Comments for Palaeontology 2.0

Comment on pdflatex errors and R by Germán

Germán — Thu, 12 Apr 2012 21:53:14 +0000

Thanks! Same here, the problem was solved by installing texinfo.

Comment on MrBayes and multicore processors by Seth

Seth — Tue, 28 Feb 2012 03:12:21 +0000

After issuing the make command the first few lines look like this:
root@ubuntu:/usr/local/bin/mrbayes_3.2.1/src# make
mpicc -O3 -ffast-math -Wall -DNDEBUG -I/usr/local/include/libhmsbeagle-1 -DUSECONFIG_H -c -o bayes.o bayes.c
mpicc -O3 -ffast-math -Wall -DNDEBUG -I/usr/local/include/libhmsbeagle-1 -DUSECONFIG_H -c -o command.o command.c
command.c: In function ‘FreeCharacters’:
command.c:9236:10: warning: variable ‘memoryLetFree’ set but not used [-Wunused-but-set-variable]
command.c: In function ‘ParseCommand’:
command.c:13792:12: warning: ‘numMatches’ may be used uninitialized in this function [-Wuninitialized]
mpicc -O3 -ffast-math -Wall -DNDEBUG -I/usr/local/include/libhmsbeagle-1 -DUSECONFIG_H

Then there is a long list of errors including in:

mbbeagle.c:(.text+0x1f02): undefined reference to `beagleSetCategoryRates’
mbbeagle.c:(.text+0x204a): undefined reference to `beagleUpdateTransitionMatrices’
mbbeagle.o: In function `LaunchBEAGLELogLikeForDivision’:
mbbeagle.c:(.text+0x23b8): undefined reference to `beagleResetScaleFactors’
mbbeagle.c:(.text+0×2559): undefined reference to `beagleResetScaleFactors’
best.o: In function `LnPriorProbGeneTree’:
best.c:(.text+0x1a1e): undefined reference to `log’

…and…

best.c:(.text+0×3027): undefined reference to `log’
best.c:(.text+0×3072): undefined reference to `log’
best.c:(.text+0x358a): undefined reference to `log’
best.o:best.c:(.text+0x35b6): more undefined references to `log’ follow
best.o: In function `Move_SpeciesTree’:
best.c:(.text+0×3971): undefined reference to `exp’
best.c:(.text+0x398c): undefined reference to `log’
collect2: ld returned 1 exit status
make: *** [mb] Error 1

I’ve tried running with and without beagle and I get the undefined log and exp in both cases.

Thank you for taking a look.

Comment on MrBayes and multicore processors by mvavrek

mvavrek — Sat, 25 Feb 2012 22:22:05 +0000

Can you post the error that it throws and the last few lines before that? That might help to get an idea about what is going on. More than likely it’s a package somewhere that needs to be tracked down and installed.

Comment on MrBayes and multicore processors by Seth

Seth — Sat, 25 Feb 2012 22:17:43 +0000

I am trying to compile MrBayes in parallel mode in Ubuntu (your site has been a huge help) but I get an error when I give the make command. It chugs along for a while then comes back with a long list of errors about an undefined reference to log. Have you come across this before or have any suggestions?

Comment on MrBayes and Ubuntu by Ross Mounce (@rmounce)

Ross Mounce (@rmounce) — Tue, 20 Dec 2011 14:08:18 +0000

PS I compiled it from source too on my Ubuntu 64-bit machine! Does the software centre install method correctly compile and install the optional BEAGLE libraries? I couldn’t correctly do this bit when I compiled and installed from source so I’m apparently not making full use of all my cores :/

http://code.google.com/p/beagle-lib/

Comment on TNT and Ubuntu by Ross Mounce (@rmounce)

Ross Mounce (@rmounce) — Tue, 20 Dec 2011 14:04:15 +0000

Hi Matthew,

Good to see people posting helpful tutorials on how to use TNT. It’s not the easiest program to get to grips with, in my experience.

However, a small note of correction – your method is not the only one with which you can calculate (Goodman)Bremer support in TNT. On the official TNT wiki manual website, under the “scripts” page there’s a nice little script written by Goloboff that’ll calculate it for you: http://tnt.insectmuseum.org/index.php/Scripts

Note also; scripts to calculate partitioned (Goodman)Bremer support, the Incongruence Length Difference test, and other useful data exploration tools. I’ve written a post of my own, (along with my research poster) on how to do these tests in TNT here: http://sites.google.com/site/rossmounce/palass2011

I hope it might be of some use to someone out there – I certainly think these are useful and interesting methods.

Comment on pdflatex errors and R by andrewgriffin

andrewgriffin — Mon, 26 Sep 2011 17:42:17 +0000

Cheers for the information. I had a similar problem with R on a Fedora 15 distribution and this pointed me in the right direction.

The culprit in this case was the texinfo-tex (4.13a-15.fc15) package.

Comment on MrBayes and multicore processors by mvavrek

mvavrek — Wed, 17 Aug 2011 01:53:05 +0000

I’ll check it out. Another one of those things that I never really thought about though, since palaeo data usually consist of a few hundred values, not hundred thousand.

Comment on MrBayes and multicore processors by Julien

Julien — Wed, 17 Aug 2011 01:49:41 +0000

Thanks for the spp.est package. Very useful. I use it in microbial ecology and I have a suggestion (if its feasible and if it makes sense!). There exist a package called mothur (oriented for microbial ecology) into which there is a rarefaction module. I think its basically the same module as spp.est but with an extra parameter which is the frequency. For instance if you only want to output the data every n species). So Lets say we have a table representing a total of 500,000 species and we want only 10 points on our rarefaction curve we would calculate values every 50,000 values. The resulting rarefaction curve would not be as detailed as if using every value, but would still give a good idea… and be faster.
Cheers!

Comment on pdflatex errors and R by synapseandsyntax

synapseandsyntax — Fri, 12 Aug 2011 20:19:38 +0000

Hi. Thanks for this post– it helped me to discover that I was missing a texlive package when I encountered the same problem. For what it’s worth, it’s probably not necessary to install texlive-full, which is over 1GB. It’s (at least one of) the following packages:

Installed the following packages:
debiandoc-sgml (1.2.15)
libroman-perl (1.23-1)
libsgmls-perl (1.03ii-32)
libsp1c2 (1.3.4-1.2.1-47build3)
libtext-format-perl (0.52-21)
sgmlspl (1.03ii-32)
sp (1.3.4-1.2.1-47build3)
texinfo (4.13a.dfsg.1-6ubuntu3)
texlive-formats-extra (2009-10ubuntu1)
texlive-generic-extra (2009-10ubuntu1)
texlive-lang-other (2009-3)
texlive-plain-extra (2009-10ubuntu1)
texlive-xetex (2009-11)

Cheers.