[package - main-armv6-default][biology/paml] Failed for paml-4.9j in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Mon, 13 Sep 2021 06:06:14 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jrm@FreeBSD.org
Log URL: http://beefy8.nyi.freebsd.org/data/main-armv6-default/p37fb990074a9_s98168a6e6c/logs/paml-4.9j.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=p37fb990074a9_s98168a6e6c
Log:
=>> Building biology/paml
build started at Mon Sep 13 05:47:11 UTC 2021
port directory: /usr/ports/biology/paml
package name: paml-4.9j
building for: FreeBSD main-armv6-default-job-03 14.0-CURRENT FreeBSD 14.0-CURRENT 1400032 arm
maintained by: jrm@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1300121
Jail OSVERSION: 1400032
Job Id: 03
!!! Jail is newer than host. (Jail: 1400032, Host: 1300121) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1400032
UNAME_v=FreeBSD 14.0-CURRENT 1400032
UNAME_r=14.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
QEMU_EMULATING=1
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-21-g883afb07
MASTERMNT=/usr/local/poudriere/data/.m/main-armv6-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=main-armv6-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for paml-4.9j:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jrm@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/paml/work HOME=/wrkdirs/usr/ports/biology/paml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/paml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/paml/work HOME=/wrkdirs/usr/ports/biology/paml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/paml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
PORTDOCS="" PORTEXAMPLES="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/paml" EXAMPLESDIR="share/examples/paml" DATADIR="share/paml" WWWDIR="www/paml" ETCDIR="etc/paml"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/paml DOCSDIR=/usr/local/share/doc/paml EXAMPLESDIR=/usr/local/share/examples/paml WWWDIR=/usr/local/www/paml ETCDIR=/usr/local/etc/paml
--End SUB_LIST--
---Begin make.conf---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=arm
MACHINE_ARCH=armv6
ARCH=${MACHINE_ARCH}
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_9d218390=FreeBSD clang version 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=FreeBSD clang version 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_9d218390_58173849=yes
CC_OUTPUT_9d218390_9bdba57c=yes
CC_OUTPUT_9d218390_6a4fe7f5=yes
CC_OUTPUT_9d218390_6bcac02b=yes
CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
CC_OUTPUT_9d218390_f00456e5=yes
CC_OUTPUT_9d218390_65ad290d=yes
CC_OUTPUT_9d218390_f2776b26=yes
CC_OUTPUT_9d218390_b2657cc3=yes
CC_OUTPUT_9d218390_380987f7=yes
CC_OUTPUT_9d218390_160933ec=yes
CC_OUTPUT_9d218390_fb62803b=yes
_OBJC_CCVERSION_9d218390=FreeBSD clang version 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin
_OBJC_ALTCCVERSION_9d218390=none
ARCH=armv6
OPSYS=FreeBSD
_OSRELEASE=14.0-CURRENT
OSREL=14.0
OSVERSION=1400032
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 33554432
stack size (kbytes, -s) 524288
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 1024
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> paml-4.9j depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.1.pkg
[main-armv6-default-job-03] Installing pkg-1.17.1...
[main-armv6-default-job-03] Extracting pkg-1.17.1: .......... done
===> paml-4.9j depends on file: /usr/local/sbin/pkg - found
===> Returning to build of paml-4.9j
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by paml-4.9j for building
<snip>
printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
^~~~~~~~~~
./paml.h:150:63: note: passing argument to parameter 'spnames' here
void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
^
In file included from yn00.c:70:
./treesub.c:1404:7: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
zt = (char*)malloc(com.ls*lpatt * sizeof(char));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./treesub.c:1427:27: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:85:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from yn00.c:70:
./treesub.c:1427:41: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:85:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from yn00.c:70:
./treesub.c:1476:24: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:85:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from yn00.c:70:
./treesub.c:1476:38: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:85:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from yn00.c:70:
./treesub.c:2282:33: warning: assigning to 'char *' from 'unsigned char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
for (il = ig*lline, pz = z[is] + il; lt < lline && il < ls; il++, lt++, pz++) {
^ ~~~~~~~~~~
yn00.c:252:18: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
CountSites(com.z[k==0?is:js], com.pi, &St, &Nt, fbSt, fbNt);
^~~~~~~~~~~~~~~~~
yn00.c:27:21: note: passing argument to parameter 'z' here
int CountSites(char z[],double pi[],double*Stot,double*Ntot,
^
yn00.c:282:18: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
CountDiffs(com.z[is], com.z[js], &Sdts, &Sdtv, &Ndts, &Ndtv, PMat);
^~~~~~~~~
yn00.c:30:21: note: passing argument to parameter 'z1' here
int CountDiffs(char z1[],char z2[],
^
yn00.c:282:29: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
CountDiffs(com.z[is], com.z[js], &Sdts, &Sdtv, &Ndts, &Ndtv, PMat);
^~~~~~~~~
yn00.c:30:31: note: passing argument to parameter 'z2' here
int CountDiffs(char z1[],char z2[],
^
12 warnings generated.
cc -O3 -o chi2 chi2.c -lm
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/paml/work/paml4.9j/src'
In file included from evolver.c:66:
./treesub.c:86:7: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
zt = (char*)malloc(com.ls*lpatt * sizeof(char));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./treesub.c:105:24: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:85:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from evolver.c:66:
./treesub.c:105:38: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:85:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from evolver.c:66:
./treesub.c:143:21: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:85:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from evolver.c:66:
./treesub.c:143:35: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:85:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from evolver.c:66:
./treesub.c:256:7: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
zt = (char*)malloc(npatt0*lpatt * sizeof(char));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./treesub.c:280:24: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:85:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from evolver.c:66:
./treesub.c:280:38: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:85:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from evolver.c:66:
./treesub.c:313:21: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:85:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from evolver.c:66:
./treesub.c:313:35: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:85:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from evolver.c:66:
./treesub.c:3106:37: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
if (!strcmp(line, com.spname[i])) break;
^~~~~~~~~~~~~
/usr/include/string.h:85:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from evolver.c:66:
./treesub.c:3115:23: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
strcpy(com.spname[cnode = tip++], line);
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:87:31: note: passing argument to parameter here
char *strcpy(char * __restrict, const char * __restrict);
^
In file included from evolver.c:67:
./treespace.c:131:18: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
sprintf(com.spname[i], "%d", i+1);
^~~~~~~~~~~~~
/usr/include/stdio.h:286:31: note: passing argument to parameter here
int sprintf(char * __restrict, const char * __restrict, ...);
^
evolver.c:121:21: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
com.spname[i] = (char*)malloc(LSPNAME * sizeof(char*));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
evolver.c:184:54: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
for (i = 0; i < com.ns; i++) sprintf(com.spname[i], "%c", (i < 26 ? 'A' + i : 'a' + i - 26));
^~~~~~~~~~~~~
/usr/include/stdio.h:286:31: note: passing argument to parameter here
int sprintf(char * __restrict, const char * __restrict, ...);
^
evolver.c:186:54: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
for (i = 0; i < com.ns; i++) sprintf(com.spname[i], "S%d", i + 1);
^~~~~~~~~~~~~
/usr/include/stdio.h:286:31: note: passing argument to parameter here
int sprintf(char * __restrict, const char * __restrict, ...);
^
evolver.c:299:26: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
if ((p = strstr(com.spname[i], key))
^~~~~~~~~~~~~
/usr/include/string.h:129:26: note: passing argument to parameter here
char *strstr(const char *, const char *) __pure;
^
evolver.c:634:18: warning: passing 'unsigned char [512]' to parameter of type 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
fdaa = gfopen(com.daafile, "r");
^~~~~~~~~~~
./paml.h:209:20: note: passing argument to parameter 'filename' here
FILE *gfopen(char *filename, char *mode);
^
evolver.c:670:19: warning: initializing 'unsigned char *' with an expression of type 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
unsigned char *pch = (com.seqtype == 2 ? AAs : BASEs);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
evolver.c:672:34: warning: passing 'unsigned char [12]' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
FILE *frootseq = (FILE*)fopen(rootseqf, "r");
^~~~~~~~
/usr/include/stdio.h:259:36: note: passing argument to parameter here
FILE *fopen(const char * __restrict, const char * __restrict);
^
evolver.c:827:15: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
sprintf(com.spname[i], "S%d", i + 1);
^~~~~~~~~~~~~
/usr/include/stdio.h:286:31: note: passing argument to parameter here
int sprintf(char * __restrict, const char * __restrict, ...);
^
evolver.c:1062:15: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
MakeSeq(com.z[tree.root], com.ls);
^~~~~~~~~~~~~~~~
evolver.c:662:19: note: passing argument to parameter 'z' here
void MakeSeq(char*z, int ls)
^
22 warnings generated.
ld: error: /tmp/evolver-656d0c.o is incompatible with /usr/lib/crt1.o
ld: error: /tmp/tools-b6acb8.o is incompatible with /usr/lib/crt1.o
cc: error: linker command failed with exit code 1 (use -v to see invocation)
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/paml