search

abacus-gene / paml

PAML is a program package for model fitting and phylogenetic tree reconstruction using DNA and protein sequence data. Please report only **technical issues** on this repository (e.g., compiling, programs abort or do not run at all, etc.). Problems with input data and general questions should be posted at https://groups.google.com/g/pamlsoftware?pli
GNU General Public License v3.0
103 stars 19 forks source link

Fix build with Clang/LLVM version 11 #3

Closed Jehops closed 1 year ago

Jehops commented 3 years ago

Merging of tentative definitions by the linker gives multiple-definition errors with Clang/LLVM version 11, which uses -fno-common by default.

These tentative definitions of anonymous enums are included multiple times in the translation unit, resulting in the error above. Since they are unused, switch them to non-anonymous enums without any declaration or definition.

Submitted by: Kyle Evans (to the FreeBSD port)

Jehops commented 3 years ago

Hello Dr. Yang,

Since these definitions of anonymous enums are unused, if you prefer them to be removed, please just let me know and I will update the pull request.

Here is a log of the errors in case they are useful: https://ftfl.ca/misc/paml-4.9j.log

Joseph

ziheng-yang commented 3 years ago

hi joe, does this problem occur with the code at the dev/ branch?
thanks, ziheng

Jehops commented 3 years ago

The linking error also occurs in the dev branch because there are still multiple tentative definitions with the same name. Starting with gcc version 10, -fno-common is the default as well, so I believe this is also a problem with newer versions of gcc.

Jehops commented 3 years ago

I can confirm the problem exists with gcc version 10.2 and that the patch fixes the problem.

Without patch:

jrm@storage2 ~/scm/nm/paml/src [dev|✚1] % make
gcc10 -O3 -o baseml baseml.c tools.c -lm
In file included from baseml.c:137:
treesub.c: In function 'IdenticalSeqs':
treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types]
 1310 |       printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
      |                              ~~~^~~~~~~
      |                                 |
      |                                 char **
In file included from baseml.c:11:
paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **'
  150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
      |                                                ~~~~~~~~~~~~~~~^~~~~~~~~
/usr/local/bin/ld: /tmp//ccSL5Igk.o:(.bss+0x4540): multiple definition of `OutTreeOptions'; /tmp//ccz9P7Vg.o:(.bss+0x2a0dfe8): first defined here
/usr/local/bin/ld: /tmp//ccSL5Igk.o:(.bss+0x4544): multiple definition of `SeqTypes'; /tmp//ccz9P7Vg.o:(.bss+0x2a0dfec): first defined here
collect2: error: ld returned 1 exit status
*** Error code 1

Stop.
make: stopped in /tank2/home/jrm/scm/nm/paml/src

With patch:

jrm@storage2 ~/scm/nm/paml/src [dev|✚2] % make
gcc10 -O3 -o baseml baseml.c tools.c -lm
In file included from baseml.c:137:
treesub.c: In function 'IdenticalSeqs':
treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types]
 1310 |       printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
      |                              ~~~^~~~~~~
      |                                 |
      |                                 char **
In file included from baseml.c:11:
paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **'
  150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
      |                                                ~~~~~~~~~~~~~~~^~~~~~~~~
gcc10 -O3 -o codeml codeml.c tools.c -lm
In file included from codeml.c:243:
treesub.c: In function 'IdenticalSeqs':
treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types]
 1310 |       printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
      |                              ~~~^~~~~~~
      |                                 |
      |                                 char **
In file included from codeml.c:17:
paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **'
  150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
      |                                                ~~~~~~~~~~~~~~~^~~~~~~~~
gcc10 -O3 -o basemlg basemlg.c tools.c -lm
In file included from basemlg.c:80:
treesub.c: In function 'ReadSeq':
treesub.c:858:31: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types]
  858 |             printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL);
      |                            ~~~^~~~~~~
      |                               |
      |                               unsigned char **
In file included from basemlg.c:11:
paml.h:153:31: note: expected 'char **' but argument is of type 'unsigned char **'
  153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype,
      |                          ~~~~~^~~~~~~~
In file included from basemlg.c:80:
treesub.c:866:28: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types]
  866 |          printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL);
      |                         ~~~^~~~~~~
      |                            |
      |                            unsigned char **
In file included from basemlg.c:11:
paml.h:153:31: note: expected 'char **' but argument is of type 'unsigned char **'
  153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype,
      |                          ~~~~~^~~~~~~~
In file included from basemlg.c:80:
treesub.c: In function 'printPatterns':
treesub.c:1093:25: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types]
 1093 |       printsma(fout, com.spname, com.z, com.ns, com.npatt, com.npatt, gap, com.seqtype, 1, 0, NULL);
      |                      ~~~^~~~~~~
      |                         |
      |                         unsigned char **
In file included from basemlg.c:11:
paml.h:153:31: note: expected 'char **' but argument is of type 'unsigned char **'
  153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype,
      |                          ~~~~~^~~~~~~~
In file included from basemlg.c:80:
treesub.c: In function 'AllPatterns':
treesub.c:1361:25: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types]
 1361 |       printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 1, 0, NULL);
      |                      ~~~^~~~~~~
      |                         |
      |                         unsigned char **
In file included from basemlg.c:11:
paml.h:153:31: note: expected 'char **' but argument is of type 'unsigned char **'
  153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype,
      |                          ~~~~~^~~~~~~~
gcc10 -O3 -o mcmctree mcmctree.c tools.c -lm
In file included from mcmctree.c:215:
treesub.c: In function 'IdenticalSeqs':
treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types]
 1310 |       printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
      |                              ~~~^~~~~~~
      |                                 |
      |                                 char **
In file included from mcmctree.c:22:
paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **'
  150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
      |                                                ~~~~~~~~~~~~~~~^~~~~~~~~
gcc10 -O3 -o infinitesites -D INFINITESITES mcmctree.c tools.c -lm
In file included from mcmctree.c:215:
treesub.c: In function 'IdenticalSeqs':
treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types]
 1310 |       printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
      |                              ~~~^~~~~~~
      |                                 |
      |                                 char **
In file included from mcmctree.c:22:
paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **'
  150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
      |                                                ~~~~~~~~~~~~~~~^~~~~~~~~
gcc10 -O3 -o pamp pamp.c tools.c -lm
In file included from pamp.c:66:
treesub.c: In function 'IdenticalSeqs':
treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types]
 1310 |       printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
      |                              ~~~^~~~~~~
      |                                 |
      |                                 char **
In file included from pamp.c:8:
paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **'
  150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
      |                                                ~~~~~~~~~~~~~~~^~~~~~~~~
gcc10 -O3 -o evolver evolver.c tools.c -lm
gcc10 -O3 -o yn00 yn00.c tools.c -lm
In file included from yn00.c:70:
treesub.c: In function 'IdenticalSeqs':
treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types]
 1310 |       printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
      |                              ~~~^~~~~~~
      |                                 |
      |                                 char **
In file included from yn00.c:13:
paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **'
  150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
      |                                                ~~~~~~~~~~~~~~~^~~~~~~~~
gcc10 -O3 -o chi2 chi2.c -lm
make  73.88s user 1.38s system 99% cpu 1:15.28 total
jrm@storage2 ~/scm/nm/paml/src [dev|✚2…9] %
ziheng-yang commented 3 years ago

hi joe, i posted an update to remove some of the compiler warnings. i hope this fixes the clang errors as well. could you check.
thanks and best wishes, ziheng

Jehops commented 3 years ago

Hi Dr. Yang,

This build finishes without errors and the output is cleaner with many of the warnings fixed. There is a link below to the build output using clang 8.0.2, which looks very similar to the output using gcc 10.2.0 now.

J.

http://pkg.awarnach.mathstat.dal.ca/data/12amd64-default/2020-09-08_15h53m05s/logs/paml-4.9j.log