Package Details: phyml 1:3.3.20220408-1

Git Clone URL: https://aur.archlinux.org/phyml.git (read-only, click to copy)
Package Base: phyml
Description: Builds phylogenies from DNA or protein sequences using a maximum likelihood approach
Upstream URL: https://github.com/stephaneguindon/phyml
Licenses: GPL2
Submitter: None
Maintainer: mschu
Last Packager: mschu
Votes: 6
Popularity: 0.000000
First Submitted: 2009-04-02 01:54 (UTC)
Last Updated: 2022-04-11 08:17 (UTC)

Dependencies (0)

Required by (4)

Sources (1)

Latest Comments

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malacology commented on 2022-04-11 02:41 (UTC)

it someone do it in a clean chroot, I think maybe it won't be include, I am not sure

Rhinoceros commented on 2022-04-09 01:47 (UTC)

@malacology makedepends already assumes that base-devel is installed. base-devel contains make.

malacology commented on 2022-04-08 22:30 (UTC)

make should be in makepedends

maximtrp commented on 2020-12-19 18:41 (UTC)

Checksum verification fails:

==> Making package: phyml 1:3.3.20200621-1 (Sat 19 Dec 2020 08:17:24 PM MSK)
==> Retrieving sources...
  -> Found phyml-3.3.20200621.tar.gz
==> Validating source files with sha256sums...
    phyml-3.3.20200621.tar.gz ... FAILED
==> ERROR: One or more files did not pass the validity check!
error downloading sources: phyml

mschu commented on 2020-07-13 11:19 (UTC) (edited on 2020-07-13 11:19 (UTC) by mschu)

Confirmed & updated! (also the upstream release has a changed checksum compared to 2 days ago)

Rhinoceros commented on 2020-07-13 02:52 (UTC)

Some info in this issue, but I did get the new version of (vanilla) phyml to build with the instructions on the main page, i.e. ./autogen.sh, ./configure --enable-phyml, make

mschu commented on 2020-07-12 19:31 (UTC)

I can get it to link if I comment out @src/utilities.h#L97-98 and instead add int CALL @src/lk.c

However, I think there must be a better solution - I'll check a bit more and then update.

Rhinoceros commented on 2020-07-09 13:16 (UTC)

@mschu There's a new version out, but I can't seem to get the new version nor this old version building any more. I'm getting a bunch of ld errors, ending with collect2: error: ld returned 1 exit status. The old version built fine in the past. Can you build either?

Rhinoceros commented on 2020-03-08 00:26 (UTC)

Hi @linearleopard. Unfortunately I'm not sure how much I can help. I tested the build again on three different systems, and it worked fine for me in all three. I Googled inlining failed in call to always_inline, and I came up with several possible solutions, but since I can't make the build fail, I'm not really in a position to test.

Please have a search and test, and if you come up with a solution, I'm happy to incorporate it into the PKGBUILD. One thing I might suggest is trying a manual makepkg -s rather than using a AUR helper.

linearleopard commented on 2020-03-07 14:59 (UTC)

Hello. Thank you for you work.

I've tried to install the package, but I got the following error: .: Building [phyml-mpi]. Version 3.3.20190909 :.

mpicc -I. -I.. -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -MT avx.o -MD -MP -MF .deps/avx.Tpo -c -o avx.o avx.c In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.1/include/immintrin.h:107, from utilities.h:38, from avx.h:18, from avx.c:14: avx.c: In function ‘AVX_Lk_dLk_Core_One_Class_Eigen_Lr’: /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.1/include/fmaintrin.h:47:1: error: inlining failed in call to always_inline ‘_mm256_fmadd_pd’: target specific option mismatch 47 | _mm256_fmadd_pd (__m256d __A, __m256d __B, __m256d __C) | ^~~~~~~~~~~~~~~ avx.c:287:12: note: called from here 287 | _z = _mm256_fmadd_pd(_x,_y,_z); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.1/include/immintrin.h:107, from utilities.h:38, from avx.h:18, from avx.c:14: /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.1/include/fmaintrin.h:47:1: error: inlining failed in call to always_inline ‘_mm256_fmadd_pd’: target specific option mismatch 47 | _mm256_fmadd_pd (__m256d __A, __m256d __B, __m256d __C) | ^~~~~~~~~~~~~~~ avx.c:287:12: note: called from here 287 | _z = _mm256_fmadd_pd(_x,_y,_z); | ^~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [Makefile:1718: avx.o] Error 1 make[2]: Leaving directory '/home/my/.cache/yay/phyml-mpi/src/phyml-3.3.20190909/src' make[1]: [Makefile:363: all-recursive] Error 1 make[1]: Leaving directory '/home/my/.cache/yay/phyml-mpi/src/phyml-3.3.20190909' make: *** [Makefile:304: all] Error 2

Could you specify, what am I doing wrong, or change install script?

Thank you.

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