[package - 142amd64-default][devel/R-cran-Hmisc] Failed for R-cran-Hmisc-4.7.0_2 in stage
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Date: Sun, 25 May 2025 02:32:12 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: skreuzer@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy22/data/142amd64-default/a2459aa0a93e/logs/R-cran-Hmisc-4.7.0_2.log
Build URL: https://pkg-status.freebsd.org/beefy22/build.html?mastername=142amd64-default&build=a2459aa0a93e
Log:
=>> Building devel/R-cran-Hmisc
build started at Sun May 25 02:29:05 UTC 2025
port directory: /usr/ports/devel/R-cran-Hmisc
package name: R-cran-Hmisc-4.7.0_2
building for: FreeBSD 142amd64-default-job-40 14.2-RELEASE-p3 FreeBSD 14.2-RELEASE-p3 amd64
maintained by: skreuzer@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 764 Feb 20 01:01 /usr/ports/devel/R-cran-Hmisc/Makefile
Ports top last git commit: a2459aa0a9
Ports top unclean checkout: no
Port dir last git commit: 1bb147345d
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2-12-g74a54a88
Host OSVERSION: 1500035
Jail OSVERSION: 1402000
Job Id: 40
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skreuzer@FreeBSD.org
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--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/devel/R-cran-Hmisc/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/devel/R-cran-Hmisc/work XDG_CACHE_HOME=/wrkdirs/usr/ports/devel/R-cran-Hmisc/work/.cache HOME=/wrkdirs/usr/ports/devel/R-cran-Hmisc/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/devel/R-cran-Hmisc/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/devel/R-cran-Hmisc/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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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/Hmisc OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/Hmisc" EXAMPLESDIR="share/examples/Hmisc" DATADIR="share/Hmisc" WWWDIR="www/Hmisc" ETCDIR="etc/Hmisc"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/Hmisc DOCSDIR=/usr/local/share/doc/Hmisc EXAMPLESDIR=/usr/local/share/examples/Hmisc WWWDIR=/usr/local/www/Hmisc ETCDIR=/usr/local/etc/Hmisc
--End SUB_LIST--
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PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
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#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
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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 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> R-cran-Hmisc-4.7.0_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.1.3.pkg
[142amd64-default-job-40] Installing pkg-2.1.3...
[142amd64-default-job-40] Extracting pkg-2.1.3: .......... done
===> R-cran-Hmisc-4.7.0_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of R-cran-Hmisc-4.7.0_2
===========================================================================
=======================<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 GPLv3 accepted by the user
===> Fetching all distfiles required by R-cran-Hmisc-4.7.0_2 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 GPLv3 accepted by the user
===> Fetching all distfiles required by R-cran-Hmisc-4.7.0_2 for building
=> SHA256 Checksum OK for Hmisc_4.7-0.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 GPLv3 accepted by the user
===> Fetching all distfiles required by R-cran-Hmisc-4.7.0_2 for building
===> Extracting for R-cran-Hmisc-4.7.0_2
=> SHA256 Checksum OK for Hmisc_4.7-0.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-Hmisc-4.7.0_2
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-latticeExtra>0 - not found
===> Installing existing package /packages/All/R-cran-latticeExtra-0.6.29_1.pkg
[142amd64-default-job-40] Installing R-cran-latticeExtra-0.6.29_1...
[142amd64-default-job-40] `-- Installing R-4.5.0...
[142amd64-default-job-40] | `-- Installing cairo-1.18.2,3...
[142amd64-default-job-40] | | `-- Installing fontconfig-2.15.0_3,1...
[142amd64-default-job-40] | | `-- Installing expat-2.7.1...
[142amd64-default-job-40] | | `-- Extracting expat-2.7.1: .......... done
[142amd64-default-job-40] | | `-- Installing freetype2-2.13.3...
[142amd64-default-job-40] | | | `-- Installing brotli-1.1.0,1...
[142amd64-default-job-40] | | | `-- Extracting brotli-1.1.0,1: .......... done
[142amd64-default-job-40] | | | `-- Installing png-1.6.48...
[142amd64-default-job-40] | | | `-- Extracting png-1.6.48: .......... done
[142amd64-default-job-40] | | `-- Extracting freetype2-2.13.3: .......... done
[142amd64-default-job-40] | | `-- Extracting fontconfig-2.15.0_3,1: .......... done
[142amd64-default-job-40] | | `-- Installing gettext-runtime-0.23.1...
[142amd64-default-job-40] | | `-- Installing indexinfo-0.3.1_1...
[142amd64-default-job-40] | | `-- Extracting indexinfo-0.3.1_1: .... done
[142amd64-default-job-40] | | `-- Extracting gettext-runtime-0.23.1: .......... done
[142amd64-default-job-40] | | `-- Installing glib-2.84.1_2,2...
[142amd64-default-job-40] | | `-- Installing libffi-3.4.8...
[142amd64-default-job-40] | | `-- Extracting libffi-3.4.8: .......... done
[142amd64-default-job-40] | | `-- Installing libiconv-1.17_1...
[142amd64-default-job-40] | | `-- Extracting libiconv-1.17_1: .......... done
[142amd64-default-job-40] | | `-- Installing libinotify-20240724_1...
<snip>
[142amd64-default-job-40] `-- Installing R-cran-digest-0.6.37...
[142amd64-default-job-40] `-- Extracting R-cran-digest-0.6.37: .......... done
[142amd64-default-job-40] `-- Installing R-cran-ellipsis-0.3.2_1...
[142amd64-default-job-40] `-- Extracting R-cran-ellipsis-0.3.2_1: .......... done
[142amd64-default-job-40] `-- Installing R-cran-fastmap-1.2.0...
[142amd64-default-job-40] `-- Extracting R-cran-fastmap-1.2.0: .......... done
[142amd64-default-job-40] Extracting R-cran-htmltools-0.5.8.1: .......... done
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-htmltools>0 - found
===> Returning to build of R-cran-Hmisc-4.7.0_2
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-data.table>0 - not found
===> Installing existing package /packages/All/R-cran-data.table-1.17.2.pkg
[142amd64-default-job-40] Installing R-cran-data.table-1.17.2...
[142amd64-default-job-40] Extracting R-cran-data.table-1.17.2: .......... done
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-data.table>0 - found
===> Returning to build of R-cran-Hmisc-4.7.0_2
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-htmlTable>0 - not found
===> Installing existing package /packages/All/R-cran-htmlTable-2.4.0_1.pkg
[142amd64-default-job-40] Installing R-cran-htmlTable-2.4.0_1...
[142amd64-default-job-40] `-- Installing R-cran-checkmate-2.1.0_1...
[142amd64-default-job-40] | `-- Installing R-cran-backports-1.5.0...
[142amd64-default-job-40] | `-- Extracting R-cran-backports-1.5.0: .......... done
[142amd64-default-job-40] `-- Extracting R-cran-checkmate-2.1.0_1: .......... done
[142amd64-default-job-40] `-- Installing R-cran-htmlwidgets-1.6.4...
[142amd64-default-job-40] | `-- Installing R-cran-jsonlite-2.0.0...
[142amd64-default-job-40] | `-- Extracting R-cran-jsonlite-2.0.0: .......... done
[142amd64-default-job-40] | `-- Installing R-cran-knitr-1.50...
[142amd64-default-job-40] | | `-- Installing R-cran-evaluate-1.0.3...
[142amd64-default-job-40] | | `-- Extracting R-cran-evaluate-1.0.3: .......... done
[142amd64-default-job-40] | | `-- Installing R-cran-highr-0.11...
[142amd64-default-job-40] | | `-- Installing R-cran-xfun-0.52...
[142amd64-default-job-40] | | `-- Extracting R-cran-xfun-0.52: .......... done
[142amd64-default-job-40] | | `-- Extracting R-cran-highr-0.11: .......... done
[142amd64-default-job-40] | | `-- Installing R-cran-yaml-2.3.10...
[142amd64-default-job-40] | | `-- Extracting R-cran-yaml-2.3.10: .......... done
[142amd64-default-job-40] | `-- Extracting R-cran-knitr-1.50: .......... done
[142amd64-default-job-40] | `-- Installing R-cran-rmarkdown-2.29...
[142amd64-default-job-40] | | `-- Installing R-cran-bslib-0.9.0...
[142amd64-default-job-40] | | `-- Installing R-cran-cachem-1.1.0...
[142amd64-default-job-40] | | `-- Extracting R-cran-cachem-1.1.0: .......... done
[142amd64-default-job-40] | | `-- Installing R-cran-jquerylib-0.1.4_1...
[142amd64-default-job-40] | | `-- Extracting R-cran-jquerylib-0.1.4_1: .......... done
[142amd64-default-job-40] | | `-- Installing R-cran-memoise-2.0.1_1...
[142amd64-default-job-40] | | `-- Extracting R-cran-memoise-2.0.1_1: .......... done
[142amd64-default-job-40] | | `-- Installing R-cran-mime-0.13...
[142amd64-default-job-40] | | `-- Extracting R-cran-mime-0.13: .......... done
[142amd64-default-job-40] | | `-- Installing R-cran-sass-0.4.10...
[142amd64-default-job-40] | | | `-- Installing R-cran-fs-1.6.6...
[142amd64-default-job-40] | | | `-- Extracting R-cran-fs-1.6.6: .......... done
[142amd64-default-job-40] | | | `-- Installing R-cran-rappdirs-0.3.3_1...
[142amd64-default-job-40] | | | `-- Extracting R-cran-rappdirs-0.3.3_1: .......... done
[142amd64-default-job-40] | | `-- Extracting R-cran-sass-0.4.10: .......... done
[142amd64-default-job-40] | | `-- Extracting R-cran-bslib-0.9.0: .......... done
[142amd64-default-job-40] | | `-- Installing R-cran-fontawesome-0.5.3...
[142amd64-default-job-40] | | `-- Extracting R-cran-fontawesome-0.5.3: .......... done
[142amd64-default-job-40] | | `-- Installing R-cran-stringr-1.5.1...
[142amd64-default-job-40] | | `-- Installing R-cran-stringi-1.8.7...
[142amd64-default-job-40] | | `-- Extracting R-cran-stringi-1.8.7: .......... done
[142amd64-default-job-40] | | `-- Extracting R-cran-stringr-1.5.1: .......... done
[142amd64-default-job-40] | | `-- Installing R-cran-tinytex-0.57...
[142amd64-default-job-40] | | `-- Extracting R-cran-tinytex-0.57: .......... done
[142amd64-default-job-40] | | `-- Installing hs-pandoc-3.6.4...
[142amd64-default-job-40] | | `-- Extracting hs-pandoc-3.6.4: .......... done
[142amd64-default-job-40] | `-- Extracting R-cran-rmarkdown-2.29: .......... done
[142amd64-default-job-40] `-- Extracting R-cran-htmlwidgets-1.6.4: .......... done
[142amd64-default-job-40] `-- Installing R-cran-rstudioapi-0.17.1...
[142amd64-default-job-40] `-- Extracting R-cran-rstudioapi-0.17.1: .......... done
[142amd64-default-job-40] Extracting R-cran-htmlTable-2.4.0_1: .......... done
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-htmlTable>0 - found
===> Returning to build of R-cran-Hmisc-4.7.0_2
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-Formula>0 - not found
===> Installing existing package /packages/All/R-cran-Formula-1.2.5.pkg
[142amd64-default-job-40] Installing R-cran-Formula-1.2.5...
[142amd64-default-job-40] Extracting R-cran-Formula-1.2.5: .......... done
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-Formula>0 - found
===> Returning to build of R-cran-Hmisc-4.7.0_2
===> R-cran-Hmisc-4.7.0_2 depends on file: /usr/local/bin/R - found
===> R-cran-Hmisc-4.7.0_2 depends on executable: gfortran13 - found
===> R-cran-Hmisc-4.7.0_2 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-Hmisc-4.7.0_2
===========================================================================
=======================<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-Hmisc-4.7.0_2 depends on package: R-cran-latticeExtra>0 - found
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-gridExtra>0 - found
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-viridis>0 - found
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-htmltools>0 - found
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-data.table>0 - found
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-htmlTable>0 - found
===> R-cran-Hmisc-4.7.0_2 depends on package: R-cran-Formula>0 - found
===> R-cran-Hmisc-4.7.0_2 depends on file: /usr/local/bin/R - found
===> R-cran-Hmisc-4.7.0_2 depends on executable: gfortran13 - found
===========================================================================
=======================<phase: stage >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Staging for R-cran-Hmisc-4.7.0_2
===> Generating temporary packing list
* installing *source* package 'Hmisc' ...
** this is package 'Hmisc' version '4.7-0'
** package 'Hmisc' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)'
using Fortran compiler: 'GNU Fortran (FreeBSD Ports Collection) 13.3.0'
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 Hmisc.c -o Hmisc.o
gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c cidxcn.f -o cidxcn.o
gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c cidxcp.f -o cidxcp.o
gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c hoeffd.f -o hoeffd.o
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 init.c -o init.o
gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c jacklins.f -o jacklins.o
gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c largrec.f -o largrec.o
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 mChoice.c -o mChoice.o
gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c maxempr.f -o maxempr.o
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 nstr.c -o nstr.o
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 ranksort.c -o ranksort.o
ranksort.c:3:12: error: unknown type name 'np'
3 | void sort2(np,ra,rb)
| ^
ranksort.c:3:15: error: unknown type name 'ra'
3 | void sort2(np,ra,rb)
| ^
ranksort.c:3:18: error: unknown type name 'rb'
3 | void sort2(np,ra,rb)
| ^
ranksort.c:3:21: error: expected ';' after top level declarator
3 | void sort2(np,ra,rb)
| ^
| ;
ranksort.c:7:1: error: expected identifier or '('
7 | {
| ^
ranksort.c:49:12: error: unknown type name 'np'
49 | void crank(np, w)
| ^
ranksort.c:49:16: error: unknown type name 'w'
49 | void crank(np, w)
| ^
ranksort.c:49:18: error: expected ';' after top level declarator
49 | void crank(np, w)
| ^
| ;
ranksort.c:53:1: error: expected identifier or '('
53 | {
| ^
ranksort.c:76:20: error: unknown type name 'np'
76 | void F77_SUB(rank)(np, x, w, ix, r)
| ^
ranksort.c:76:24: error: unknown type name 'x'
76 | void F77_SUB(rank)(np, x, w, ix, r)
| ^
ranksort.c:76:27: error: unknown type name 'w'
76 | void F77_SUB(rank)(np, x, w, ix, r)
| ^
ranksort.c:76:30: error: unknown type name 'ix'
76 | void F77_SUB(rank)(np, x, w, ix, r)
| ^
ranksort.c:76:34: error: unknown type name 'r'
76 | void F77_SUB(rank)(np, x, w, ix, r)
| ^
ranksort.c:76:36: error: expected ';' after top level declarator
76 | void F77_SUB(rank)(np, x, w, ix, r)
| ^
| ;
ranksort.c:80:1: error: expected identifier or '('
80 | {
| ^
ranksort.c:5:8: warning: tentative array definition assumed to have one element
5 | double ra[];
| ^
ranksort.c:6:5: warning: tentative array definition assumed to have one element
6 | int rb[];
| ^
ranksort.c:78:16: warning: tentative array definition assumed to have one element
78 | double x[],r[],w[];
| ^
ranksort.c:77:10: warning: tentative array definition assumed to have one element
77 | int *np, ix[];
| ^
ranksort.c:78:8: warning: tentative array definition assumed to have one element
78 | double x[],r[],w[];
| ^
ranksort.c:78:12: warning: tentative array definition assumed to have one element
78 | double x[],r[],w[];
| ^
6 warnings and 16 errors generated.
gmake: *** [/usr/local/lib/R/etc/Makeconf:202: ranksort.o] Error 1
ERROR: compilation failed for package 'Hmisc'
* removing '/wrkdirs/usr/ports/devel/R-cran-Hmisc/work/stage/usr/local/lib/R/library/Hmisc'
*** Error code 1
Stop.
make: stopped in /usr/ports/devel/R-cran-Hmisc