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2023-08-28gnu: r-nlme: Update to 3.1-163.Ricardo Wurmus
* gnu/packages/statistics.scm (r-nlme): Update to 3.1-163.
2023-08-28gnu: r-matrix: Update to 1.6-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-matrix): Update to 1.6-1.
2023-08-28gnu: r-httr: Update to 1.4.7.Ricardo Wurmus
* gnu/packages/statistics.scm (r-httr): Update to 1.4.7.
2023-08-28gnu: r-gtable: Update to 0.3.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gtable): Update to 0.3.4.
2023-08-28gnu: r-cairo: Add optional libraries.Ricardo Wurmus
* gnu/packages/statistics.scm (r-cairo)[inputs]: Remove libxt; add harfbuzz, icu4c, libjpeg-turbo, and libtiff.
2023-08-28gnu: r-cairo: Update to 1.6-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-cairo): Update to 1.6-1.
2023-08-28gnu: r-quantreg: Update to 5.97.Ricardo Wurmus
* gnu/packages/statistics.scm (r-quantreg): Update to 5.97. [arguments]: Quote phases instead of argument list.
2023-08-28gnu: r-acepack: Update to 1.4.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-acepack): Update to 1.4.2. [properties]: Protect gfortran input from updater.
2023-08-28gnu: r-spatial: Update to 7.3-17.Ricardo Wurmus
* gnu/packages/statistics.scm (r-spatial): Update to 7.3-17.
2023-08-28gnu: r-survival: Update to 3.5-7.Ricardo Wurmus
* gnu/packages/statistics.scm (r-survival): Update to 3.5-7.
2023-08-28gnu: r-ggplot2: Update to 3.4.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-ggplot2): Update to 3.4.3.
2023-08-05gnu: python-pymc: Update to 5.7.1.Vinicius Monego
* gnu/packages/statistics.scm (python-pymc): Update to 5.7.1.
2023-07-29gnu: python-pymc: Update to 5.6.1.Vinicius Monego
* gnu/packages/statistics.scm (python-pymc): Update to 5.6.1.
2023-07-29gnu: python-arviz: Update to 0.16.1.Vinicius Monego
* gnu/packages/statistics.scm (python-arviz): Update to 0.16.1.
2023-07-18gnu: Rationalize texlive-updmap.cfg and texlive-tiny inputs.Nicolas Goaziou
TEXLIVE-UPDMAP.CFG and TEXLIVE-TINY should only be used as native inputs. Also remove texlive packages already provided by them. * doc/build.scm (pdf-manual): * gnu/packages/algebra.scm (pari-gp): * gnu/packages/bioinformatics.scm (discrover): (phyml): (velvet): * gnu/packages/chemistry.scm (yaehmop): * gnu/packages/chez.scm (stex-bootstrap): (chez-web): (chez-sockets): * gnu/packages/cran.scm (r-prereg): * gnu/packages/docbook.scm (dblatex): * gnu/packages/emacs-xyz.scm (emacs-auctex): * gnu/packages/engineering.scm (fastcap): * gnu/packages/fsf.scm (book-faif): * gnu/packages/graphviz.scm (dot2tex): * gnu/packages/maths.scm (hypre): * gnu/packages/ocaml.scm (unison): (ocaml-bibtex2html): * gnu/packages/plotutils.scm (asymptote): * gnu/packages/python-xyz.scm (python-nbconvert): (python-pypandoc): * gnu/packages/radio.scm (gnuradio): (libosmo-dsp): * gnu/packages/statistics.scm (r-with-tests): * gnu/packages/tex.scm (texlive-makecmds): (texlive-innerscript): (teximpatient): (texlive-xkeyval): Remove texlive packages already provided by TEXLIVE-UPDMAP.CFG. Don't add TEXLIVE-TINY or TEXLIVE-UPDMAP.CFG as inputs.
2023-07-18gnu: Replace texlive-latex-base with texlive-latex-bin.Nicolas Goaziou
Although `latex-base' is clearly defined on CTAN, it isn't a proper TeX Live package. Since we're trying to follow as closely as possible this TeX distribution, we replace the package with the closest one, which is `texlive-latex-bin'. As a consequence, the #:TEXLIVE-LATEX-BASE argument becomes #:TEXLIVE-LATEX-BIN?, emphasizing the fact that the meaningful values for it are booleans. * gnu/packages/graphviz.scm (dot2tex)[propagated-inputs]: Remove TEXLIVE-GRAPHICS, TEXLIVE-LATEX-BASE. Add TEXLIVE-LATEX-BIN. * gnu/packages/plotutils.scm (asymptote)[native-inputs]: Remove TEXLIVE-LATEX-BASE, TEXLIVE-GRAPHICS, TEXLIVE-L3BACKEND. Use TEXLIVE-UPDMAP.CFG. * gnu/packages/sphinx.scm (python-sphinx)[propagated-inputs]: Remove TEXLIVE-GRAPHICS, TEXLIVE-LATEX-BASE. Add TEXLIVE-LATEX-BIN. * gnu/packages/tex.scm (texlive-latex-base): Deprecate variable. (texlive-hyphen-complete): (texlive-tex): (texlive-latex): (texlive-docstrip): (texlive-unicode-data): (texlive-hyphen-base): (texlive-tex-ini-files): (texlive-metafont): (texlive-modes): (texlive-knuth-lib): (texlive-latex-fonts): (texlive-etex): (texlive-plain): (texlive-kpathsea): (texlive-latexconfig): (texlive-latex-bin): (texlive-l3kernel): (texlive-l3backend): (texlive-l3packages): (texlive-luatex): (texlive-luahbtex): (texlive-babel): (texlive-cyrillic): (texlive-pdftex): (texlive-cm)[arguments]: Replace #:TEXLIVE-LATEX-BASE with #:TEXLIVE-LATEX-BIN?. (texlive-lm): (texlive-lua-alt-getopt): (texlive-luaotfload): (texlive-graphics-def): (texlive-graphics-cfg): Set #:TEXLIVE-LATEX-BIN? to #F. (texlive-graphics): (texlive-lualibs): (texlive-firstaid): (texlive-atveryend)[arguments]: Set #:TEXLIVE-LATEX-BIN? to #F. [native-inputs]: Add TEXLIVE-DOCSTRIP, TEXLIVE-PDFTEX. (texlive-updmap.cfg): Remove TEXLIVE-CM, TEXLIVE-GRAPHICS, TEXLIVE-LATEX-BASE. Add TEXLIVE-LATEX-BIN. (texlive-atbegshi)[arguments]: Set #:TEXLIVE-LATEX-BIN? to #F. [native-inputs]: Add TEXLIVE-DOCSTRIP, TEXLIVE-PDFTEX. [propagated-inputs]: Remove TEXLIVE-IFTEX, TEXLIVE-INFWARERR and TEXLIVE-LTXCMDS. (texlive-everyshi)[arguments]: Build package with a temporary "latex.fmt" file. (texlive-cyrillic): Set #:TEXLIVE-LATEX-BIN? to #T. * guix/build-system/texlive.scm (default-texlive-latex-base): Rename to TEXLIVE-LATEX-BIN. (lower): Set default value for TEXLIVE-LATEX-BIN? to #TRUE. * gnu/packages/statistics.scm (r-with-tests): Remove TEXLIVE-LATEX-BASE and TEXLIVE-GRAPHICS. * doc/guix.texi (Build Systems): Document #:TEXLIVE-LATEX-BIN? argument. Remove reference to #:TEXLIVE-LATEX-BASE.
2023-07-18gnu: Deprecate texlive-base in favor of texlive-scheme-basic.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-base): Deprecate variable. (texlive-updmap.cfg): Use default packages from now deprecated TEXLIVE-BASE. Also remove already implemented TODO. * doc/build.scm (pdf-manual): * gnu/packages/statistics.scm: Replace TEXLIVE-BASE with call to TEXLIVE-UPDMAP.CFG. * guix/profiles.scm (texlive-font-maps): Trigger TeX Live hook whenever a texlive package is included in the manifest.
2023-07-18gnu: texlive-jknappen: Deprecate package.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-jknappen): Deprecate variable. (texlive-paralist): (texlive-jadetex): (texlive-xindy): * gnu/packages/maths.scm (hypre): * gnu/packages/python-xyz.scm (python-nbconvert): Use TEXLIVE-JKNAPLTX instead.
2023-07-18gnu: texlive-latex-xkeyval -> texlive-xkeyval.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-xkeyval): New variable. (texlive-latex-xkeyval): Deprecate variable. (texlive-bidi): (texlive-pstool): (texlive-polyglossia): (texlive-zref): (texlive-standalone): (texlive-todonotes): (texlive-adjustbox): (texlive-qrcode): (texlive-breakurl): * gnu/packages/graphviz.scm (dot2tex): * gnu/packages/statistics.scm (r-with-tests): Use new name.
2023-07-18gnu: texlive-fonts-ec -> texlive-ec.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-ec): New variable. (texlive-fonts-ec): Deprecate variable. (lyx): (biber): * gnu/packages/python-xyz.scm (python-pypandoc): * gnu/packages/statistics.scm (r-with-tests): * doc/build.scm (pdf-manual): * gnu/packages/bioinformatics.scm (discrover): (phyml): (velvet): * gnu/packages/chemistry.scm (yaehmop): * gnu/packages/chez.scm (stex-bootstrap): * gnu/packages/ocaml.scm (unison): (ocaml-bibtex2html): * gnu/packages/plotutils.scm (asymptote): Use new name.
2023-07-18gnu: texlive-latex-upquote -> texlive-upquote.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-upquote): New variable. (texlive-latex-upquote): Deprecate variable. * gnu/packages/cran.scm (r-prereg): * gnu/packages/maths.scm (hypre): * gnu/packages/python-xyz.scm (python-nbconvert): * gnu/packages/sphinx.scm (python-sphinx): * gnu/packages/statistics.scm (r-with-tests): Use new name.
2023-07-17gnu: r-puniform: Update to 0.2.6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-puniform): Update to 0.2.6.
2023-07-17gnu: r-clubsandwich: Update to 0.5.9.Ricardo Wurmus
* gnu/packages/statistics.scm (r-clubsandwich): Update to 0.5.9.
2023-07-17gnu: r-matrixmodels: Update to 0.5-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-matrixmodels): Update to 0.5-2.
2023-07-17gnu: r-deoptimr: Update to 1.1-0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-deoptimr): Update to 1.1-0.
2023-07-17gnu: r-mgcv: Update to 1.9-0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mgcv): Update to 1.9-0.
2023-07-17gnu: r-openssl: Update to 2.1.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-openssl): Update to 2.1.0. [properties]: Add hint to keep openssl input. [inputs]: Add zlib.
2023-07-16gnu: r-with-tests: Update to 4.3.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-tests): Update to 4.3.1.
2023-07-16gnu: r-with-tests: Fix reference to grep.Ricardo Wurmus
detectCores.R fails to return the number of cores when running R in a container without grep. Reported-by: Jonas Freimuth. * gnu/packages/statistics.scm (r-with-tests)[arguments]: Fix references to grep and wc in detectCores.R. [inputs]: Add grep.
2023-07-12gnu: r-norm: Update to 1.0-11.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-norm): Update to 1.0-11.1.
2023-07-12gnu: r-logspline: Update to 2.1.20.Ricardo Wurmus
* gnu/packages/statistics.scm (r-logspline): Update to 2.1.20.
2023-07-12gnu: r-pbapply: Update to 1.7-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-pbapply): Update to 1.7-2.
2023-07-12gnu: r-robust: Update to 0.7-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-robust): Update to 0.7-2.
2023-07-12gnu: r-rrcov: Update to 1.7-4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rrcov): Update to 1.7-4.
2023-07-12gnu: r-robustbase: Update to 0.99-0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-robustbase): Update to 0.99-0.
2023-07-12gnu: r-deoptimr: Update to 1.0-14.Ricardo Wurmus
* gnu/packages/statistics.scm (r-deoptimr): Update to 1.0-14.
2023-07-12gnu: r-mvtnorm: Update to 1.2-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.2-2.
2023-07-12gnu: r-rmarkdown: Update to 2.23.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.23.
2023-07-12gnu: r-rcpparmadillo: Update to 0.12.4.1.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.12.4.1.0.
2023-07-12gnu: r-rstudioapi: Update to 0.15.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rstudioapi): Update to 0.15.0.
2023-07-12gnu: r-xml2: Update to 1.3.5.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml2): Update to 1.3.5.
2023-07-12gnu: r-locfit: Update to 1.5-9.8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-locfit): Update to 1.5-9.8.
2023-07-12gnu: r-dbplyr: Update to 2.3.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dbplyr): Update to 2.3.3.
2023-07-12gnu: r-testthat: Update to 3.1.10.Ricardo Wurmus
* gnu/packages/statistics.scm (r-testthat): Update to 3.1.10.
2023-07-12gnu: r-matrix: Update to 1.6-0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-matrix): Update to 1.6-0.
2023-07-12gnu: r-kernsmooth: Update to 2.23-22.Ricardo Wurmus
* gnu/packages/statistics.scm (r-kernsmooth): Update to 2.23-22.
2023-07-12gnu: r-lme4: Update to 1.1-34.Ricardo Wurmus
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-34.
2023-07-12gnu: r-digest: Update to 0.6.33.Ricardo Wurmus
* gnu/packages/statistics.scm (r-digest): Update to 0.6.33. [native-inputs]: Add r-simplermarkdown.
2023-07-12gnu: r-plotly: Update to 4.10.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-plotly): Update to 4.10.2.
2023-07-07gnu: python-statsmodels: Update to 0.14.0.Ricardo Wurmus
* gnu/packages/statistics.scm (python-statsmodels): Update to 0.14.0. [source]: Simplify snippet. [build-system]: Use pyproject-build-system. [arguments]: Remove trailing #T from build phase. [propagated-inputs]: Add python-packaging; remove python-matplotlib. [native-inputs]: Add python-colorama, python-flake8, python-isort, python-joblib, python-matplotlib, python-pytest, python-pytest-randomly, python-pytest-xdist, and python-setuptools-scm; remove python-nose and python-sphinx.
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