[package - main-armv6-default][biology/paml] Failed for paml-4.9j in stage
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Date: Sat, 31 Jul 2021 22:49:46 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/pe8cfea34d340_s297e9f364b/logs/paml-4.9j.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=pe8cfea34d340_s297e9f364b
Log:
=>> Building biology/paml
build started at Sat Jul 31 22:28:57 UTC 2021
port directory: /usr/ports/biology/paml
package name: paml-4.9j
building for: FreeBSD main-armv6-default-job-07 14.0-CURRENT FreeBSD 14.0-CURRENT 1400025 arm
maintained by: jrm@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-8-gaf08dbda
Host OSVERSION: 1300121
Jail OSVERSION: 1400025
Job Id: 07
!!! Jail is newer than host. (Jail: 1400025, Host: 1300121) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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---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--
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--End CONFIGURE_ENV--
--MAKE_ENV--
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--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--
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=======================<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-1.17.0.pkg
[main-armv6-default-job-07] Installing pkg-1.17.0...
[main-armv6-default-job-07] Extracting pkg-1.17.0: .......... 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>
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:126:26: 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)
^
23 warnings generated.
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:82:25: 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:82:39: 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:82:25: 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:82:39: 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:82:25: 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:82:39: 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:82:25: 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:82:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from evolver.c:66:
./treesub.c:2973:19: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if (line[i] == EOF)
~~~~~~~ ^ ~~~
./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:82:39: 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:84:31: 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:126:26: 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)
^
23 warnings generated.
===========================================================================
=======================<phase: run-depends >============================
===========================================================================
=======================<phase: stage >============================
===> Staging for paml-4.9j
===> Generating temporary packing list
install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/src/baseml /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin
install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/src/basemlg /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin
install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/src/chi2 /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin
install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/src/codeml /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin
install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/src/evolver /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin
install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/src/evolverNSbranches /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin
install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/src/evolverNSbranchsites /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin
install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/src/evolverNSsites /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin
install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/src/pamp /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin
install -s -m 555 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/src/yn00 /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/bin
install -m 0644 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/doc/* /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/share/doc/paml
install -m 0644 /wrkdirs/usr/ports/biology/paml/work/paml4.9j/README.txt /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/share/doc/paml
(cd /wrkdirs/usr/ports/biology/paml/work/paml4.9j && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE "dat Technical" /wrkdirs/usr/ports/biology/paml/work/stage/usr/local/share/examples/paml)
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/paml