[package - main-amd64-default][science/R-cran-eco] Failed for R-cran-eco-4.0.3 in stage
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Date: Tue, 20 May 2025 03:51:03 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: wen@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p641386d44e51_s2a042fab4f9/logs/R-cran-eco-4.0.3.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p641386d44e51_s2a042fab4f9
Log:
=>> Building science/R-cran-eco
build started at Tue May 20 03:48:16 UTC 2025
port directory: /usr/ports/science/R-cran-eco
package name: R-cran-eco-4.0.3
building for: FreeBSD main-amd64-default-job-06 15.0-CURRENT FreeBSD 15.0-CURRENT 1500042 amd64
maintained by: wen@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 384 May 21 2023 /usr/ports/science/R-cran-eco/Makefile
Ports top last git commit: 641386d44e5
Ports top unclean checkout: no
Port dir last git commit: fb1969a894d
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2-12-g74a54a88
Host OSVERSION: 1500035
Jail OSVERSION: 1500042
Job Id: 06
!!! Jail is newer than host. (Jail: 1500042, Host: 1500035) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500042
UNAME_v=FreeBSD 15.0-CURRENT 1500042
UNAME_r=15.0-CURRENT
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
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.2-12-g74a54a88
MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
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POUDRIERE_PKGNAME=poudriere-git-3.4.2-12-g74a54a88
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
wen@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
F77="gfortran13" F90="gfortran13" FC="gfortran13" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc13" XDG_DATA_HOME=/wrkdirs/usr/ports/science/R-cran-eco/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/R-cran-eco/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/R-cran-eco/work/.cache HOME=/wrkdirs/usr/ports/science/R-cran-eco/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/R-cran-eco/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/R-cran-eco/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="gfortran13" F90="gfortran13" FC="gfortran13" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc13" XDG_DATA_HOME=/wrkdirs/usr/ports/science/R-cran-eco/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/R-cran-eco/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/R-cran-eco/work/.cache HOME=/wrkdirs/usr/ports/science/R-cran-eco/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/R-cran-eco/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/R-cran-eco/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/objco
py" 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 CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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/eco OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/eco" EXAMPLESDIR="share/examples/eco" DATADIR="share/eco" WWWDIR="www/eco" ETCDIR="etc/eco"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/eco DOCSDIR=/usr/local/share/doc/eco EXAMPLESDIR=/usr/local/share/examples/eco WWWDIR=/usr/local/www/eco ETCDIR=/usr/local/etc/eco
--End SUB_LIST--
---Begin 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.
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# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# 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 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
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) 8192
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
pipebuf (-y) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> R-cran-eco-4.0.3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.1.2.pkg
[main-amd64-default-job-06] Installing pkg-2.1.2...
[main-amd64-default-job-06] Extracting pkg-2.1.2: .......... done
===> R-cran-eco-4.0.3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of R-cran-eco-4.0.3
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by R-cran-eco-4.0.3 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by R-cran-eco-4.0.3 for building
=> SHA256 Checksum OK for eco_4.0-3.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by R-cran-eco-4.0.3 for building
===> Extracting for R-cran-eco-4.0.3
=> SHA256 Checksum OK for eco_4.0-3.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for R-cran-eco-4.0.3
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> R-cran-eco-4.0.3 depends on file: /usr/local/bin/R - not found
===> Installing existing package /packages/All/R-4.5.0.pkg
[main-amd64-default-job-06] Installing R-4.5.0...
[main-amd64-default-job-06] `-- Installing cairo-1.18.2,3...
[main-amd64-default-job-06] | `-- Installing fontconfig-2.15.0_3,1...
[main-amd64-default-job-06] | | `-- Installing expat-2.7.1...
[main-amd64-default-job-06] | | `-- Extracting expat-2.7.1: .......... done
[main-amd64-default-job-06] | | `-- Installing freetype2-2.13.3...
[main-amd64-default-job-06] | | `-- Installing brotli-1.1.0,1...
<snip>
[main-amd64-default-job-06] | | `-- Extracting avahi-app-0.8_6: .......... done
[main-amd64-default-job-06] | | `-- Installing gnutls-3.8.9...
[main-amd64-default-job-06] | | `-- Installing libtasn1-4.20.0_1...
[main-amd64-default-job-06] | | `-- Extracting libtasn1-4.20.0_1: .......... done
[main-amd64-default-job-06] | | `-- Installing nettle-3.10.1...
[main-amd64-default-job-06] | | `-- Extracting nettle-3.10.1: .......... done
[main-amd64-default-job-06] | | `-- Installing p11-kit-0.25.5...
[main-amd64-default-job-06] | | `-- Extracting p11-kit-0.25.5: .......... done
[main-amd64-default-job-06] | | `-- Extracting gnutls-3.8.9: .......... done
[main-amd64-default-job-06] | | `-- Installing libpaper-1.1.28_1...
[main-amd64-default-job-06] | | `-- Extracting libpaper-1.1.28_1: .......... done
===> Creating groups
Creating group 'cups' with gid '193'
===> Creating users
Creating user 'cups' with uid '193'
[main-amd64-default-job-06] | `-- Extracting cups-2.4.11_1: .......... done
[main-amd64-default-job-06] | `-- Installing jbig2dec-0.20_1...
[main-amd64-default-job-06] | `-- Extracting jbig2dec-0.20_1: .......... done
[main-amd64-default-job-06] | `-- Installing jpeg-turbo-3.1.0...
[main-amd64-default-job-06] | `-- Extracting jpeg-turbo-3.1.0: .......... done
[main-amd64-default-job-06] | `-- Installing lcms2-2.17...
[main-amd64-default-job-06] | | `-- Installing tiff-4.7.0...
[main-amd64-default-job-06] | | `-- Installing jbigkit-2.1_3...
[main-amd64-default-job-06] | | `-- Extracting jbigkit-2.1_3: .......... done
[main-amd64-default-job-06] | | `-- Installing lerc-4.0.0...
[main-amd64-default-job-06] | | `-- Extracting lerc-4.0.0: ........ done
[main-amd64-default-job-06] | | `-- Installing libdeflate-1.22...
[main-amd64-default-job-06] | | `-- Extracting libdeflate-1.22: .......... done
[main-amd64-default-job-06] | | `-- Extracting tiff-4.7.0: .......... done
[main-amd64-default-job-06] | `-- Extracting lcms2-2.17: .......... done
[main-amd64-default-job-06] | `-- Installing libXt-1.3.0,1...
[main-amd64-default-job-06] | `-- Extracting libXt-1.3.0,1: .......... done
[main-amd64-default-job-06] | `-- Installing libidn-1.43...
[main-amd64-default-job-06] | `-- Extracting libidn-1.43: .......... done
[main-amd64-default-job-06] | `-- Installing openjpeg-2.5.3...
[main-amd64-default-job-06] | `-- Extracting openjpeg-2.5.3: .......... done
[main-amd64-default-job-06] | `-- Installing poppler-data-0.4.12...
[main-amd64-default-job-06] | `-- Extracting poppler-data-0.4.12: .......... done
[main-amd64-default-job-06] | `-- Installing urw-base35-fonts-20200910...
[main-amd64-default-job-06] | | `-- Installing mkfontscale-1.2.3...
[main-amd64-default-job-06] | | `-- Installing libfontenc-1.1.8...
[main-amd64-default-job-06] | | `-- Extracting libfontenc-1.1.8: ......... done
[main-amd64-default-job-06] | | `-- Extracting mkfontscale-1.2.3: ....... done
[main-amd64-default-job-06] | `-- Extracting urw-base35-fonts-20200910: .......... done
[main-amd64-default-job-06] `-- Extracting ghostscript10-10.05.1: .......... done
[main-amd64-default-job-06] `-- Installing gmake-4.4.1...
[main-amd64-default-job-06] `-- Extracting gmake-4.4.1: .......... done
[main-amd64-default-job-06] `-- Installing harfbuzz-10.3.0...
[main-amd64-default-job-06] | `-- Installing graphite2-1.3.14...
[main-amd64-default-job-06] | `-- Extracting graphite2-1.3.14: .......... done
[main-amd64-default-job-06] `-- Extracting harfbuzz-10.3.0: .......... done
[main-amd64-default-job-06] `-- Installing icu-76.1,1...
[main-amd64-default-job-06] `-- Extracting icu-76.1,1: .......... done
[main-amd64-default-job-06] `-- Installing libXScrnSaver-1.2.4_1...
[main-amd64-default-job-06] `-- Extracting libXScrnSaver-1.2.4_1: .......... done
[main-amd64-default-job-06] `-- Installing libXmu-1.1.4,1...
[main-amd64-default-job-06] `-- Extracting libXmu-1.1.4,1: .......... done
[main-amd64-default-job-06] `-- Installing pango-1.56.1...
[main-amd64-default-job-06] | `-- Installing fribidi-1.0.16...
[main-amd64-default-job-06] | `-- Extracting fribidi-1.0.16: .......... done
[main-amd64-default-job-06] | `-- Installing libXft-2.3.8...
[main-amd64-default-job-06] | `-- Extracting libXft-2.3.8: .......... done
[main-amd64-default-job-06] | `-- Installing libthai-0.1.29_1...
[main-amd64-default-job-06] | | `-- Installing libdatrie-0.2.13_2...
[main-amd64-default-job-06] | | `-- Extracting libdatrie-0.2.13_2: .......... done
[main-amd64-default-job-06] | `-- Extracting libthai-0.1.29_1: .......... done
[main-amd64-default-job-06] `-- Extracting pango-1.56.1: .......... done
[main-amd64-default-job-06] `-- Installing tcl86-8.6.16_2...
[main-amd64-default-job-06] `-- Extracting tcl86-8.6.16_2: .......... done
[main-amd64-default-job-06] `-- Installing tk86-8.6.16...
[main-amd64-default-job-06] `-- Extracting tk86-8.6.16: .......... done
[main-amd64-default-job-06] Extracting R-4.5.0: .......... done
==> Running trigger: fontconfig.ucl
Running fc-cache to build fontconfig cache...
==> Running trigger: gio-modules.ucl
Generating GIO modules cache
==> Running trigger: glib-schemas.ucl
Compiling glib schemas
No schema files found: doing nothing.
=====
Message from freetype2-2.13.3:
--
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 libinotify-20240724_1:
--
You might want to consider increasing the kern.maxfiles tunable if you plan
to use this library for applications that need to monitor activity of a lot
of files.
=====
Message from python311-3.11.12:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py311-gdbm databases/py-gdbm@py311
py311-sqlite3 databases/py-sqlite3@py311
py311-tkinter x11-toolkits/py-tkinter@py311
=====
Message from gcc13-13.3.0_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/gcc13
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
=====
Message from ghostscript10-10.05.1:
--
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.
===> R-cran-eco-4.0.3 depends on file: /usr/local/bin/R - found
===> Returning to build of R-cran-eco-4.0.3
===> R-cran-eco-4.0.3 depends on executable: gfortran13 - found
===> R-cran-eco-4.0.3 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for R-cran-eco-4.0.3
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===========================================================================
=======================<phase: run-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> R-cran-eco-4.0.3 depends on file: /usr/local/bin/R - found
===> R-cran-eco-4.0.3 depends on executable: gfortran13 - found
===========================================================================
=======================<phase: stage >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Staging for R-cran-eco-4.0.3
===> Generating temporary packing list
* installing *source* package 'eco' ...
** this is package 'eco' version '4.0-3'
** package 'eco' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)'
cc -std=gnu23 -I"/usr/local/lib/R/include" -DNDEBUG -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 bayes.c -o bayes.o
bayes.c:73:3: error: use of undeclared identifier 'Free'; did you mean 'free'?
73 | Free(Ybar);
| ^~~~
| free
/usr/include/stdlib.h:96:7: note: 'free' declared here
96 | void free(void *);
| ^
bayes.c:74:3: error: use of undeclared identifier 'Free'; did you mean 'free'?
74 | Free(mun);
| ^~~~
| free
/usr/include/stdlib.h:96:7: note: 'free' declared here
96 | void free(void *);
| ^
2 errors generated.
gmake: *** [/usr/local/lib/R/etc/Makeconf:202: bayes.o] Error 1
ERROR: compilation failed for package 'eco'
* removing '/wrkdirs/usr/ports/science/R-cran-eco/work/stage/usr/local/lib/R/library/eco'
*** Error code 1
Stop.
make: stopped making "stage" in /usr/ports/science/R-cran-eco