Date: Fri, 20 Jan 2017 04:52:06 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][biology/molden] Failed for molden-5.7_4, 1 in build Message-ID: <201701200452.v0K4q67x007805@beefy8.nyi.freebsd.org>
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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: pi@FreeBSD.org Last committer: gerald@FreeBSD.org Ident: $FreeBSD: head/biology/molden/Makefile 428057 2016-12-07 13:24:56Z gerald $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p431452_s312087/logs/molden-5.7_4,1.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p431452_s312087 Log: ====>> Building biology/molden build started at Fri Jan 20 03:56:28 UTC 2017 port directory: /usr/ports/biology/molden building for: FreeBSD head-armv6-default-job-21 12.0-CURRENT FreeBSD 12.0-CURRENT r312087 arm maintained by: pi@FreeBSD.org Makefile ident: $FreeBSD: head/biology/molden/Makefile 428057 2016-12-07 13:24:56Z gerald $ Poudriere version: 3.1.14 Host OSVERSION: 1200010 Jail OSVERSION: 1200020 Job Id: 21 !!! Jail is newer than host. (Jail: 1200020, Host: 1200010) !!! !!! 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 UNAME_v=FreeBSD 12.0-CURRENT r312087 UNAME_r=12.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=armv6 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref QEMU_EMULATING=1 UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=molden-5.7_4,1 OSREL=12.0 _OSRELEASE=12.0-CURRENT PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=24 PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=1200020 ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for molden-5.7_4,1: DATA=on: Install data files DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran49" FC="gfortran49" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc49" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc49" MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/molden/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/molden/work HOME=/wrkdirs/usr/ports/biology/molden/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran49" FC="gfortran49" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc49" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc49" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/molden/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/molden/work HOME=/wrkdirs/usr/ports/biology/molden/work TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -DFREEBSD -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -I/usr/local/include -Wno-return-type -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 -B/usr/local/bin" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -DFREEBSD -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -I/usr/local/include -Wno-return-type -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/molden" EXAMPLESDIR="share/examples/molden" DATADIR="share/molden" WWWDIR="www/molden" ETCDIR="etc/molden" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/molden DOCSDIR=/usr/local/share/doc/molden EXAMPLESDIR=/usr/local/share/examples/molden WWWDIR=/usr/local/www/molden ETCDIR=/usr/local/etc/molden --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 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 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++ AS=/nxb-bin/usr/bin/as 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 READELF=/nxb-bin/usr/bin/readelf 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--- =======================<phase: check-sanity >============================ ===> License Molden accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> molden-5.7_4,1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.4_1.txz [head-armv6-default-job-21] Installing pkg-1.9.4_1... [head-armv6-default-job-21] Extracting pkg-1.9.4_1: .......... done ===> molden-5.7_4,1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of molden-5.7_4,1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License Molden accepted by the user => molden5.7.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.7.tar.gz molden5.7.tar.gz 0 B 0 Bps ===> Fetching all distfiles required by molden-5.7_4,1 for building =========================================================================== =======================<phase: checksum >============================ ===> License Molden accepted by the user ===> Fetching all distfiles required by molden-5.7_4,1 for building => SHA256 Checksum OK for molden5.7.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License Molden accepted by the user ===> Fetching all distfiles required by molden-5.7_4,1 for building ===> Extracting for molden-5.7_4,1 => SHA256 Checksum OK for molden5.7.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for molden-5.7_4,1 ===> Applying FreeBSD patches for molden-5.7_4,1 =========================================================================== =======================<phase: build-depends >============================ ===> molden-5.7_4,1 depends on executable: gfortran49 - not found ===> Installing existing package /packages/All/gcc-4.9.4.txz [head-armv6-default-job-21] Installing gcc-4.9.4... [head-armv6-default-job-21] `-- Installing indexinfo-0.2.6... [head-armv6-default-job-21] `-- Extracting indexinfo-0.2.6: .... done [head-armv6-default-job-21] `-- Installing mpc-1.0.3... [head-armv6-default-job-21] | `-- Installing gmp-5.1.3_3... [head-armv6-default-job-21] | `-- Extracting gmp-5.1.3_3: .......... done [head-armv6-default-job-21] | `-- Installing mpfr-3.1.5... [head-armv6-default-job-21] | `-- Extracting mpfr-3.1.5: .......... done [head-armv6-default-job-21] `-- Extracting mpc-1.0.3: ...... done [head-armv6-default-job-21] `-- Installing binutils-2.27_5,1... [head-armv6-default-job-21] | `-- Installing gettext-runtime-0.19.8.1_1... [head-armv6-default-job-21] | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [head-armv6-default-job-21] `-- Extracting binutils-2.27_5,1: .......... done <snip> ^ xwin.c:48972:39: warning: implicit declaration of function 'csrft_' is invalid in C99 [-Wimplicit-function-declaration] asurf_(&hlpsrf->srfmap,&calc);csrft_(xyzp->isurf); ^ xwin.c:49124:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] initMLT() ^ xwin.c:49352:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] initPHRM() ^ xwin.c:49550:12: warning: implicit declaration of function 'initPSRCH' is invalid in C99 [-Wimplicit-function-declaration] case 7: initPSRCH(qboxes[QPHRMT].str); ^ xwin.c:49559:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] initPSRCH(query) ^ xwin.c:49787:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] dlystr_() ^ xwin.c:49798:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] delayt() ^ xwin.c:49807:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] WinName(Window win,char *wname) ^ xwin.c:50067:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] motion_screen(inct,incp) ^ xwin.c:50352:5: warning: implicit declaration of function 'ogwrmol' is invalid in C99 [-Wimplicit-function-declaration] ogwrmol(r,adjus,natoms,nat,xsym,ysym,zsym,vdwr); ^ xwin.c:50395:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] ogwrmol(double *r, double *adjus, int *natoms, int *nat, ^ xwin.c:50483:4: warning: implicit declaration of function 'BuildList' is invalid in C99 [-Wimplicit-function-declaration] BuildList(r,cnst,nnpts1,nnpts2,iorb,dens); ^ xwin.c:50516:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] parogf_(str,nlen) ^ xwin.c:50565:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] BuildList(r,cnst,nnpts1,nnpts2,iorb,dens) ^ xwin.c:56144:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] chncol(ich,col,iupd) ^ xwin.c:56159:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] wrtall() ^ xwin.c:56165:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] DeleteActiveSurfaces() ^ xwin.c:56177:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] bldlst_() ^ xwin.c:56186:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] molsrf(SurfCol,SrfArr) ^ xwin.c:56975:10: warning: implicit declaration of function 'dfirot_' is invalid in C99 [-Wimplicit-function-declaration] dfirot_(&l1); ^ xwin.c:57116:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] prresrot(eupl) ^ xwin.c:57132:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] showresrot(sol) ^ xwin.c:57224:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] opt3rot() ^ xwin.c:57397:5: warning: implicit declaration of function 'dfiflx_' is invalid in C99 [-Wimplicit-function-declaration] dfiflx_(&etot); ^ xwin.c:57593:8: warning: implicit declaration of function 'init_trr' is invalid in C99 [-Wimplicit-function-declaration] if (init_trr(filename) < 0) { ^ xwin.c:57610:9: warning: implicit declaration of function 'gfrm' is invalid in C99 [-Wimplicit-function-declaration] while(!gfrm(&iframe,step,0)) { ^ xwin.c:57822:8: warning: implicit declaration of function 'init_edr' is invalid in C99 [-Wimplicit-function-declaration] if (init_edr(filename) < 0) { ^ xwin.c:57829:9: warning: implicit declaration of function 'efrm' is invalid in C99 [-Wimplicit-function-declaration] while(!efrm(&step,&ener)) { ^ xwin.c:57872:2: warning: implicit declaration of function 'gmmcnv_' is invalid in C99 [-Wimplicit-function-declaration] gmmcnv_(geop->formax,geop->forrms,geop->dismax,geop->disrms, ^ xwin.c:57948:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] SetExplButton(win,x,y) ^ xwin.c:58091:6: warning: implicit declaration of function 'utime' is invalid in C99 [-Wimplicit-function-declaration] if (utime(temppath, &ut_buf) == -1) rval = 1; ^ xwin.c:58108:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] mvhlpat(nlines,nato1) ^ xwin.c:58237:5: warning: implicit declaration of function 'supimp_' is invalid in C99 [-Wimplicit-function-declaration] supimp_( xyzp1->coo,COOt,&iat1,&iat2, ^ xwin.c:58251:2: warning: implicit declaration of function 'cntvec_' is invalid in C99 [-Wimplicit-function-declaration] cntvec_( ^ xwin.c:58285:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] CombineStructs(str2,notaligned,new_struct) ^ xwin.c:58476:2: warning: implicit declaration of function 'getrad' is invalid in C99 [-Wimplicit-function-declaration] getrad(tmp1,xyzp1->coo,xyzp1->iatoms,&rad1); ^ xwin.c:58505:6: warning: implicit declaration of function 'trcoo_' is invalid in C99 [-Wimplicit-function-declaration] trcoo_(tmp3,&COOt[j*3]); ^ xwin.c:58766:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] AddAtom(i,j,k,bl,alpha,dih,ires) ^ xwin.c:58778:2: warning: implicit declaration of function 'atadd_' is invalid in C99 [-Wimplicit-function-declaration] atadd_(&i,&j,&k,&ONE,&bl,&alpha,&dih,&iret, ^ xwin.c:58787:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] LigandHydro(het) ^ xwin.c:60102:5: warning: implicit declaration of function 'getrng_' is invalid in C99 [-Wimplicit-function-declaration] getrng_(&iat1,&iout,xyzp->ianz,xyzp->iconn); ^ xwin.c:60119:20: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if (ic == 3 && ! ich == 1) return 1; ^ ~~ xwin.c:60119:20: note: add parentheses after the '!' to evaluate the comparison first if (ic == 3 && ! ich == 1) return 1; ^ ( ) xwin.c:60119:20: note: add parentheses around left hand side expression to silence this warning if (ic == 3 && ! ich == 1) return 1; ^ ( ) xwin.c:60880:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] LigandStruct(het) ^ xwin.c:60897:40: warning: comparison of address of 'COO[istruct]->coo' equal to a null pointer is always false [-Wtautological-pointer-compare] if (istruct == 0 && &COO[istruct]->coo == NULL) { ~~~~~~~~~~~~~~^~~ ~~~~ xwin.c:61886:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] subdivide(v1,v2,v3,c1,c2,c3,pol,pol2,psa,tsa,exs,depth) ^ xwin.c:61963:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] calpsa_(v,cval,pol,pol2,psa,tsa,exs,depth) ^ xwin.c:61993:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] tstpsa_(cval,pol,pol2,ires) ^ xwin.c:62072:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] subd(v1,v2,v3,depth) ^ xwin.c:62169:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] subd2(v1,v2,v3,psa,depth) ^ xwin.c:62341:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] tpsa_() ^ xwin.c:62489:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] fndhnmr(iat,jcut,hcont,ncont) ^ xwin.c:62543:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] javch3(ih) ^ xwin.c:62569:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] avch3() ^ xwin.c:62601:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] nmrsplit(tpeaks,tinten,npeaks,splt) ^ xwin.c:62625:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] prep_nmr() { ^ xwin.c:62680:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] click_nmr_spec(indx) ^ xwin.c:62740:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] getrad(t,coo,iatoms,dret) ^ xwin.c:62771:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] prt_(iop) ^ xwin.c:63020:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] plcnrm() ^ 1196 warnings generated. gfortran49 -o molden atomdens.o molden.o above.o actcal.o basprt.o calc.o caldis.o calfa.o cntour.o cnvgam.o cnvgau.o convzmat.o cross.o crprod.o datin.o defpc.o defrad.o del.o denmak.o densmat.o distot.o dmat.o docent.o draw.o euler.o eulerh.o files.o fndcal.o gampoi.o gaupoi.o gaussian.o geogam.o geogau.o getmul.o getpoi.o getreal.o gmmcnv.o grdcal.o gstr.o hidedr.o impsc.o locatc.o maxmin.o mdout.o mmcnv.o mopaco.o mopin.o mulprt.o occin.o oriin.o parang.o pareul.o parfc.o parori.o parpla.o parstp.o planky.o plend.o plini.o plmol.o plotgh.o plotgr.o plotin.o plpost.o prev.o proato.o procnv.o progeo.o rdbas.o rdcor.o rdgam.o rdgaus.o rdinfo.o rdpdb.o rdvect.o reada.o readel.o readvv.o renorm.o rmomen.o rota.o rotatg.o rotb.o rotc.o rotcor.o rotd.o rotfir.o rotm.o rotmom.o scback.o search.o searchd.o setang.o setbas.o settc.o shsort.o site.o slater.o stoc.o tessa.o tk4014.o tocap.o tocapf.o tomold.o under.o vaxdum.o vclr.o vec.o vlen.o vsc1.o wrinfo.o zread.o samino.o prtcal.o acts s.o actami.o plden.o heaps.o den3d.o dencnt.o plhead.o pltab.o eucmol.o pl3dm.o plbox.o selsol.o atmd.o dolift.o spaced.o snypnt.o eulstr.o calct.o coeffs.o epint.o espot.o fcij.o fmt.o genaos.o rys.o ryspol.o rysrot.o thrcen.o twocen.o ifblen.o rott.o plmolp.o wrzmat.o rdchx.o obin.o pred.o gargpl.o inferr.o freqs.o getmop.o brklin.o getzm.o xyzcoo.o geomop.o dumzm.o getxyz.o espchrg.o proxim.o rdgamu.o plvrml.o molsint.o runjob.o rdmsf.o wrmsf.o rdmolf.o adf_fun.o rotpol.o extbas.o rdcpmd.o eem.o asspmf.o srfcal.o rdqchm.o rdorca.o rdmaux.o rdnwch.o mpdum.o xwin.o -lX11 -lm xwin.o: In function `DoWGET': xwin.c:(.text+0x7c748): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() xwin.o: In function `dos2u': xwin.c:(.text+0x78ecc): warning: warning: mktemp() possibly used unsafely; consider using mkstemp() /usr/local/lib/gcc49/gcc/armv6-portbld-freebsd12.0/4.9.4/../../../libgfortran.so: undefined reference to `fpgetsticky' collect2: error: ld returned 1 exit status gmake[1]: *** [makefile:279: molden] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/molden/work/molden5.7' *** Error code 1 Stop. make: stopped in /usr/ports/biology/molden
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