------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/paml XDG_CONFIG_HOME=/construction/biology/paml HOME=/construction/biology/paml TMPDIR="/tmp" PATH=/construction/biology/paml/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/paml XDG_CONFIG_HOME=/construction/biology/paml HOME=/construction/biology/paml TMPDIR="/tmp" PATH=/construction/biology/paml/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/paml/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/paml" EXAMPLESDIR="share/examples/paml" DATADIR="share/paml" WWWDIR="www/paml" ETCDIR="etc/paml" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> paml-4.9j depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> paml-4.9j depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by paml-4.9j for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> paml-4.9j depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by paml-4.9j for building => SHA256 Checksum OK for paml4.9j.tgz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> paml-4.9j depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by paml-4.9j for building ===> Extracting for paml-4.9j => SHA256 Checksum OK for paml4.9j.tgz. Extracted Memory Use: 14.55M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for paml-4.9j ===> Converting DOS text files to UNIX text files ===> Applying ports patches for paml-4.9j from /xports/biology/paml/files SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> paml-4.9j depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> paml-4.9j depends on package: gmake>=4.3 - found ===> Configuring for paml-4.9j SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for paml-4.9j gmake[1]: Entering directory '/construction/biology/paml/paml4.9j/src' cc -O3 -o baseml baseml.c tools.c -lm In file included from baseml.c:131: treesub.c: In function 'IdenticalSeqs': treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types] printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); ~~~^~~~~~~ In file included from baseml.c:11: paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); ~~~~~~~~~~~~~~~^~~~~~~~~ cc -O3 -o codeml codeml.c tools.c -lm In file included from codeml.c:238: treesub.c: In function 'IdenticalSeqs': treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types] printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); ~~~^~~~~~~ In file included from codeml.c:17: paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); ~~~~~~~~~~~~~~~^~~~~~~~~ cc -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] printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); ~~~^~~~~~~ In file included from basemlg.c:11: paml.h:153:31: note: expected 'char **' but argument is of type 'unsigned char **' 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] printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); ~~~^~~~~~~ In file included from basemlg.c:11: paml.h:153:31: note: expected 'char **' but argument is of type 'unsigned char **' 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] printsma(fout, com.spname, com.z, com.ns, com.npatt, com.npatt, gap, com.seqtype, 1, 0, NULL); ~~~^~~~~~~ In file included from basemlg.c:11: paml.h:153:31: note: expected 'char **' but argument is of type 'unsigned char **' 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] printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 1, 0, NULL); ~~~^~~~~~~ In file included from basemlg.c:11: paml.h:153:31: note: expected 'char **' but argument is of type 'unsigned char **' int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, ~~~~~^~~~~~~~ cc -O3 -o mcmctree mcmctree.c tools.c -lm In file included from mcmctree.c:192: treesub.c: In function 'IdenticalSeqs': treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types] printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); ~~~^~~~~~~ In file included from mcmctree.c:22: paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); ~~~~~~~~~~~~~~~^~~~~~~~~ cc -O3 -o infinitesites -D INFINITESITES mcmctree.c tools.c -lm In file included from mcmctree.c:192: treesub.c: In function 'IdenticalSeqs': treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types] printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); ~~~^~~~~~~ In file included from mcmctree.c:22: paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); ~~~~~~~~~~~~~~~^~~~~~~~~ cc -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] printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); ~~~^~~~~~~ In file included from pamp.c:8: paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); ~~~~~~~~~~~~~~~^~~~~~~~~ cc -O3 -o evolver evolver.c tools.c -lm cc -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] printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); ~~~^~~~~~~ In file included from yn00.c:13: paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); ~~~~~~~~~~~~~~~^~~~~~~~~ cc -O3 -o chi2 chi2.c -lm gmake[1]: Leaving directory '/construction/biology/paml/paml4.9j/src' SUCCEEDED 00:04:16 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for paml-4.9j ===> Generating temporary packing list install -s -m 555 /construction/biology/paml/paml4.9j/src/baseml /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9j/src/basemlg /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9j/src/chi2 /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9j/src/codeml /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9j/src/evolver /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9j/src/evolverNSbranches /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9j/src/evolverNSbranchsites /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9j/src/evolverNSsites /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9j/src/pamp /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9j/src/yn00 /construction/biology/paml/stage/usr/local/bin install -m 0644 /construction/biology/paml/paml4.9j/doc/* /construction/biology/paml/stage/usr/local/share/doc/paml install -m 0644 /construction/biology/paml/paml4.9j/README.txt /construction/biology/paml/stage/usr/local/share/doc/paml (cd /construction/biology/paml/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" /construction/biology/paml/stage/usr/local/share/examples/paml) (cd /construction/biology/paml/paml4.9j/examples && /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 . /construction/biology/paml/stage/usr/local/share/examples/paml) install -m 0644 /construction/biology/paml/paml4.9j/*.aa /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9j/*.ctl /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9j/*.dat /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9j/*.nuc /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9j/*.trees /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9j/*.txt /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9j/paup* /construction/biology/paml/stage/usr/local/share/examples/paml ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for paml-4.9j file sizes/checksums [173]: 0% file sizes/checksums [173]: 57% file sizes/checksums [173]: 100% packing files [173]: 0% packing files [173]: 57% packing files [173]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:21 TOTAL TIME 00:04:41