[package - main-amd64-default][math/R-cran-NMF] Failed for R-cran-NMF-0.21.0_4 in stage
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Date: Wed, 03 May 2023 08:31:04 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/beefy18/data/main-amd64-default/pdf5b273c8e36_s83d5725005/logs/R-cran-NMF-0.21.0_4.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=pdf5b273c8e36_s83d5725005
Log:
=>> Building math/R-cran-NMF
build started at Wed May 3 08:30:53 UTC 2023
port directory: /usr/ports/math/R-cran-NMF
package name: R-cran-NMF-0.21.0_4
building for: FreeBSD main-amd64-default-job-01 14.0-CURRENT FreeBSD 14.0-CURRENT 1400088 amd64
maintained by: tota@FreeBSD.org
Makefile ident:
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=======================<phase: check-sanity >============================
===> License GPLv2+ accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> R-cran-NMF-0.21.0_4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-amd64-default-job-01] Installing pkg-1.19.1_1...
[main-amd64-default-job-01] Extracting pkg-1.19.1_1: .......... done
===> R-cran-NMF-0.21.0_4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of R-cran-NMF-0.21.0_4
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2+ accepted by the user
===> Fetching all distfiles required by R-cran-NMF-0.21.0_4 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv2+ accepted by the user
===> Fetching all distfiles required by R-cran-NMF-0.21.0_4 for building
=> SHA256 Checksum OK for NMF_0.21.0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv2+ accepted by the user
===> Fetching all distfiles required by R-cran-NMF-0.21.0_4 for building
===> Extracting for R-cran-NMF-0.21.0_4
=> SHA256 Checksum OK for NMF_0.21.0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for R-cran-NMF-0.21.0_4
===========================================================================
=======================<phase: build-depends >============================
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-pkgmaker>=0.20 - not found
===> Installing existing package /packages/All/R-cran-pkgmaker-0.32.2_1.pkg
[main-amd64-default-job-01] Installing R-cran-pkgmaker-0.32.2_1...
[main-amd64-default-job-01] `-- Installing R-4.3.0...
[main-amd64-default-job-01] | `-- Installing cairo-1.17.4_2,3...
<snip>
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_6:
--
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_10:
--
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-NMF-0.21.0_4 depends on package: R-cran-pkgmaker>=0.20 - found
===> Returning to build of R-cran-NMF-0.21.0_4
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-registry>0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-rngtools>=1.2.3 - not found
===> Installing existing package /packages/All/R-cran-rngtools-1.5.2_1.pkg
[main-amd64-default-job-01] Installing R-cran-rngtools-1.5.2_1...
[main-amd64-default-job-01] Extracting R-cran-rngtools-1.5.2_1: .......... done
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-rngtools>=1.2.3 - found
===> Returning to build of R-cran-NMF-0.21.0_4
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-stringr>=1.0.0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-digest>0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-gridBase>0 - not found
===> Installing existing package /packages/All/R-cran-gridBase-0.4.7_5.pkg
[main-amd64-default-job-01] Installing R-cran-gridBase-0.4.7_5...
[main-amd64-default-job-01] Extracting R-cran-gridBase-0.4.7_5: .......... done
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-gridBase>0 - found
===> Returning to build of R-cran-NMF-0.21.0_4
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-colorspace>0 - not found
===> Installing existing package /packages/All/R-cran-colorspace-2.0.3_1.pkg
[main-amd64-default-job-01] Installing R-cran-colorspace-2.0.3_1...
[main-amd64-default-job-01] Extracting R-cran-colorspace-2.0.3_1: .......... done
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-colorspace>0 - found
===> Returning to build of R-cran-NMF-0.21.0_4
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-RColorBrewer>0 - not found
===> Installing existing package /packages/All/R-cran-RColorBrewer-1.1.3_1.pkg
[main-amd64-default-job-01] Installing R-cran-RColorBrewer-1.1.3_1...
[main-amd64-default-job-01] Extracting R-cran-RColorBrewer-1.1.3_1: .......... done
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-RColorBrewer>0 - found
===> Returning to build of R-cran-NMF-0.21.0_4
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-foreach>0 - not found
===> Installing existing package /packages/All/R-cran-foreach-1.5.2_1.pkg
[main-amd64-default-job-01] Installing R-cran-foreach-1.5.2_1...
[main-amd64-default-job-01] `-- Installing R-cran-iterators-1.0.14_1...
[main-amd64-default-job-01] `-- Extracting R-cran-iterators-1.0.14_1: .......... done
[main-amd64-default-job-01] Extracting R-cran-foreach-1.5.2_1: .......... done
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-foreach>0 - found
===> Returning to build of R-cran-NMF-0.21.0_4
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-doParallel>0 - not found
===> Installing existing package /packages/All/R-cran-doParallel-1.0.17_1.pkg
[main-amd64-default-job-01] Installing R-cran-doParallel-1.0.17_1...
[main-amd64-default-job-01] Extracting R-cran-doParallel-1.0.17_1: .......... done
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-doParallel>0 - found
===> Returning to build of R-cran-NMF-0.21.0_4
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-ggplot2>0 - not found
===> Installing existing package /packages/All/R-cran-ggplot2-3.3.6_1.pkg
[main-amd64-default-job-01] Installing R-cran-ggplot2-3.3.6_1...
[main-amd64-default-job-01] `-- Installing R-cran-gtable-0.3.1_1...
[main-amd64-default-job-01] `-- Extracting R-cran-gtable-0.3.1_1: .......... done
[main-amd64-default-job-01] `-- Installing R-cran-isoband-0.2.5_1...
[main-amd64-default-job-01] `-- Extracting R-cran-isoband-0.2.5_1: .......... done
[main-amd64-default-job-01] `-- Installing R-cran-rlang-1.1.0_1...
[main-amd64-default-job-01] `-- Extracting R-cran-rlang-1.1.0_1: .......... done
[main-amd64-default-job-01] `-- Installing R-cran-scales-1.2.1_1...
[main-amd64-default-job-01] | `-- Installing R-cran-R6-2.5.1_1...
[main-amd64-default-job-01] | `-- Extracting R-cran-R6-2.5.1_1: .......... done
[main-amd64-default-job-01] | `-- Installing R-cran-farver-2.1.1_1...
[main-amd64-default-job-01] | `-- Extracting R-cran-farver-2.1.1_1: .......... done
[main-amd64-default-job-01] | `-- Installing R-cran-labeling-0.4.2_1...
[main-amd64-default-job-01] | `-- Extracting R-cran-labeling-0.4.2_1: .......... done
[main-amd64-default-job-01] | `-- Installing R-cran-lifecycle-1.0.3_1...
[main-amd64-default-job-01] | | `-- Installing R-cran-cli-3.6.0_1...
[main-amd64-default-job-01] | | `-- Extracting R-cran-cli-3.6.0_1: .......... done
[main-amd64-default-job-01] | `-- Extracting R-cran-lifecycle-1.0.3_1: .......... done
[main-amd64-default-job-01] | `-- Installing R-cran-munsell-0.5.0_4...
[main-amd64-default-job-01] | `-- Extracting R-cran-munsell-0.5.0_4: .......... done
[main-amd64-default-job-01] | `-- Installing R-cran-viridisLite-0.4.1_1...
[main-amd64-default-job-01] | `-- Extracting R-cran-viridisLite-0.4.1_1: .......... done
[main-amd64-default-job-01] `-- Extracting R-cran-scales-1.2.1_1: .......... done
[main-amd64-default-job-01] `-- Installing R-cran-tibble-3.2.1_1...
[main-amd64-default-job-01] | `-- Installing R-cran-fansi-1.0.3_1...
[main-amd64-default-job-01] | `-- Extracting R-cran-fansi-1.0.3_1: .......... done
[main-amd64-default-job-01] | `-- Installing R-cran-pillar-1.9.0...
[main-amd64-default-job-01] | | `-- Installing R-cran-utf8-1.2.2_1...
[main-amd64-default-job-01] | | `-- Extracting R-cran-utf8-1.2.2_1: .......... done
[main-amd64-default-job-01] | | `-- Installing R-cran-vctrs-0.6.1_1...
[main-amd64-default-job-01] | | `-- Extracting R-cran-vctrs-0.6.1_1: .......... done
[main-amd64-default-job-01] | `-- Extracting R-cran-pillar-1.9.0: .......... done
[main-amd64-default-job-01] | `-- Installing R-cran-pkgconfig-2.0.3_2...
[main-amd64-default-job-01] | `-- Extracting R-cran-pkgconfig-2.0.3_2: .......... done
[main-amd64-default-job-01] `-- Extracting R-cran-tibble-3.2.1_1: .......... done
[main-amd64-default-job-01] Extracting R-cran-ggplot2-3.3.6_1: .......... done
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-ggplot2>0 - found
===> Returning to build of R-cran-NMF-0.21.0_4
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-reshape2>0 - not found
===> Installing existing package /packages/All/R-cran-reshape2-1.4.4_2.pkg
[main-amd64-default-job-01] Installing R-cran-reshape2-1.4.4_2...
[main-amd64-default-job-01] `-- Installing R-cran-Rcpp-1.0.10_1...
[main-amd64-default-job-01] `-- Extracting R-cran-Rcpp-1.0.10_1: .......... done
[main-amd64-default-job-01] `-- Installing R-cran-plyr-1.8.7_1...
[main-amd64-default-job-01] `-- Extracting R-cran-plyr-1.8.7_1: .......... done
[main-amd64-default-job-01] Extracting R-cran-reshape2-1.4.4_2: .......... done
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-reshape2>0 - found
===> Returning to build of R-cran-NMF-0.21.0_4
===> R-cran-NMF-0.21.0_4 depends on file: /usr/local/bin/R - found
===> R-cran-NMF-0.21.0_4 depends on executable: gfortran12 - found
===> R-cran-NMF-0.21.0_4 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for R-cran-NMF-0.21.0_4
===========================================================================
=======================<phase: build >============================
===========================================================================
=======================<phase: run-depends >============================
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-pkgmaker>=0.20 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-registry>0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-rngtools>=1.2.3 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-stringr>=1.0.0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-digest>0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-gridBase>0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-colorspace>0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-RColorBrewer>0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-foreach>0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-doParallel>0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-ggplot2>0 - found
===> R-cran-NMF-0.21.0_4 depends on package: R-cran-reshape2>0 - found
===> R-cran-NMF-0.21.0_4 depends on file: /usr/local/bin/R - found
===> R-cran-NMF-0.21.0_4 depends on executable: gfortran12 - found
===========================================================================
=======================<phase: stage >============================
===> Staging for R-cran-NMF-0.21.0_4
===> Generating temporary packing list
* installing *source* package 'NMF' ...
** package 'NMF' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6)'
using C++ compiler: 'FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6)'
gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R-cran-NMF/work/NMF/src'
c++ -std=gnu++17 -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 -DLIBICONV_PLUG -isystem /usr/local/include -c distance.cpp -o distance.o
c++ -std=gnu++17 -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 -DLIBICONV_PLUG -isystem /usr/local/include -c divergence.cpp -o divergence.o
c++ -std=gnu++17 -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 -DLIBICONV_PLUG -isystem /usr/local/include -c euclidean.cpp -o euclidean.o
cc -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 registerDynamicSymbol.c -o registerDynamicSymbol.o
c++ -std=gnu++17 -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 -DLIBICONV_PLUG -isystem /usr/local/include -c utils.cpp -o utils.o
utils.cpp:118:20: error: use of undeclared identifier 'DOUBLE_EPS'
double eps = sqrt(DOUBLE_EPS);
^
1 error generated.
gmake[1]: *** [/usr/local/lib/R/etc/Makeconf:198: utils.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R-cran-NMF/work/NMF/src'
ERROR: compilation failed for package 'NMF'
* removing '/wrkdirs/usr/ports/math/R-cran-NMF/work/stage/usr/local/lib/R/library/NMF'
*** Error code 1
Stop.
make: stopped in /usr/ports/math/R-cran-NMF