Date: Wed, 23 Aug 2017 18:31:19 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110arm64-default][textproc/R-cran-XML] Failed for R-cran-XML-3.98.1.9 in stage Message-ID: <201708231831.v7NIVJTq034194@thunderx1.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: tota@FreeBSD.org Last committer: tota@FreeBSD.org Ident: $FreeBSD: head/textproc/R-cran-XML/Makefile 444545 2017-06-28 07:31:11Z tota $ Log URL: http://thunderx1.nyi.freebsd.org/data/110arm64-default/448504/logs/R-cran-XML-3.98.1.9.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=110arm64-default&build=448504 Log: ====>> Building textproc/R-cran-XML build started at Wed Aug 23 18:28:54 UTC 2017 port directory: /usr/ports/textproc/R-cran-XML building for: FreeBSD 110arm64-default-job-03 11.0-RELEASE-p1 FreeBSD 11.0-RELEASE-p1 arm64 maintained by: tota@FreeBSD.org Makefile ident: $FreeBSD: head/textproc/R-cran-XML/Makefile 444545 2017-06-28 07:31:11Z tota $ Poudriere version: 3.1.19-61-ga8829ba9 Host OSVERSION: 1200040 Jail OSVERSION: 1100122 Job Id: 03 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p1 UNAME_r=11.0-RELEASE-p1 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110arm64-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=R-cran-XML-3.98.1.9 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110arm64-default/ref/.p/pool MASTERNAME=110arm64-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.19-61-ga8829ba9 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/wrkdirs/usr/ports/textproc/R-cran-XML/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/textproc/R-cran-XML/work HOME=/wrkdirs/usr/ports/textproc/R-cran-XML/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/wrkdirs/usr/ports/textproc/R-cran-XML/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/textproc/R-cran-XML/work HOME=/wrkdirs/usr/ports/textproc/R-cran-XML/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="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin" LIBS="" CXX="c++" CXXFLAGS= "-O2 -pipe -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-- R_MOD_DIR=lib/R/library/XML GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/XML" EXAMPLESDIR="share/examples/XML" DATADIR="share/XML" WWWDIR="www/XML" ETCDIR="etc/XML" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/XML DOCSDIR=/usr/local/share/doc/XML EXAMPLESDIR=/usr/local/share/examples/XML WWWDIR=/usr/local/www/XML ETCDIR=/usr/local/etc/XML --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes #### /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 #### ARCH=aarch64 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=11.0 OSVERSION=1100122 PYTHONBASE=/usr/local UID=0 _JAVA_OS_LIST_REGEXP=native|linux _JAVA_VENDOR_LIST_REGEXP=openjdk|oracle|sun _JAVA_VERSION_LIST_REGEXP=1.6|1.7|1.8|1.6\+|1.7\+|1.8\+ _OSRELEASE=11.0-RELEASE-p1 #### Misc Poudriere #### GID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 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 BSD2CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> R-cran-XML-3.98.1.9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz [110arm64-default-job-03] Installing pkg-1.10.1... [110arm64-default-job-03] Extracting pkg-1.10.1: .......... done ===> R-cran-XML-3.98.1.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of R-cran-XML-3.98.1.9 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by R-cran-XML-3.98.1.9 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by R-cran-XML-3.98.1.9 for building => SHA256 Checksum OK for XML_3.98-1.9.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by R-cran-XML-3.98.1.9 for building ===> Extracting for R-cran-XML-3.98.1.9 => SHA256 Checksum OK for XML_3.98-1.9.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for R-cran-XML-3.98.1.9 =========================================================================== =======================<phase: build-depends >============================ ===> R-cran-XML-3.98.1.9 depends on file: /usr/local/bin/R - not found ===> Installing existing package /packages/All/R-3.4.1_4.txz [110arm64-default-job-03] Installing R-3.4.1_4... [110arm64-default-job-03] `-- Installing cairo-1.14.8_1,2... [110arm64-default-job-03] | `-- Installing dri2proto-2.8... [110arm64-default-job-03] | `-- Extracting dri2proto-2.8: .... done [110arm64-default-job-03] | `-- Installing fontconfig-2.12.1,1... [110arm64-default-job-03] | | `-- Installing expat-2.2.1... [110arm64-default-job-03] | | `-- Extracting expat-2.2.1: .......... done [110arm64-default-job-03] | | `-- Installing freetype2-2.8... [110arm64-default-job-03] | | `-- Extracting freetype2-2.8: .......... done [110arm64-default-job-03] | `-- Extracting fontconfig-2.12.1,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded [110arm64-default-job-03] | `-- Installing gettext-runtime-0.19.8.1_1... [110arm64-default-job-03] | | `-- Installing indexinfo-0.2.6... [110arm64-default-job-03] | | `-- Extracting indexinfo-0.2.6: .... done [110arm64-default-job-03] | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [110arm64-default-job-03] | `-- Installing glib-2.50.2_4,1... [110arm64-default-job-03] | | `-- Installing libffi-3.2.1... [110arm64-default-job-03] | | `-- Extracting libffi-3.2.1: .......... done [110arm64-default-job-03] | | `-- Installing libiconv-1.14_10... [110arm64-default-job-03] | | `-- Extracting libiconv-1.14_10: .......... done [110arm64-default-job-03] | | `-- Installing pcre-8.40_1... [110arm64-default-job-03] | | `-- Extracting pcre-8.40_1: .......... done [110arm64-default-job-03] | | `-- Installing perl5-5.24.2... <snip> #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Message from python27-2.7.13_7: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from ca_root_nss-3.32: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** Message from gcc5-5.4.0_3: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from trousers-0.3.14_1: To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Message from ghostscript9-agpl-base-9.16_5: Note: in order to use the script "dvipdf", dvips must be installed. This program is provided by another package print/tex-dvipsk. FAPIfontmap and FAPIcidfmap in /usr/local/share/ghostscript/9.16/Resource/Init have to be configured if you want to use FAPI feature. Message from dejavu-2.37: Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. Message from R-3.4.1_4: ======================================================================== On 11.1 and later, there is a problem downloading R packages when gfortran is chosen as the fortran compiler. Use either of these workarounds until a permanent solution is found. 1. If you are on an amd64 system, you can use flang as the fortran compiler. 2. If you choose gfortran as the fortran compiler, you can add options(download.file.method="wget") to ~/.Rprofile followed by a newline. Details: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=221127 ======================================================================== ===> R-cran-XML-3.98.1.9 depends on file: /usr/local/bin/R - found ===> Returning to build of R-cran-XML-3.98.1.9 ===> R-cran-XML-3.98.1.9 depends on executable: gfortran5 - found ===> R-cran-XML-3.98.1.9 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ ===> R-cran-XML-3.98.1.9 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) =========================================================================== =======================<phase: configure >============================ ===> Configuring for R-cran-XML-3.98.1.9 =========================================================================== =======================<phase: build >============================ =========================================================================== =======================<phase: run-depends >============================ ===> R-cran-XML-3.98.1.9 depends on file: /usr/local/bin/R - found ===> R-cran-XML-3.98.1.9 depends on executable: gfortran5 - found =========================================================================== =======================<phase: stage >============================ ===> Staging for R-cran-XML-3.98.1.9 ===> Generating temporary packing list * installing *source* package 'XML' ... ** package 'XML' successfully unpacked and MD5 sums checked checking for gcc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking how to run the C preprocessor... cpp checking for sed... /usr/bin/sed checking for pkg-config... no checking for xml2-config... /usr/local/bin/xml2-config USE_XML2 = yes SED_EXTENDED_ARG: -E Minor 9, Patch 4 for 2.9.4 Located parser file -I/usr/local/include/libxml2 -I/usr/include/parser.h Checking for 1.8: -I/usr/local/include/libxml2 -I/usr/include Using libxml2.* checking for gzopen in -lz... yes checking for xmlParseFile in -lxml2... yes checking for xmlHashSize in -lxml2... yes Using built-in xmlHashSize Checking DTD parsing (presence of externalSubset)... checking for xmlHashSize in -lxml2... yes Found xmlHashSize checking for xmlOutputBufferCreateBuffer in -lxml2... yes have xmlOutputBufferCreateBuffer() checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes checking libxml/xmlversion.h usability... yes checking libxml/xmlversion.h presence... yes checking for libxml/xmlversion.h... yes Expat: FALSE Checking for return type of xmlHashScan element routine. No return value for xmlHashScan xmlNs has a context field Checking for cetype_t enumeration Using recent version of R with cetype_t enumeration type for encoding checking for xmlsec1-config... no nodegc default xml-debug default Version has XML_WITH_ZLIB Version has xmlHasFeature() **************************************** Configuration information: Libxml settings libxml include directory: -I/usr/local/include/libxml2 -I/usr/include libxml library directory: -L/usr/local/lib -lxml2 -lz -llzma -L/usr/lib -lm -lz -lxml2 libxml 2: -DLIBXML2=1 Compilation flags: -DLIBXML -I/usr/local/include/libxml2 -I/usr/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 Link flags: -L/usr/local/lib -lxml2 -lz -llzma -L/usr/lib -lm -lz -lxml2 **************************************** configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/supports.R config.status: creating inst/scripts/RSXML.csh config.status: creating inst/scripts/RSXML.bsh ** libs gmake[1]: Entering directory '/wrkdirs/usr/ports/textproc/R-cran-XML/work/XML/src' /usr/local/bin/clang40 -I/usr/local/lib/R/include -DNDEBUG -DLIBXML -I/usr/local/include/libxml2 -I/usr/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -isystem /usr/local/include -fno-strict-aliasing -c DocParse.c -o DocParse.o gmake[1]: /usr/local/bin/clang40: Command not found gmake[1]: *** [/usr/local/lib/R/etc/Makeconf:159: DocParse.o] Error 127 gmake[1]: Leaving directory '/wrkdirs/usr/ports/textproc/R-cran-XML/work/XML/src' ERROR: compilation failed for package 'XML' * removing '/wrkdirs/usr/ports/textproc/R-cran-XML/work/stage/usr/local/lib/R/library/XML' *** Error code 1 Stop. make: stopped in /usr/ports/textproc/R-cran-XML
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