[package - 131amd64-default][math/R-cran-irlba] Failed for R-cran-irlba-2.3.5 in stage
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Date: Wed, 29 Mar 2023 12:50:19 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: tota@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy16/data/131amd64-default/1f6505161e34/logs/R-cran-irlba-2.3.5.log Build URL: https://pkg-status.freebsd.org/beefy16/build.html?mastername=131amd64-default&build=1f6505161e34 Log: =>> Building math/R-cran-irlba build started at Wed Mar 29 12:49:49 UTC 2023 port directory: /usr/ports/math/R-cran-irlba package name: R-cran-irlba-2.3.5 building for: FreeBSD 131amd64-default-job-11 13.1-RELEASE-p7 FreeBSD 13.1-RELEASE-p7 amd64 maintained by: tota@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1301000 Job Id: 11 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1301000 UNAME_v=FreeBSD 13.1-RELEASE-p7 UNAME_r=13.1-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/131amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/131amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=131amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/131amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- tota@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" XDG_DATA_HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work XDG_CACHE_HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work/.cache HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/math/R-cran-irlba/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/math/R-cran-irlba/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" XDG_DATA_HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work XDG_CACHE_HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work/.cache HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/math/R-cran-irlba/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/math/R-cran-irlba/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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="/u sr/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 CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -B/usr/local/bin -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -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/irlba OSREL=13.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/irlba" EXAMPLESDIR="share/examples/irlba" DATADIR="share/irlba" WWWDIR="www/irlba" ETCDIR="etc/irlba" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/irlba DOCSDIR=/usr/local/share/doc/irlba EXAMPLESDIR=/usr/local/share/examples/irlba WWWDIR=/usr/local/www/irlba ETCDIR=/usr/local/etc/irlba --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # 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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 #### _CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: x86_64-unknown-freebsd13.1 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: x86_64-unknown-freebsd13.1 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: x86_64-unknown-freebsd13.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.1-RELEASE-p7 OSREL=13.1 OSVERSION=1301000 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 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 GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> R-cran-irlba-2.3.5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [131amd64-default-job-11] Installing pkg-1.19.1_1... [131amd64-default-job-11] Extracting pkg-1.19.1_1: .......... done ===> R-cran-irlba-2.3.5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of R-cran-irlba-2.3.5 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by R-cran-irlba-2.3.5 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by R-cran-irlba-2.3.5 for building => SHA256 Checksum OK for irlba_2.3.5.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by R-cran-irlba-2.3.5 for building ===> Extracting for R-cran-irlba-2.3.5 => SHA256 Checksum OK for irlba_2.3.5.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for R-cran-irlba-2.3.5 =========================================================================== =======================<phase: build-depends >============================ ===> R-cran-irlba-2.3.5 depends on file: /usr/local/bin/R - not found ===> Installing existing package /packages/All/R-4.2.3.pkg [131amd64-default-job-11] Installing R-4.2.3... [131amd64-default-job-11] `-- Installing cairo-1.17.4_2,3... [131amd64-default-job-11] | `-- Installing fontconfig-2.14.2,1... [131amd64-default-job-11] | | `-- Installing expat-2.5.0... [131amd64-default-job-11] | | `-- Extracting expat-2.5.0: .......... done [131amd64-default-job-11] | | `-- Installing freetype2-2.12.1_2... [131amd64-default-job-11] | | `-- Installing brotli-1.0.9,1... [131amd64-default-job-11] | | `-- Extracting brotli-1.0.9,1: .......... done [131amd64-default-job-11] | | `-- Installing png-1.6.39... [131amd64-default-job-11] | | `-- Extracting png-1.6.39: .......... done [131amd64-default-job-11] | | `-- Extracting freetype2-2.12.1_2: .......... done [131amd64-default-job-11] | `-- Extracting fontconfig-2.14.2,1: .......... done [131amd64-default-job-11] | `-- Installing gettext-runtime-0.21.1... <snip> [131amd64-default-job-11] `-- Extracting gmake-4.3_2: .......... done [131amd64-default-job-11] `-- Installing harfbuzz-7.1.0... [131amd64-default-job-11] | `-- Installing graphite2-1.3.14... [131amd64-default-job-11] | `-- Extracting graphite2-1.3.14: .......... done [131amd64-default-job-11] `-- Extracting harfbuzz-7.1.0: .......... done [131amd64-default-job-11] `-- Installing icu-72.1,1... [131amd64-default-job-11] `-- Extracting icu-72.1,1: .......... done [131amd64-default-job-11] `-- Installing libXScrnSaver-1.2.4... [131amd64-default-job-11] `-- Extracting libXScrnSaver-1.2.4: .......... done [131amd64-default-job-11] `-- Installing libXmu-1.1.3,1... [131amd64-default-job-11] | `-- Installing libXt-1.2.1,1... [131amd64-default-job-11] | `-- Extracting libXt-1.2.1,1: .......... done [131amd64-default-job-11] `-- Extracting libXmu-1.1.3,1: .......... done [131amd64-default-job-11] `-- Installing pango-1.50.9_1... [131amd64-default-job-11] | `-- Installing encodings-1.0.5,1... [131amd64-default-job-11] | `-- Extracting encodings-1.0.5,1: .......... done [131amd64-default-job-11] | `-- Installing fribidi-1.0.12... [131amd64-default-job-11] | `-- Extracting fribidi-1.0.12: .......... done [131amd64-default-job-11] | `-- Installing libXft-2.3.7... [131amd64-default-job-11] | `-- Extracting libXft-2.3.7: .......... done [131amd64-default-job-11] | `-- Installing libthai-0.1.29... [131amd64-default-job-11] | | `-- Installing libdatrie-0.2.13_1... [131amd64-default-job-11] | | `-- Extracting libdatrie-0.2.13_1: .......... done [131amd64-default-job-11] | `-- Extracting libthai-0.1.29: .......... done [131amd64-default-job-11] | `-- Installing xorg-fonts-truetype-7.7_1... [131amd64-default-job-11] | | `-- Installing dejavu-2.37_1... [131amd64-default-job-11] | | `-- Installing mkfontscale-1.2.1... [131amd64-default-job-11] | | | `-- Installing libfontenc-1.1.4... [131amd64-default-job-11] | | | `-- Extracting libfontenc-1.1.4: ......... done [131amd64-default-job-11] | | `-- Extracting mkfontscale-1.2.1: ....... done [131amd64-default-job-11] | | `-- Extracting dejavu-2.37_1: .......... done [131amd64-default-job-11] | | `-- Installing font-bh-ttf-1.0.3_4... [131amd64-default-job-11] | | `-- Extracting font-bh-ttf-1.0.3_4: .......... done [131amd64-default-job-11] | | `-- Installing font-misc-ethiopic-1.0.4... [131amd64-default-job-11] | | `-- Extracting font-misc-ethiopic-1.0.4: ...... done [131amd64-default-job-11] | | `-- Installing font-misc-meltho-1.0.3_4... [131amd64-default-job-11] | | `-- Extracting font-misc-meltho-1.0.3_4: .......... done [131amd64-default-job-11] | `-- Extracting xorg-fonts-truetype-7.7_1: ... done [131amd64-default-job-11] `-- Extracting pango-1.50.9_1: .......... done [131amd64-default-job-11] `-- Installing tcl86-8.6.13... [131amd64-default-job-11] `-- Extracting tcl86-8.6.13: .......... done [131amd64-default-job-11] `-- Installing tk86-8.6.13... [131amd64-default-job-11] `-- Extracting tk86-8.6.13: .......... done [131amd64-default-job-11] Extracting R-4.2.3: .......... done Running fc-cache to build fontconfig cache... Generating GIO modules cache Compiling glib schemas No schema files found: doing nothing. ===== Message from freetype2-2.12.1_2: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from python39-3.9.16_2: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===== Message from ca_root_nss-3.89: -- 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. 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 gcc12-12.2.0_5: -- 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/gcc12 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from ghostscript9-agpl-base-9.56.1_8: -- This package installs a script named dvipdf that depends on dvips. If you want to use this script you need to install print/tex-dvipsk. ===== Message from libthai-0.1.29: -- ===> NOTICE: The libthai 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from dejavu-2.37_1: -- 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. ===> R-cran-irlba-2.3.5 depends on file: /usr/local/bin/R - found ===> Returning to build of R-cran-irlba-2.3.5 ===> R-cran-irlba-2.3.5 depends on executable: gfortran12 - found ===> R-cran-irlba-2.3.5 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for R-cran-irlba-2.3.5 =========================================================================== =======================<phase: build >============================ =========================================================================== =======================<phase: run-depends >============================ ===> R-cran-irlba-2.3.5 depends on file: /usr/local/bin/R - found ===> R-cran-irlba-2.3.5 depends on executable: gfortran12 - found =========================================================================== =======================<phase: stage >============================ ===> Staging for R-cran-irlba-2.3.5 ===> Generating temporary packing list * installing *source* package 'irlba' ... ** package 'irlba' successfully unpacked and MD5 sums checked ** using staged installation ** libs gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R-cran-irlba/work/irlba/src' cc -I"/usr/local/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/library/Matrix/include' -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c irlb.c -o irlb.o irlb.c:590:11: error: too many arguments to function call, expected 0, have 7 sdmult (cha, t, one, zero, &chb, &chc, &chol_c); ~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 error generated. gmake[1]: *** [/usr/local/lib/R/etc/Makeconf:169: irlb.o] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R-cran-irlba/work/irlba/src' ERROR: compilation failed for package 'irlba' * removing '/wrkdirs/usr/ports/math/R-cran-irlba/work/stage/usr/local/lib/R/library/irlba' *** Error code 1 Stop. make: stopped in /usr/ports/math/R-cran-irlba