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Maintainer: po...@freebsd.org Last committer: pa...@freebsd.org Ident: $FreeBSD: head/biology/ncbi-toolkit/Makefile 348888 2014-03-23 20:50:54Z pawel $ Log URL: http://beefy6.nyi.freebsd.org/data/101amd64-default/416942/logs/ncbi-toolkit-2012.06.20.log Build URL: http://beefy6.nyi.freebsd.org/build.html?mastername=101amd64-default&build=416942 Log: ====>> Building biology/ncbi-toolkit build started at Thu Jun 16 02:13:38 UTC 2016 port directory: /usr/ports/biology/ncbi-toolkit building for: FreeBSD 101amd64-default-job-18 10.1-RELEASE-p36 FreeBSD 10.1-RELEASE-p36 amd64 maintained by: po...@freebsd.org Makefile ident: $FreeBSD: head/biology/ncbi-toolkit/Makefile 348888 2014-03-23 20:50:54Z pawel $ Poudriere version: 3.1.12 Host OSVERSION: 1100109 Jail OSVERSION: 1001000 ---Begin Environment--- SHELL=/bin/csh UNAME_v=FreeBSD 10.1-RELEASE-p36 UNAME_r=10.1-RELEASE-p36 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=amd64 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/101amd64-default/ref UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/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=ncbi-toolkit-2012.06.20 OSREL=10.1 _OSRELEASE=10.1-RELEASE-p36 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=24 PWD=/usr/local/poudriere/data/.m/101amd64-default/ref/.p/pool HAVE_COMPAT_IA32_KERN=YES LINUX_OSRELEASE=2.6.32 MASTERNAME=101amd64-default SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.12 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=1001000 ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for ncbi-toolkit-2012.06.20: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- MOTIFLIB="-L/usr/local/lib -lXm -lXp" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work TMPDIR="/tmp" NO_PIE=yes WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-DLIBICONV_PLUG" LDFLAGS=" -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing -DLIBICONV_PLUG" 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=10.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/ncbi-toolkit" EXAMPLESDIR="share/examples/ncbi-toolkit" DATADIR="share/ncbi-toolkit" WWWDIR="www/ncbi-toolkit" ETCDIR="etc/ncbi-toolkit" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ncbi-toolkit DOCSDIR=/usr/local/share/doc/ncbi-toolkit EXAMPLESDIR=/usr/local/share/examples/ncbi-toolkit WWWDIR=/usr/local/www/ncbi-toolkit ETCDIR=/usr/local/etc/ncbi-toolkit --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ ===> NOTICE: The ncbi-toolkit port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port =========================================================================== =======================<phase: pkg-depends >============================ ===> ncbi-toolkit-2012.06.20 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.5_1.txz [101amd64-default-job-18] Installing pkg-1.8.5_1... [101amd64-default-job-18] Extracting pkg-1.8.5_1: .......... done ===> ncbi-toolkit-2012.06.20 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-toolkit-2012.06.20 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> NOTICE: The ncbi-toolkit port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by ncbi-toolkit-2012.06.20 for building =========================================================================== =======================<phase: checksum >============================ ===> NOTICE: The ncbi-toolkit port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by ncbi-toolkit-2012.06.20 for building => SHA256 Checksum OK for ncbi-toolkit-2012.06.20/ncbi.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> NOTICE: The ncbi-toolkit port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by ncbi-toolkit-2012.06.20 for building ===> Extracting for ncbi-toolkit-2012.06.20 => SHA256 Checksum OK for ncbi-toolkit-2012.06.20/ncbi.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for ncbi-toolkit-2012.06.20 ===> Applying FreeBSD patches for ncbi-toolkit-2012.06.20 =========================================================================== =======================<phase: build-depends >============================ ===> ncbi-toolkit-2012.06.20 depends on package: libiconv>=1.14_9 - not found ===> Installing existing package /packages/All/libiconv-1.14_9.txz [101amd64-default-job-18] Installing libiconv-1.14_9... [101amd64-default-job-18] Extracting libiconv-1.14_9: .......... done ===> ncbi-toolkit-2012.06.20 depends on package: libiconv>=1.14_9 - found ===> Returning to build of ncbi-toolkit-2012.06.20 ===> ncbi-toolkit-2012.06.20 depends on file: /usr/local/libdata/pkgconfig/xpm.pc - not found ===> Installing existing package /packages/All/libXpm-3.5.11_4.txz [101amd64-default-job-18] Installing libXpm-3.5.11_4... [101amd64-default-job-18] `-- Installing xproto-7.0.28... [101amd64-default-job-18] `-- Extracting xproto-7.0.28: .......... done [101amd64-default-job-18] `-- Installing libXt-1.1.5,1... [101amd64-default-job-18] | `-- Installing libSM-1.2.2_3,1... [101amd64-default-job-18] | | `-- Installing libICE-1.0.9_1,1... [101amd64-default-job-18] | | `-- Extracting libICE-1.0.9_1,1: .......... done [101amd64-default-job-18] | `-- Extracting libSM-1.2.2_3,1: .......... done [101amd64-default-job-18] | `-- Installing libX11-1.6.3,1... <snip> switch (wiz->cultured_kingdom) { ^ sequin1.c:16488:11: warning: enumeration values 'eVirusFeat_None' and 'eVirusFeat_CDS' not handled in switch [-Wswitch] switch (wiz->virus_feat) { ^ sequin1.c:20709:13: warning: enumeration value 'eVirusClass_Unknown' not handled in switch [-Wswitch] switch (wiz->virus_class) { ^ sequin1.c:20814:13: warning: enumeration value 'eCulturedKingdom_Unknown' not handled in switch [-Wswitch] switch (wiz->cultured_kingdom) { ^ sequin1.c:21083:10: warning: illegal character encoding in string literal [-Winvalid-source-encoding] -Use the <93>Import Source Table<94> button to import a tab-delimited table\n\ ^~~~ ~~~~ sequin1.c:21241:10: warning: illegal character encoding in string literal [-Winvalid-source-encoding] -Use the <93>Import Source Table<94> button to import a tab-delimited table\n\ ^~~~ ~~~~ sequin1.c:21321:10: warning: illegal character encoding in string literal [-Winvalid-source-encoding] -Use the <93>Import Source Table<94> button to import a tab-delimited table\n\ ^~~~ ~~~~ sequin1.c:21962:65: warning: use of logical '||' with constant operand [-Wconstant-logical-operand] if (rval && (wiz->wizard_type == eWizardType_Microsatellite || eWizardType_DLoop)) { ^ ~~~~~~~~~~~~~~~~~ sequin1.c:21962:65: note: use '|' for a bitwise operation if (rval && (wiz->wizard_type == eWizardType_Microsatellite || eWizardType_DLoop)) { ^~ | sequin1.c:25697:11: warning: enumeration values 'eWizardType_TSA' and 'eWizardType_Microsatellite' not handled in switch [-Wswitch] switch (wiz->wizard_type) { ^ sequin1.c:26622:13: warning: enumeration values 'eWizardType_TSA', 'eWizardType_Microsatellite', and 'eWizardType_DLoop' not handled in switch [-Wswitch] switch (wiz->wizard_type) { ^ sequin1.c:26655:11: warning: 4 enumeration values not handled in switch: 'eWizardType_UnculturedSamples', 'eWizardType_TSA', 'eWizardType_Microsatellite'... [-Wswitch] switch (wiz->wizard_type) { ^ sequin1.c:26717:11: warning: 4 enumeration values not handled in switch: 'eWizardType_UnculturedSamples', 'eWizardType_TSA', 'eWizardType_Microsatellite'... [-Wswitch] switch (wiz->wizard_type) { ^ sequin1.c:29939:7: warning: illegal character encoding in string literal [-Winvalid-source-encoding] Click <91>Import Nucleotide Alignment<92> to load your nucleotide alignment file.\n\ ^~~~ ~~~~ sequin1.c:29940:7: warning: illegal character encoding in string literal [-Winvalid-source-encoding] Click <91>Custom Alignment Settings<92> if there is trouble reading your alignment file.\n\ ^~~~ ~~~~ sequin1.c:30287:11: warning: 5 enumeration values not handled in switch: 'eWizardType_UnculturedSamples', 'eWizardType_Viruses', 'eWizardType_CulturedSamples'... [-Wswitch] switch (frm->wiz->wizard_type) { ^ 19 warnings generated. sequin2.c:7871:56: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion] if (sep == NULL || StringHasNoText (valname)) return FALSE; ^~~~~ ./include/ncbistd.h:278:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin2.c:7872:33: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion] if (! IS_Bioseq (sep)) return FALSE; ^~~~~ ./include/ncbistd.h:278:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin2.c:7874:68: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion] if (bsp == NULL || bsp->mol != mol || bsp->descr == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:278:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin2.c:7876:57: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion] if (vnp == NULL || vnp->data.ptrvalue == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:278:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin2.c:27635:57: warning: expression which evaluates to zero treated as a null pointer constant of type 'BioseqPtr' (aka 'struct bioseq *') [-Wnon-literal-null-conversion] if (sep == NULL || sep->data.ptrvalue == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:278:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin2.c:27650:32: warning: expression which evaluates to zero treated as a null pointer constant of type 'BioseqPtr' (aka 'struct bioseq *') [-Wnon-literal-null-conversion] if (!IS_Bioseq (sep)) return FALSE; ^~~~~ ./include/ncbistd.h:278:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin2.c:28350:13: warning: '&&' within '||' [-Wlogical-op-parentheses] && StringCmp (oip->str, "ProjectID") == 0 || StringCmp (oip->str, "ParentID") == 0) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ sequin2.c:28350:13: note: place parentheses around the '&&' expression to silence this warning && StringCmp (oip->str, "ProjectID") == 0 || StringCmp (oip->str, "ParentID") == 0) { ^ sequin2.c:29035:21: warning: implicit conversion from enumeration type 'enum EBlastStage' to different enumeration type 'enum blast_hint' [-Wenum-conversion] options->hint = eNone; ~ ^~~~~ 8 warnings generated. sequin3.c:9351:26: warning: '&&' within '||' [-Wlogical-op-parentheses] || must_have_stops && !HasInternalStops (sfp)) ~~ ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ sequin3.c:9351:26: note: place parentheses around the '&&' expression to silence this warning || must_have_stops && !HasInternalStops (sfp)) ^ ( ) sequin3.c:18822:60: warning: cast to 'Nlm_VoidPtr' (aka 'void *') from smaller integer type 'Nlm_Int4' (aka 'int') [-Wint-to-void-pointer-cast] GatherItem (sel->entityID, sel->itemID, sel->itemtype, (Pointer) (Int4) align_type, AddBlastTag); ^ 2 warnings generated. sequin4.c:5396:52: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion] salp = Sequin_GlobalAlign2Seq(bsp, sbp->bsp, FALSE); ^~~~~ ./include/ncbistd.h:278:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin4.c:5400:49: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion] salp = Sqn_GlobalAlign2Seq(bsp, sbp->bsp, FALSE); ^~~~~ ./include/ncbistd.h:278:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin4.c:16733:67: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion] salp = Sequin_GlobalAlign2Seq(master_bsp, vnp->data.ptrvalue, FALSE); ^~~~~ ./include/ncbistd.h:278:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ 3 warnings generated. sequin5.c:18449:12: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion] return FALSE; ^~~~~ ./include/ncbistd.h:278:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin5.c:20038:12: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion] return FALSE; ^~~~~ ./include/ncbistd.h:278:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ 2 warnings generated. sequin7.c:14803:48: warning: '&&' within '||' [-Wlogical-op-parentheses] || best_left == fcontext.left && best_right < fcontext.right) { ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin7.c:14803:48: note: place parentheses around the '&&' expression to silence this warning || best_left == fcontext.left && best_right < fcontext.right) { ^ ( ) sequin7.c:16288:46: warning: '&&' within '||' [-Wlogical-op-parentheses] || word_break - t->suggested_fix == 10 && StringNICmp (t->suggested_fix, "uncultured ", 11) == 0) { ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin7.c:16288:46: note: place parentheses around the '&&' expression to silence this warning || word_break - t->suggested_fix == 10 && StringNICmp (t->suggested_fix, "uncultured ", 11) == 0) { ^ ( ) 2 warnings generated. sequin8.c:10738:39: warning: self-comparison always evaluates to true [-Wtautological-compare] } else if (left2 <= left1 && right2 >= right2) { ^ sequin8.c:11080:69: warning: self-comparison always evaluates to false [-Wtautological-compare] if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) { ^ sequin8.c:11086:69: warning: self-comparison always evaluates to false [-Wtautological-compare] if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) { ^ sequin8.c:15341:11: warning: enumeration value 'eReportTypeTSA' not handled in switch [-Wswitch] switch (report_type) { ^ sequin8.c:15372:11: warning: enumeration value 'eReportTypeTSA' not handled in switch [-Wswitch] switch (report_type) { ^ sequin8.c:15390:11: warning: enumeration value 'eReportTypeTSA' not handled in switch [-Wswitch] switch (report_type) { ^ sequin8.c:16944:11: warning: enumeration value 'eReportTypeTSA' not handled in switch [-Wswitch] switch (report_type) { ^ sequin8.c:16968:11: warning: enumeration value 'eReportTypeTSA' not handled in switch [-Wswitch] switch (report_type) { ^ 8 warnings generated. sequin9.c:14092:49: warning: implicit conversion from 'unsigned long' to 'Nlm_Uint4' (aka 'unsigned int') changes value from 18446744073709551607 to 4294967287 [-Wconstant-conversion] PRINTID_REPORT, sizeof (id_txt) - 50); ~~~~~~~~~~~~~~~~^~~~ 1 warning generated. /usr/bin/ld: cannot find -lpng cc: error: linker command failed with exit code 1 (use -v to see invocation) *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/build FAILURE primary make status = 0, demo = 0, threaded_demo = 0, net = 1 ####### # ##### ##### #### ##### # # # # # # # # # ##### # # # # # # # # # ##### ##### # # ##### # # # # # # # # # ####### # # # # #### # # *** Error code 1 Stop. make: stopped in /usr/ports/biology/ncbi-toolkit _______________________________________________ freebsd-pkg-fallout@freebsd.org mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "freebsd-pkg-fallout-unsubscr...@freebsd.org"
