[Debian-med-packaging] Problems building latest phyml

[Andreas Tille]

Hi Stephane,

On Tue, Jun 27, 2017 at 10:05:57AM +0200, Stephane Guindon wrote:
> I am not so surprised that the BEAGLE-enabled version of PhyML does not
> compile. I did not work on integrating BEAGLE to PhyML and I am thus not
> sure how to fix this issue. My suggestion would be that the Debian package
> does not incorporate phyml-beagle. Would that make sense?

Its fine for me to drop beagle support if you confirm that it is not
really supported.  Unfortunately I have build issues also without
beagle.


...
gcc  -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -march=native  -Wl,-z,relro -Wl,-z,now -o phytime main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o times.o m4.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o date.o sse.o avx.o xml.o -lm -lm 
main.o: In function `main':
main.c:(.text.startup+0x5): undefined reference to `PHYREX_Main'
lk.o: In function `Lk':
lk.c:(.text+0xd851): undefined reference to `PHYREX_Ldsk_To_Tree'
mcmc.o: In function `MCMC_Copy_To_New_Param_Val':
mcmc.c:(.text+0xc636): undefined reference to `PHYREX_Neighborhood_Size'
mcmc.c:(.text+0xc674): undefined reference to `PHYREX_Update_Sigsq'
mcmc.o: In function `MCMC_PHYREX_Lbda':
mcmc.c:(.text+0x10df6): undefined reference to `PHYREX_Wrap_Lk'
mcmc.o: In function `MCMC_PHYREX_Mu':
mcmc.c:(.text+0x10e56): undefined reference to `PHYREX_Wrap_Lk'
mcmc.o: In function `MCMC_PHYREX_Radius':
mcmc.c:(.text+0x10eb6): undefined reference to `PHYREX_Wrap_Lk'
mcmc.o: In function `MCMC_PHYREX_Sigsq':
mcmc.c:(.text+0x10f2a): undefined reference to `PHYREX_Wrap_Lk'
mcmc.c:(.text+0x10f42): undefined reference to `PHYREX_Update_Radius'
mcmc.o: In function `MCMC_PHYREX_Delete_Disk':
mcmc.c:(.text+0x110dd): undefined reference to `PHYREX_Remove_Disk'
mcmc.c:(.text+0x1114c): undefined reference to `PHYREX_Tree_Height'
mcmc.c:(.text+0x111b7): undefined reference to `PHYREX_Lk'
mcmc.c:(.text+0x114a0): undefined reference to `PHYREX_Insert_Disk'
mcmc.c:(.text+0x114e6): undefined reference to `PHYREX_Insert_Disk'
mcmc.c:(.text+0x114f6): undefined reference to `PHYREX_Insert_Disk'
mcmc.c:(.text+0x11506): undefined reference to `PHYREX_Insert_Disk'
mcmc.c:(.text+0x11516): undefined reference to `PHYREX_Insert_Disk'
mcmc.o:mcmc.c:(.text+0x11526): more undefined references to `PHYREX_Insert_Disk' follow
mcmc.o: In function `MCMC_PHYREX_Delete_Disk':
mcmc.c:(.text+0x115d4): undefined reference to `PHYREX_Update_Lindisk_List'
mcmc.c:(.text+0x1164d): undefined reference to `PHYREX_Lk'
mcmc.o: In function `MCMC_PHYREX_Insert_Disk':
mcmc.c:(.text+0x11738): undefined reference to `PHYREX_Tree_Height'
mcmc.c:(.text+0x11855): undefined reference to `PHYREX_Insert_Disk'
mcmc.c:(.text+0x11990): undefined reference to `PHYREX_Lk'
mcmc.c:(.text+0x11a44): undefined reference to `PHYREX_Remove_Disk'
mcmc.c:(.text+0x11a97): undefined reference to `PHYREX_Remove_Disk'
mcmc.c:(.text+0x11aad): undefined reference to `PHYREX_Remove_Disk'
mcmc.c:(.text+0x11ac3): undefined reference to `PHYREX_Remove_Disk'
mcmc.c:(.text+0x11ad9): undefined reference to `PHYREX_Remove_Disk'
mcmc.o:mcmc.c:(.text+0x11aef): more undefined references to `PHYREX_Remove_Disk' follow
mcmc.o: In function `MCMC_PHYREX_Insert_Disk':
mcmc.c:(.text+0x11be7): undefined reference to `PHYREX_Update_Lindisk_List'
mcmc.c:(.text+0x11c7a): undefined reference to `PHYREX_Lk'
mcmc.o: In function `MCMC_PHYREX_Indel_Disk':
mcmc.c:(.text+0x11d0e): undefined reference to `PHYREX_Tree_Height'
mcmc.c:(.text+0x11d8c): undefined reference to `PHYREX_Total_Number_Of_Hit_Disks'
mcmc.c:(.text+0x11d97): undefined reference to `PHYREX_Total_Number_Of_Intervals'
mcmc.o: In function `MCMC_PHYREX_Move_Disk_Updown':
mcmc.c:(.text+0x12b00): undefined reference to `PHYREX_Lk'
mcmc.o: In function `MCMC_PHYREX_Scale_Times':
...

I'm CCing Debian Med maintainers since I'll be mostly offline the next
two weeks.

Kind regards

       Andreas.


-- 
http://fam-tille.de