to install PDL::Stats via metacpan (cpanm PDL::Stats), but it failed (see cpanmbuild_PDLStats_2015-08-13.txt, which is the /home/fame/.cpanm/build.log mentioned at the end of the file itself). Does anyone has a solution to help me installing this missing dependency? Thank you very much in advance. Isabelle -- Isabelle KIEFFER, Ingénieur de Recherche CNRS ESRF - ligne CRG FAME (BM30B) BP 220 - 38 043 Grenoble CEDEX - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50
On 08/13/2015 10:51 AM, Isabelle Kieffer wrote:
Dear Bruce, dear all,
After installing demeter on my computer, I am now trying to install it on our beamline: a Ubuntu 12.04 machine. I followed https://gist.github.com/waveform80/3959252 instructions and I have a problem with PDL::Stats that persists as "not installed" dependency (see depsPDL_errors_2015-08-13.txt).
I can find the corresponding package (libpdl-stats-perl) only for later Ubuntu versions thus I tried to install PDL::Stats via metacpan (cpanm PDL::Stats), but it failed (see cpanmbuild_PDLStats_2015-08-13.txt, which is the /home/fame/.cpanm/build.log mentioned at the end of the file itself).
Does anyone has a solution to help me installing this missing dependency?
Thank you very much in advance.
Hi Isabelle, You have the option of simply ignoring this problem. If the module in question is absent, Athena et al should still run. However, the PCA tool in Athena will be disabled. That said, I got curious about the problem, so I used perlbrew to install perl 5.14.4. That's the closest version available under perlbrew to the perl version you are using on your computer, which is 5.14.2. I then installed PDL. I then tried to install PDL::Stats and ran into the same problem you are reporting. I have a solution, but it is requires you to do a bit of work. Download the PDL::Stats package from https://metacpan.org/pod/PDL::Stats (there is a download link about 1/2 way down on the left). Unpack it and cd into the new subdirectory. Open the file GLM/glm.pp in a text editor. At line 105 change PDL->propogate_badflag( b, 0 ); to PDL->propagate_badflag( b, 0 ); That is, correct the misspelling of the word "propagate". Do the same at line 172. (You can fix the typos at lines 103 and 170, but those are comment lines. Not necessary, unless you have particularly severe OCD!) Then do the standard incantation: perl Makefile.PL make make test make install # or sudo make install Worked for me. I have not yet installed all of Demeter under 5.14.4, so I have not yet tested whether PCA works after all this. It's getting kind of late, so I'll try that in the morning. Hopefully, this will get you over this hurdle. Presumably, the debian package did all that.... Please report back to the list about what happens. Good luck, B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Thank you very much: everything seems OK. We just have to play with it now. Isabelle On 13.08.2015 23:21, Bruce Ravel wrote:
On 08/13/2015 10:51 AM, Isabelle Kieffer wrote:
Dear Bruce, dear all,
After installing demeter on my computer, I am now trying to install it on our beamline: a Ubuntu 12.04 machine. I followed https://gist.github.com/waveform80/3959252 instructions and I have a problem with PDL::Stats that persists as "not installed" dependency (see depsPDL_errors_2015-08-13.txt).
I can find the corresponding package (libpdl-stats-perl) only for later Ubuntu versions thus I tried to install PDL::Stats via metacpan (cpanm PDL::Stats), but it failed (see cpanmbuild_PDLStats_2015-08-13.txt, which is the /home/fame/.cpanm/build.log mentioned at the end of the file itself).
Does anyone has a solution to help me installing this missing dependency?
Thank you very much in advance.
Hi Isabelle,
You have the option of simply ignoring this problem. If the module in question is absent, Athena et al should still run. However, the PCA tool in Athena will be disabled.
That said, I got curious about the problem, so I used perlbrew to install perl 5.14.4. That's the closest version available under perlbrew to the perl version you are using on your computer, which is 5.14.2.
I then installed PDL. I then tried to install PDL::Stats and ran into the same problem you are reporting. I have a solution, but it is requires you to do a bit of work.
Download the PDL::Stats package from https://metacpan.org/pod/PDL::Stats (there is a download link about 1/2 way down on the left). Unpack it and cd into the new subdirectory.
Open the file GLM/glm.pp in a text editor. At line 105 change
PDL->propogate_badflag( b, 0 );
to
PDL->propagate_badflag( b, 0 );
That is, correct the misspelling of the word "propagate". Do the same at line 172. (You can fix the typos at lines 103 and 170, but those are comment lines. Not necessary, unless you have particularly severe OCD!)
Then do the standard incantation:
perl Makefile.PL make make test make install # or sudo make install
Worked for me.
I have not yet installed all of Demeter under 5.14.4, so I have not yet tested whether PCA works after all this. It's getting kind of late, so I'll try that in the morning.
Hopefully, this will get you over this hurdle. Presumably, the debian package did all that....
Please report back to the list about what happens.
Good luck, B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973
Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Isabelle KIEFFER, Ingénieur de Recherche CNRS ESRF - ligne CRG FAME (BM30B) BP 220 - 38 043 Grenoble CEDEX - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50
participants (2)
-
Bruce Ravel -
Isabelle Kieffer