sysutils/xentools418: replace /usr/pkg in CHECK_RELRO_SKIP with ${PREFIX}

Currently, the package fails to build if ${PREFIX} is not /usr/pkg,
because one file is not skipped in the RELRO check.

(brook)

netcdf: Add libexecinfo/buildlink3.mk in buildlink3.mk

Netcdf is built with libexecinfo, which is exposed to at least the
geography/gdal-lib package.  Include libexecinfo/buildlink3.mk in its
buildlink3.mk file so that linking against netcdf will succeed.

(brook)

gdal-lib: fix CONFIGURE_ARGS reference to non-existent directory

The configure script for gdal-lib specifies locations for various
required libraries via command line arguments.  For example, the
configure script defines compiler flags for the location of libz based
upon the --with-libz argument as follows:

EXTRA_INCLUDES="-I$with_libz -I$with_libz/include $EXTRA_INCLUDES"

Since the origin of the package, the location of libz has been
specified in Makefile.common as follows:

CONFIGURE_ARGS+= --with-libz=${BUILDLINK_PREFIX.zlib}/include

In a typical pkgsrc installation, the configure script is run with the
argument --with-libz=/usr/pkg/include, which leads to the following
compiler flags:

  -I/usr/pkg/include -I/usr/pkg/include/include

The latter directory of course generally never exists.  Although this
has apparently worked in the past, gcc12 exits with an error.

This patch removes the extra /include suffix from the libz location
specified in CONFIGURE_ARGS.  As a result, libz now matches the way
other libraries are specified, none of which include the /include
suffix and all of which are handled in the configure script in similar
ways.

(brook)

math/R-nimble: Add tool dependency on gmake.

A library, libnimble.a, is compiled by this package using a Gnu makefile.
Add a tool dependency on gmake to avoid syntax errors.

(brook)

u-boot-beagleboneblack: Update sysutils/u-boot-beagleboneblack to 2022.04.

Previously the u-boot-beagleboneblack package used the default U-Boot
version, which was 2018.11.  However, that version failed to boot with
the NetBSD UEFI bootloader, efiboot.  Updating to U-Boot version
2022.04 enables UEFI booting.

(brook)

devel/bison: do not suggest nls option on Darwin

The previous commit message included the following comment:

    TODO: avoid suggesting nls on macOS/x86_64 versions where bison
    will crash.

Additionally, options.mk contains a comment suggesting the crash only
occurs for versions less than or equal to approximately 11.6.  This
commit adds conditionals to options.mk to suggest the nls option only
when crashes are not expected.

(brook)

mariadb105-client: no need to special case __APPLE__ for pkgsrc builds

The file client/mysql.cc uses the readline library, but it has preprocessor
conditionals specially for __APPLE__.  Pkgsrc expects a common readline,
however, and so the build fails.  Removing the special case handles __APPLE__
the same as other platforms.

(brook)

mariadb106-client: no need to special case __APPLE__ for pkgsrc builds

The file client/mysql.cc uses the readline library, but it has preprocessor
conditionals specially for __APPLE__.  Pkgsrc expects a common readline,
however, and so the build fails.  Removing the special case handles __APPLE__
the same as other platforms.

(brook)

cad/oce: fixes for Darwin

Currently cad/oce does not build on Darwin, in part because sed
substitutions in CMakeFiles fail because the suffixes (.dylib) differ
from expected (.so).  There are, however, two additional problems.
First, frameworks are not used by pkgsrc, yet CMakeLists.txt expects
them on Darwin and uses special installation steps.  Instead, use the
standard installation steps.  Additionally, there are a few PLIST
differences between Darwin and other platforms, which are handled with
PLIST.* variables that differentiate Darwin from other systems.

(brook)

math/R: fix compiler flags embedded within Makeconf

The R package installs the file lib/R/etc/Makeconf, which is intended
to be used by R packages that themselves compile programs.  This
feature is rarely used, but the math/R-nimble package is an example of
one that does.  For this to work, the compiler flags embedded within
Makeconf must be compatible with the system compiler.  At least on
MacOS, this is not the case by default, and so nimble compilations
fail.  This substitutes ${COMPILER_RPATH_FLAG} into configure.ac, so
that it is used when creating Makeconf.  Since neither R itself nor
most R packages compile other programs, Makeconf is generally not used
and this fix will have no impact.

(brook)

graphics/Coin: build without framework support on Darwin.

By default, Coin is installed on Darwin as a framework, which is a completely
different file layout incompatible with pkgsrc.  Add a configure argument to
prevent this and select a standard layout compatible with pkgsrc.

(brook)

biology/minimap2: install minimap2 program instead of python binding

The distfile for minimap2 includes two different components: (i) the
minimap2 sequence mapping program itself, and (ii) a python binding
generally referred to as mappy.  The initial version of this package
included only the python binding.  However, it is more appropriate
that the minimap2 package should contain the program of the same name,
and a new package be created with the name mappy for the python
binding.  Splitting these into two packages makes sense, because this
allows users to install the minimap2 package without python
dependencies.

(brook)

doc: Added biology/filter-fastq version 0.0.0.20210527

(brook)

biology/filter-fastq: add filter-fastq version 0.0.0.20210527

(brook)

biology/filter-fastq: add filter-fastq version 0.0.0.20210527

Filter reads from a FASTQ file using a list of identifiers.

Each entry in the input FASTQ file (or files) is checked against all
entries in the identifier list. Matches are included by default, or
excluded if the --invert flag is supplied. Paired-end files are kept
consistent (in order).

This is almost certainly not the most efficient way to implement this
filtering procedure. I tested a few different strategies and this one
seemed the fastest. Current timing with 16 processes is about 10
minutes per 1M paired reads with gzip'd input and output, depending on
the length of the identifier list to filter by.

usage: filter_fastq.py [-h] [-i INPUT] [-1 READ1] [-2 READ2] [-p NUM_THREADS]
                      [-o OUTPUT] [-f FILTER_FILE] [-v] [--gzip]

(brook)

doc: Added biology/beagle version 5.2

(brook)

Added biology/beagle version 5.2

(brook)

biology/beagle: added beagle 5.2

Introduction

Beagle is a software package for phasing genotypes and for imputing
ungenotyped markers. Beagle version 5.2 provides significantly faster
genotype phasing than version 5.1

Citation

If you use Beagle in a published analysis, please report the program
version and cite the appropriate article.

The Beagle 5.2 genotype imputation method is described in:

  B L Browning, Y Zhou, and S R Browning (2018). A one-penny imputed
  genome from next generation reference panels. Am J Hum Genet
  103(3):338-348. doi:10.1016/j.ajhg.2018.07.015

The most recent reference for Beagle's phasing method is:

  S R Browning and B L Browning (2007) Rapid and accurate haplotype
  phasing and missing data inference for whole genome association
  studies by use of localized haplotype clustering. Am J Hum Genet
  81:1084-1097. doi:10.1086/521987

This reference will be updated when the Beagle version 5 phasing
method is published.

(brook)

doc: Added biology/racon version 1.4.3

(brook)

Added biology/racon 1.4.3

(brook)

biology/racon: add racon 1.4.3

## Description

Racon is intended as a standalone consensus module to correct raw
contigs generated by rapid assembly methods which do not include a
consensus step. The goal of Racon is to generate genomic consensus
which is of similar or better quality compared to the output generated
by assembly methods which employ both error correction and consensus
steps, while providing a speedup of several times compared to those
methods. It supports data produced by both Pacific Biosciences and
Oxford Nanopore Technologies.

Racon can be used as a polishing tool after the assembly with **either
Illumina data or data produced by third generation of
sequencing**. The type of data inputed is automatically detected.

Racon takes as input only three files: contigs in FASTA/FASTQ format,
reads in FASTA/FASTQ format and overlaps/alignments between the reads
and the contigs in MHAP/PAF/SAM format. Output is a set of polished
contigs in FASTA format printed to stdout. All input files **can be
compressed with gzip** (which will have impact on parsing time).

Racon can also be used as a read error-correction tool. In this
scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps
between reads **including dual overlaps**.

A **wrapper script** is also available to enable easier usage to the
end-user for large datasets. It has the same interface as racon but
adds two additional features from the outside. Sequences can be
**subsampled** to decrease the total execution time (accuracy might be
lower) while target sequences can be **split** into smaller chunks and
run sequentially to decrease memory consumption. Both features can be
run at the same time as well.

(brook)

doc: Added biology/minimap2 version 2.18

(brook)

Add biology/minimap2 2.18

(brook)

biology/minimap2: add minimap 2.18

## Users' Guide

Minimap2 is a versatile sequence alignment program that aligns DNA or
mRNA sequences against a large reference database. Typical use cases
include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
human genome; (2) finding overlaps between long reads with error rate
up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore
cDNA or Direct RNA reads against a reference genome; (4) aligning
Illumina single- or paired-end reads; (5) assembly-to-assembly
alignment; (6) full-genome alignment between two closely related
species with divergence below ~15%.

For ~10kb noisy reads sequences, minimap2 is tens of times faster than
mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and
GMAP. It is more accurate on simulated long reads and produces
biologically meaningful alignment ready for downstream analyses. For
>100bp Illumina short reads, minimap2 is three times as fast as
BWA-MEM and Bowtie2, and as accurate on simulated data.  Detailed
evaluations are available from the minimap2 paper or the preprint.

Release 2.18-r1015 (9 April 2021)
---------------------------------

This release fixes multiple rare bugs in minimap2 and adds additional
functionality to paftools.js.

Changes to minimap2:

* Bugfix: a rare segfault caused by an off-by-one error (#489)

* Bugfix: minimap2 segfaulted due to an uninitilized variable (#622 and #625).

* Bugfix: minimap2 parsed spaces as field separators in BED (#721). This led
  to issues when the BED name column contains spaces.

* Bugfix: minimap2 `--split-prefix` did not work with long reference names
  (#394).

* Bugfix: option `--junc-bonus` didn't work (#513)

* Bugfix: minimap2 didn't return 1 on I/O errors (#532)

* Bugfix: the `de:f` tag (sequence divergence) could be negative if there were
  ambiguous bases

* Bugfix: fixed two undefined behaviors caused by calling memcpy() on
  zero-length blocks (#443)

* Bugfix: there were duplicated SAM @SQ lines if option `--split-prefix` is in
  use (#400 and #527)

* Bugfix: option -K had to be smaller than 2 billion (#491). This was caused
  by a 32-bit integer overflow.

* Improvement: optionally compile against SIMDe (#597). Minimap2 should work
  with IBM POWER CPUs, though this has not been tested. To compile with SIMDe,
  please use `make -f Makefile.simde`.

* Improvement: more informative error message for I/O errors (#454) and for
  FASTQ parsing errors (#510)

* Improvement: abort given malformatted RG line (#541)

* Improvement: better formula to estimate the `dv:f` tag (approximate sequence
  divergence). See DOI:10.1101/2021.01.15.426881.

* New feature: added the `--mask-len` option to fine control the removal of
  redundant hits (#659). The default behavior is unchanged.

Changes to mappy:

* Bugfix: mappy caused segmentation fault if the reference index is not
  present (#413).

* Bugfix: fixed a memory leak via 238b6bb3

* Change: always require Cython to compile the mappy module (#723). Older
  mappy packages at PyPI bundled the C source code generated by Cython such
  that end users did not need to install Cython to compile mappy. However, as
  Python 3.9 is breaking backward compatibility, older mappy does not work
  with Python 3.9 anymore. We have to add this Cython dependency as a
  workaround.

Changes to paftools.js:

* Bugfix: the "part10-" line from asmgene was wrong (#581)

* Improvement: compatibility with GTF files from GenBank (#422)

* New feature: asmgene also checks missing multi-copy genes

* New feature: added the misjoin command to evaluate large-scale misjoins and
  megabase-long inversions.

Although given the many bug fixes and minor improvements, the core algorithm
stays the same. This version of minimap2 produces nearly identical alignments
to v2.17 except very rare corner cases.

Now unimap is recommended over minimap2 for aligning long contigs against a
reference genome. It often takes less wall-clock time and is much more
sensitive to long insertions and deletions.

(2.18: 9 April 2021, r1015)

(brook)

doc: Added biology/miniasm version 0.3

(brook)

Add biology/miniasm 0.3.

(brook)

biology/miniasm: add miniasm 0.3

Miniasm is a very fast OLC-based *de novo* assembler for noisy long
reads. It takes all-vs-all read self-mappings (typically by minimap)
as input and outputs an assembly graph in the GFA format. Different
from mainstream assemblers, miniasm does not have a consensus step. It
simply concatenates pieces of read sequences to generate the final
unitig sequences. Thus the per-base error rate is similar to the raw
input reads.

So far miniasm is in early development stage. It has only been tested
on a dozen of PacBio and Oxford Nanopore (ONT) bacterial data
sets. Including the mapping step, it takes about 3 minutes to assemble
a bacterial genome. Under the default setting, miniasm assembles 9 out
of 12 PacBio datasets and 3 out of 4 ONT datasets into a single
contig. The 12 PacBio data sets are [PacBio E.  coli
sample][PB-151103], [ERS473430][ERS473430], [ERS544009][ERS544009],
[ERS554120][ERS554120], [ERS605484][ERS605484],
[ERS617393][ERS617393], [ERS646601][ERS646601],
[ERS659581][ERS659581], [ERS670327][ERS670327],
[ERS685285][ERS685285], [ERS743109][ERS743109] and a deprecated PacBio
E.  coli data set. ONT data are acquired from the Loman Lab.

For a *C. elegans* PacBio data set (only 40X are used, not the whole
dataset), miniasm finishes the assembly, including reads overlapping,
in ~10 minutes with 16 CPUs. The total assembly size is 105Mb; the N50
is 1.94Mb. In comparison, the HGAP3 produces a 104Mb assembly with N50
1.61Mb. This dotter plot gives a global view of the miniasm assembly
(on the X axis) and the HGAP3 assembly (on Y). They are broadly
comparable. Of course, the HGAP3 consensus sequences are much more
accurate. In addition, on the whole data set (assembled in ~30 min),
the miniasm N50 is reduced to 1.79Mb. Miniasm still needs
improvements.

Miniasm confirms that at least for high-coverage bacterial genomes, it
is possible to generate long contigs from raw PacBio or ONT reads
without error correction. It also shows that minimap can be used as a
read overlapper, even though it is probably not as sensitive as the
more sophisticated overlapers such as MHAP and DALIGNER.  Coupled with
long-read error correctors and consensus tools, miniasm may also be
useful to produce high-quality assemblies.

## Algorithm Overview

1. Crude read selection. For each read, find the longest contiguous region
  covered by three good mappings. Get an approximate estimate of read
  coverage.

2. Fine read selection. Use the coverage information to find the good regions
  again but with more stringent thresholds. Discard contained reads.

3. Generate a string graph. Prune tips, drop weak overlaps and
  collapse short bubbles. These procedures are similar to those
  implemented in short-read assemblers.

4. Merge unambiguous overlaps to produce unitig sequences.

## Limitations

1. Consensus base quality is similar to input reads (may be fixed with a
  consensus tool).

2. Only tested on a dozen of high-coverage PacBio/ONT data sets (more testing
  needed).

3. Prone to collapse repeats or segmental duplications longer than input reads
  (hard to fix without error correction).

(brook)

devel/scmcvs: do not require mkinstalldirs

Two m4 files add requirements for mkinstalldirs, but it has long been
replaced.

(brook)

security/mit-krb5: revert previous commit

The fix in the previous patch was already in the updated package, despite
information from upstream.

(brook)

security/mit-krb5: update patch-aclocal.m4 to avoid empty conditional branch.

Mainline autoconf generates no shell code for AC_CONFIG_AUX_DIR().
Call it unconditionally to avoid a syntax error.  See
https://github.com/krb5/krb5/commit/f78edbe30816f049e1360cb6e203fabfdf7b98df.

(brook)

parallel/fastflow: Replace bash in scripts

(brook)

doc: Added biology/R-popbio version 2.7

(brook)

biology/R-popbio: import R-popbio-2.7

Construct and analyze projection matrix models from a demography study
of marked individuals classified by age or stage. The package covers
methods described in Matrix Population Models by Caswell (2001) and
Quantitative Conservation Biology by Morris and Doak (2002).

(brook)

geography/R-maps: remove MASTER_SITES

MASTER_SITES is defined in math/R/Makefile.extension, which should be
included by all R packages.  Therefore, MASTER_SITES should not normally
be defined in the Makefile for an R package.

(brook)

math/R-tensor: remove MASTER_SITES

MASTER_SITES is defined in math/R/Makefile.extension, which should be
included by all R packages.  Therefore, MASTER_SITES should not normally
be defined in the Makefile for an R package.

(brook)

math/R-goftest: remove MASTER_SITES

MASTER_SITES is defined in math/R/Makefile.extension, which should be
included by all R packages.  Therefore, MASTER_SITES should not normally
be defined in the Makefile for an R package.

(brook)

math/R-LearnBayes: remove MASTER_SITES

MASTER_SITES is defined in math/R/Makefile.extension, which should be
included by all R packages.  Therefore, MASTER_SITES should not normally
be defined in the Makefile for an R package.

(brook)

graphics/R-polyclip: remove MASTER_SITES

MASTER_SITES is defined in math/R/Makefile.extension, which should be
included by all R packages.  Therefore, MASTER_SITES should not normally
be defined in the Makefile for an R package.

(brook)

geography/R-mapdata: remove MASTER_SITES

MASTER_SITES is defined in math/R/Makefile.extension, which should be
included by all R packages.  Therefore, MASTER_SITES should not normally
be defined in the Makefile for an R package.

(brook)

geography/R-geosphere: remove MASTER_SITES

MASTER_SITES is defined in math/R/Makefile.extension, which should be
included by all R packages.  Therefore, MASTER_SITES should not normally
be defined in the Makefile for an R package.

(brook)

Add URLs to the MASTER_SITE_R_CRAN list

At some point CRAN added the https protocol to its repositories, but
this was never reflected in MASTER_SITE_R_CRAN.  Add analogues for
all the http sites with responsive https servers.

(brook)

math/R-psych: remove MASTER_SITES

MASTER_SITES is defined in math/R/Makefile.extension, which should be
included by all R packages.  Therefore, MASTER_SITES should not be
defined in a Makefile for an R package.

(brook)

math/R-mnormt: remove MASTER_SITES

MASTER_SITES is defined in math/R/Makefile.extension, which should be
included by all R packages.  Therefore, MASTER_SITES should not be
define in a Makefile for an R package.

(brook)

geography/R-deldir: remove MASTER_SITES

MASTER_SITES is defined in math/R/Makefile.extension, which should be
included by all R packages.  Therefore, MASTER_SITES should not normally
be defined in the Makefile for an R package.

(brook)

doc: Added parallel/fastflow version 3.0.0

(brook)

parallel/fastflow: import fastflow-3.0.0

FastFlow: high-performance parallel patterns and building blocks in C++

FastFlow is a programming library implemented in modern C++ and
targeting multi/many-cores (there exists an experimental version based
on ZeroMQ targeting distributed systems). It offers both a set of
high-level ready-to-use parallel patterns and a set of mechanisms and
composable components (called building blocks) to support low-latency
and high-throughput data-flow streaming networks.

FastFlow simplifies the development of parallel applications modelled
as a structured directed graph of processing nodes. The graph of
concurrent nodes is constructed by the assembly of sequential and
parallel building blocks as well as higher-level easy-to-use
components (i.e. parallel patterns) modelling typical schemas of
parallel computations (e.g., pipeline, task-farm, parallel-for,
etc.). FastFlow efficiency stems from the optimized implementation of
the base communication and synchronization mechanisms and from its
layered software design.

(brook)

doc: Added geography/R-rnaturalearthhires version 0.2.0

(brook)

geography/R-rnaturalearthhires: import R-rnaturalearthhires-0.2.0

High Resolution World Vector Map Data from Natural Earth used in rnaturalearth.

Facilitates mapping by making natural earth map data from
http://www.naturalearthdata.com/ more easily available to R
users. Focuses on vector data.

(brook)

doc: Added geography/R-rnaturalearth version 0.1.0

(brook)

geography/R-rnaturalearth: import R-rnaturalearth-0.1.0

Facilitates mapping by making natural earth map data from
<http://www.naturalearthdata.com/> more easily available to R users.

(brook)

doc: Added geography/R-rnaturalearthdata version 0.1.0

(brook)

geography/R-rnaturalearthdata: import R-rnaturalearthdata-0.1.0

Vector map data from <http://www.naturalearthdata.com/>. Access
functions are provided in the accompanying package 'rnaturalearth'.

(brook)

Add geography/R-stars.

(brook)

doc: Added geography/R-stars version 0.4.3

(brook)

geography/R-stars: import R-stars-0.4.3

Reading, manipulating, writing and plotting spatiotemporal arrays
(raster and vector data cubes) in 'R', using 'GDAL' bindings provided
by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.

(brook)

doc: Added geography/R-osmdata version 0.1.3

(brook)

geography/R-osmdata: import R-osmdata-0.1.3

Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp'
objects.  'OSM' data are extracted from the 'Overpass' web server and
processed with very fast 'C++' routines for return to 'R'.

(brook)

doc: Added geography/R-osmar version 1.1.7

(brook)

geography/R-osmar: import R-osmar-1.1.7

This package provides infrastructure to access OpenStreetMap data from
different sources, to work with the data in common R manner, and to
convert data into available infrastructure provided by existing R
packages (e.g., into sp and igraph objects).

(brook)

doc: Added geography/R-ggspatial version 1.0.3

(brook)

geography/R-ggspatial: import R-ggspatial-1.0.3

Spatial data plus the power of the ggplot2 framework means easier
mapping when input data are already in the form of spatial objects.

(brook)

doc: Added geography/R-spData version 0.3.3

(brook)

geography/R-spData: import R-spData-0.3.3

Diverse spatial datasets for demonstrating, benchmarking and teaching
spatial data analysis. It includes R data of class sf (defined by the
package 'sf'), Spatial ('sp'), and nb ('spdep'). Unlike other spatial
data packages such as 'rnaturalearth' and 'maps', it also contains
data stored in a range of file formats including GeoJSON, ESRI
Shapefile and GeoPackage. Some of the datasets are designed to
illustrate specific analysis techniques. cycle_hire() and
cycle_hire_osm(), for example, is designed to illustrate point pattern
analysis techniques.

(brook)

doc: Added geography/R-lwgeom version 0.2.5

(brook)

geography/R-lwgeom: import R-lwgeom-0.2.5

Access to selected functions found in 'liblwgeom'
<https://github.com/postgis/postgis/tree/master/liblwgeom>, the
light-weight geometry library used by 'PostGIS' <http://postgis.net/>.

(brook)

doc: Added geography/R-raster version 3.0.12

(brook)

geography/R-raster: import R-raster-3.0.12

Reading, writing, manipulating, analyzing and modeling of gridded
spatial data. The package implements basic and high-level functions.
Processing of very large files is supported. There is a also support
for vector data operations such as intersections. See the manual and
tutorials on <https://rspatial.org/> to get started.

(brook)

Add geography/R-rosm.

(brook)

doc: Added geography/R-rosm version 0.2.5

(brook)

geography/R-rosm: import R-rosm-0.2.5

Download and plot Open Street Map <http://www.openstreetmap.org/>,
Bing Maps <http://www.bing.com/maps> and other tiled map sources. Use
to create basemaps quickly and add hillshade to vector-based maps.

(brook)

doc: Added geography/R-rgdal version 1.4.8

(brook)

geography/R-rgdal: import R-rgdal-1.4.8

Provides bindings to the 'Geospatial' Data Abstraction Library
('GDAL') (>= 1.11.4) and access to projection/transformation
operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4'
libraries are external to the package, and, when installing the
package from source, must be correctly installed first. From 'rgdal'
1.4.1, provision is made for 'PROJ6' accommodation, with 'PROJ6'
functionality to follow; from 1.4.1 'rgdal' will build and function
when 'PROJ' >= 6. Both 'GDAL' raster and 'OGR' vector map data can be
imported into R, and 'GDAL' raster data and 'OGR' vector data
exported. Use is made of classes defined in the 'sp' package. Windows
and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat')
are provided on 'CRAN'.

(brook)

doc: Added geography/R-sf version 0.9.5

(brook)

geography/R-sf: import R-sf-0.9.5

Support for simple features, a standardized way to encode spatial
vector data. Binds to 'GDAL' for reading and writing data, to 'GEOS'
for geometrical operations, and to 'PROJ' for projection conversions
and datum transformations. Optionally uses the 's2' package for
spherical geometry operations on geographic coordinates.

(brook)

doc: Updated graphics/ncview to 2.1.7

(brook)

doc: Added math/R-units version 0.6.5

(brook)

math/R-units: import R-units-0.6.5

Support for measurement units in R vectors, matrices and arrays:
automatic propagation, conversion, derivation and simplification of
units; raising errors in case of unit incompatibility. Compatible with
the POSIXct, Date and difftime classes. Uses the UNIDATA udunits
library and unit database for unit compatibility checking and
conversion.

(brook)

graphics/ncview: update to 2.1.7.

2.0: 21 Jan 2010

* ncview now REQUIRES netcdf version 4 with full HDF5 support.  I am not
  going to maintain two code bases, one of which supports netcdf-4 and
  one of which doesn't.  If you need a vesion of ncview that works even
  without a full netcdf v4/HDF-5 install, use ncview version 1.93h.

* If a udunits library is supplied, ncview now requires that it be the
  udunits-2 library.  Support for the udunits-1 library has been dropped.

* Many thanks to Magnus Hagdorn for changes to the package that make it
  more compatible with GNU standards!  All failures in that respect are
  mine; Magnus' contributions were exemplary.

1.93d: 13 June 2008

* Thanks to Seth Olsen for contributing the code to sort the variables
  menus.

(brook)

doc: Updated math/udunits to 2.2.26

(brook)

math/udunits: update to udunits2 v2.2.26.

The UDUNITS-2 package differs from the previous UDUNITS package in the
following ways:

    Support for non-ASCII characters. The original UDUNITS package only
    supports the ASCII character set. The UDUNITS-2 package supports
    the following character sets: ASCII, ISO 8859-1 (Latin 1), and the
    UTF-8 encoding of ISO 10646 (Unicode). This means that unit string
    specifications like "µ°F·Ω⁻¹" are now supported (your viewer
    must support UTF-8 to display this string correctly).

    Support for logarithmic units. The unit string specification
    "0.1 lg(re 1 mW)" specifies a deciBel unit with a one milliwatt
    reference level.  Meteorologists should note that the unit "dBZ"
    (i.e., "0.1 lg(re um^3)") is now supported.

    Persistent value converters. It is now possible to obtain a converter
    data-object, which can be used to convert numeric values in one
    unit to numeric values in another, compatible unit. The values can
    be float, double, or one-dimensional arrays of floats or doubles.

    Improved API. Due to the above changes, it was not possible to keep
    the application programming interface of the original UDUNITS
    package.  Beginning with version 2.1.0, however, the package
    contains a thin UDUNITS API to the UDUNITS-2 library, so code
    written to the original API can simply be recompiled and relinked
    against the new package.  Because the original UDUNITS API uses the
    "utUnit" data-structure and the UDUNITS-2 API uses pointers to
    "ut_unit" data-structures, a small memory-leak is possible in code
    that creates many units.  This leak can be avoided by calling the
    new method utFree(utUnit*) when the unit is no longer needed.

    XML unit database. The unit database is encoded using human-readable
    XML rather than a custom format. The XML parser included in the
    package supports an <import> element to allow easy and convenient
    customization.

One thing that has not changed is that all unit string specifications
understood by the original UDUNITS package are also understood by the
new UDUNITS-2 package.

(brook)

geographcy/R-maps: use gmake and remove the patch.

The patch made it possible to comple R-maps with bmake.  However, the
intent of upstream is to use gmake, which requires no patches.  Therefore,
add USE_TOOLS=gmake and remove the patch.

(brook)

geographcy/R-mapdata: use gmake and remove the patch.

The patch made it possible to comple R-mapdata with bmake.  However, the
intent of upstream is to use gmake, which requires no patches.  Therefore,
add USE_TOOLS=gmake and remove the patch.

(brook)

doc: Added geography/R-spatstat version 1.63.2

(brook)

geography/R-spatstat: import R-spatstat-1.63.2

Comprehensive open-source toolbox for analysing Spatial Point
Patterns. Focused mainly on two-dimensional point patterns, including
multitype/marked points, in any spatial region. Also supports
three-dimensional point patterns, space-time point patterns in any
number of dimensions, point patterns on a linear network, and patterns
of other geometrical objects. Supports spatial covariate data such as
pixel images. Contains over 2000 functions for plotting spatial data,
exploratory data analysis, model-fitting, simulation, spatial
sampling, model diagnostics, and formal inference. Many data types and
exploratory methods are supported.  Formal hypothesis tests of random
pattern and tests for covariate effects are also supported. Parametric
models can be fitted to point pattern data using the functions ppm(),
kppm(), slrm(), dppm() similar to glm(). Types of models include
Poisson, Gibbs and Cox point processes, Neyman-Scott cluster
processes, and determinantal point processes. Models may involve
dependence on covariates, inter-point interaction, cluster formation
and dependence on marks. Models are fitted by maximum likelihood,
logistic regression, minimum contrast, and composite likelihood
methods. A model can be fitted to a list of point patterns (replicated
point pattern data) using the function mppm(). The model can include
random effects and fixed effects depending on the experimental design,
in addition to all the features listed above.  Fitted point process
models can be simulated, automatically. Formal hypothesis tests of a
fitted model are supported along with basic tools for model selection.

(brook)

doc: Added geography/R-spatstat.data version 1.4.3

(brook)

geography/R-spatstat.data: import R-spatstat.data-1.4.3

Contains all the datasets for the 'spatstat' package.

(brook)

doc: Added geography/R-spatstat.utils version 1.17.0

(brook)

geography/R-spatstat.utils: import R-spatstat.utils-1.17.0

Contains utility functions for the 'spatstat' package which may also
be useful for other purposes.

(brook)

doc: Added graphics/R-png version 0.1.7

(brook)

graphics/R-png: import R-png-0.1.7

This package provides an easy and simple way to read, write and
display bitmap images stored in the PNG format. It can read and write
both files and in-memory raw vectors.

(brook)

doc: Added geography/R-prettymapr version 0.2.2

(brook)

geography/R-prettymapr: import R-prettymapr-0.2.2

Automates the process of creating a scale bar and north arrow in any
package that uses base graphics to plot in R. Bounding box tools help
find and manipulate extents. Finally, there is a function to automate
the process of setting margins, plotting the map, scale bar, and north
arrow, and resetting graphic parameters upon completion.

(brook)

doc: Added geography/R-rgeos version 0.5.2

(brook)

geography/R-rgeos: import R-rgeos-0.5.2

Interface to Geometry Engine - Open Source ('GEOS') using the C 'API'
for topology operations on geometries. The 'GEOS' library is external
to the package, and, when installing the package from source, must be
correctly installed first. Windows and Mac Intel OS X binaries are
provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS'
3.7.1, topological operations succeeded with some invalid geometries
for which the same operations fail from and including 'GEOS' 3.7.2.
The 'checkValidity=' argument defaults and structure have been
changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2
(no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is
also provided that may be used, assigned globally using
'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L'
argument, to attempt zero-width buffer repair if invalid geometries
are found. The previous default (FALSE, now '0L') is fastest and used
for 'GEOS' < 3.7.2, but will not warn users of possible problems
before the failure of topological operations that previously
succeeded.

(brook)

doc: Added math/R-nimble version 0.9.0

(brook)

math/R-nimble: import R-nimble-0.9.0

A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate
models and do basic R-style math, and compiling both models and
nimbleFunctions via custom- generated C++. 'NIMBLE' includes default
methods for MCMC, particle filtering, Monte Carlo Expectation
Maximization, and some other tools. The nimbleFunction system makes it
easy to do things like implement new MCMC samplers from R, customize
the assignment of samplers to different parts of a model from R, and
compile the new samplers automatically via C++ alongside the samplers
'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by
making it extensible: New distributions and functions can be added,
including as calls to external compiled code. Although most people
think of MCMC as the main goal of the 'BUGS'/'JAGS' language for
writing models, one can use 'NIMBLE' for writing arbitrary other kinds
of model-generic algorithms as well. A full User Manual is available
at <https://r-nimble.org>.

(brook)

doc: Added math/R-LearnBayes version 2.15.1

(brook)

math/R-LearnBayes: import R-LearnBayes-2.15.1

LearnBayes contains a collection of functions helpful in learning the
basic tenets of Bayesian statistical inference.  It contains functions
for summarizing basic one and two parameter posterior distributions
and predictive distributions.  It contains MCMC algorithms for
summarizing posterior distributions defined by the user.  It also
contains functions for regression models, hierarchical models,
Bayesian tests, and illustrations of Gibbs sampling.

(brook)

doc: Added math/R-goftest version 1.2.2

(brook)

math/R-goftest: import R-goftest-1.2.2

Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit for
continuous univariate distributions, using efficient algorithms.

(brook)

doc: Added math/R-psych version 1.9.12.31

(brook)

math/R-psych: import R-psych-1.9.12.31

A general purpose toolbox for personality, psychometric theory and
experimental psychology.  Functions are primarily for multivariate
analysis and scale construction using factor analysis, principal
component analysis, cluster analysis and reliability analysis,
although others provide basic descriptive statistics. Item Response
Theory is done using factor analysis of tetrachoric and polychoric
correlations. Functions for analyzing data at multiple levels include
within and between group statistics, including correlations and factor
analysis.  Functions for simulating and testing particular item and
test structures are included. Several functions serve as a useful
front end for structural equation modeling.  Graphical displays of
path diagrams, factor analysis and structural equation models are
created using basic graphics. Some of the functions are written to
support a book on psychometric theory as well as publications in
personality research. For more information, see the
personality-project.org/r web page.

(brook)

doc: Added math/R-mnormt version 1.5.6

(brook)

math/R-mnormt: import R-mnormt-1.5.6

Functions are provided for computing the density and the distribution
function of multivariate normal and "t" random variables, and for
generating random vectors sampled from these distributions.
Probabilities are computed via non-Monte Carlo methods; different
routines are used in the case d=1, d=2, d>2, if d denotes the number
of dimensions.

(brook)

doc: Added math/R-tensor version 1.5

(brook)

math/R-tensor: import R-tensor-1.5

The tensor product of two arrays is notionally an outer product of the
arrays collapsed in specific extents by summing along the appropriate
diagonals.

(brook)

doc: Added textproc/R-rjson version 0.2.20

(brook)

textproc/R-rjson: import R-rjson-0.2.20

Converts R object into JSON objects and vice-versa.

(brook)

doc: Added time/R-lubridate version 1.7.4

(brook)

time/R-lubridate: import R-lubridate-1.7.4

Functions to work with date-times and time-spans: fast and user
friendly parsing of date-time data, extraction and updating of
components of a date-time (years, months, days, hours, minutes, and
seconds), algebraic manipulation on date-time and time-span objects.
The 'lubridate' package has a consistent and memorable syntax that
makes working with dates easy and fun. Parts of the 'CCTZ' source
code, released under the Apache 2.0 License, are included in this
package. See <https://github.com/google/cctz> for more details.

(brook)

doc: Added www/R-rvest version 0.3.5

(brook)

www/R-rvest: import R-rvest-0.3.5

Wrappers around the 'xml2' and 'httr' packages to make it easy to
download, then manipulate, HTML and XML.

(brook)

doc: Added www/R-RCurl version 1.98.1.1

(brook)

www/R-RCurl: import R-RCurl-1.98.1.1

A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/> Provides
functions to allow one to compose general HTTP requests and provides
convenient functions to fetch URIs, get & post forms, etc. and process
the results returned by the Web server. This provides a great deal of
control over the HTTP/FTP/... connection and the form of the request
while providing a higher-level interface than is available just using
R socket connections.  Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies,
redirects, authentication, etc.

(brook)

doc: Added geography/R-mapdata version 2.3.0

(brook)

geography/R-mapdata: import R-mapdata-2.3.0

Supplement to maps package, providing the larger and/or
higher-resolution databases.

(brook)

doc: Added geography/R-maps version 3.3.0

(brook)

geography/R-maps: import R-maps-3.3.0

Display of maps.  Projection code and larger maps are in separate
packages ('mapproj' and 'mapdata').

(brook)

doc: Added geography/R-geosphere version 1.5.10

(brook)

geography/R-geosphere: import R-geosphere-1.5.10

Spherical trigonometry for geographic applications. That is, compute
distances and related measures for angular (longitude/latitude)
locations.

(brook)

doc: Added geography/R-deldir version 0.1.25

(brook)

geography/R-deldir: import R-deldir-0.1.25

Calculates the Delaunay triangulation and the Dirichlet or Voronoi
tessellation (with respect to the entire plane) of a planar point set.
Plots triangulations and tessellations in various ways.  Clips
tessellations to sub-windows. Calculates perimeters of tessellations.

(brook)

doc: Added devel/R-caTools version 1.18.0

(brook)

devel/R-caTools: import R-caTools-1.18.0

Contains several basic utility functions including: moving (rolling,
running) window statistic functions, read/write for GIF and ENVI
binary files, fast calculation of AUC, LogitBoost classifier, base64
encoder/decoder, round-off-error-free sum and cumsum, etc.

(brook)

math/R-sp: add a buildlink3.mk file for dependencies.

The R-sp package installs header and library files, which may be needed
by dependencies.  Add a buildlink3.mk file for such dependencies to
include.

(brook)

Add R-ggthemes.

(brook)

Add R-polyclip.

(brook)

doc: Added graphics/R-ggthemes version 4.2.0

(brook)

graphics/R-ggthemes: import R-ggthemes-4.2.0

Some extra themes, geoms, and scales for 'ggplot2'. Provides 'ggplot2'
themes and scales that replicate the look of plots by Edward Tufte,
Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata', 'Excel', and
'The Wall Street Journal', among others. Provides 'geoms' for Tufte's
box plot and range frame.

(brook)

doc: Added graphics/R-polyclip version 1.10.0

(brook)

graphics/R-polyclip: import R-polyclip-1.10.0

R port of Angus Johnson's open source library Clipper. Performs
polygon clipping operations (intersection, union, set minus, set
difference) for polygonal regions of arbitrary complexity, including
holes. Computes offset polygons (spatial buffer zones, morphological
dilations, Minkowski dilations) for polygonal regions and polygonal
lines. Computes Minkowski Sum of general polygons. There is a function
for removing self-intersections from polygon data.

(brook)

doc: Added graphics/R-jpeg version 0.1.8.1

(brook)

graphics/R-jpeg: import R-jpeg-0.1.8.1

This package provides an easy and simple way to read, write and
display bitmap images stored in the JPEG format. It can read and write
both files and in-memory raw vectors.

(brook)

doc: Updated math/R-tidyr to 1.0.2

(brook)

R-tidyr: update from 0.8.3 to 1.0.2.

Many changes are identified for the update to 1.0.0; see News.md for
details.

Apparently, these include some breaking changes.  See
`vignette("in-packages")` for a detailed transition guide.

(brook)

doc: Updated math/R-dplyr to 1.0.0

(brook)

R-dplyr: updated to 1.0.0.

(brook)

doc: Added math/R-generics version 0.0.2

(brook)

R-generics: initial import of v0.0.2.

In order to reduce potential package dependencies and conflicts,
generics provides a number of commonly used S3 generics.

(brook)

Fix incorrect entry for graphics/R-farver.

(brook)

doc: Updated graphics/R-scales to 1.1.0

(brook)

R-scales: update to 1.1.0.

(brook)

doc: Updated graphics/R-farver to 2.0.3

(brook)

R-farver: initial import of v2.0.3.

(brook)

doc: Updated devel/R-tidyselect to 1.1.0

(brook)

R-tidyselect: update to 1.1.0.

(brook)

doc: Updated math/R-classInt to 0.4.2

(brook)

R-classInt: update to 0.4.2.

(brook)

doc: Updated math/R-vctrs to 0.3.2

(brook)

R-vctrs: update to 0.3.2.

(brook)

doc: Added devel/R-lifecycle version 0.2.0

(brook)

R-lifecycle: Add new package for version 0.2.0.

Manage the life cycle of your exported functions with shared
conventions, documentation badges, and non-invasive deprecation
warnings. The 'lifecycle' package defines four development stages
(experimental, maturing, stable, and questioning) and three
deprecation stages (soft-deprecated, deprecated, and defunct). It
makes it easy to insert badges corresponding to these stages in your
documentation. Usage of deprecated functions are signalled with
increasing levels of non-invasive verbosity.

(brook)

doc: Updated www/R-curl to 4.3

(brook)

R-curl: update to 4.3.

(brook)

doc: Updated textproc/R-stringi to 1.4.6

(brook)

R-stringi: update to 1.4.6.

(brook)

doc: Updated security/R-digest to 0.6.25

(brook)

R-digest: update to 0.6.25.

(brook)

doc: Updated math/R-plyr to 1.8.6

(brook)

R-plyr: update to 1.8.6.

(brook)

doc: Updated devel/R-rlang to 0.4.7

(brook)

R-rlang: update to 0.4.7.

(brook)

doc: Updated devel/R-purrr to 0.3.3

(brook)

R-purrr: update to 0.3.3.

(brook)

doc: Updated devel/R-glue to 1.4.1

(brook)

R-glue: update to 1.4.1.

(brook)

doc: Updated devel/R-R6 to 2.4.1

(brook)

R-R6: update to 2.4.1.

(brook)

Conditionally define WRKSRC.

Conditionally define WRKSRC so that R packages with an unusual organization
can override the default.

(brook)

Fix issues with a nonstandard compiler and umask.

If the compiler is in a nonstandard location, libtool may choose the
incorrect mode.  This is described in libtool documentation:
    https://www.gnu.org/software/libtool/manual/html_node/Tags.html
The correct fix is to use --tag to explicitly set the mode.  See
https://sourceforge.net/p/openjade/patches/48/

Write permissions are removed when the package is built.  However, the
command chmod -w does not affect bits set in umask.  The correct usage
is to explicitly identify the users to which the command applies.  See
https://sourceforge.net/p/openjade/patches/49/

(brook)

qt5-qscintilla: Update distinfo for new patch added in prior commit.

(brook)

Select fields explicitly from df.depends in make.df.depends().

The function make.df.depends() constructs a dataframe for DEPENDS lines in
the updated Makefile.  That dataframe is combined with other dataframes for
different portions of the Makefile.  Consequently, all the dataframes must
have the same fields or combining with rbind() fails.  Previously, the
dataframe had the wrong set of fields; this explicitly selects the correct
set that matches the other dataframes so that they can all be combined
correctly.

(brook)

Add full path to installed library names on Darwin.

(brook)

Explicitly include bsd.prefs.mk before using ${OPSYS}.

(brook)

x11/qt5-qscintilla: add dependency on x11/qt5-qtmacextras for Darwin.

(brook)

Define RPKG, not rpkg, in the environment for R2pkg.R

When reading the environment, R2pkg.R expects RPKG to be the name of the
R package.  Fix the inadvertent use of lower case in the variable name.

(brook)

Add a hyphen (-) to each stored argument so recursive calls work.

In order for recursive calls of R2pkg to work, they must receive the same
set of arguments as the original.  Previous argument handling stripped the
hyphen (-) from each argument; this explicitly restores it.

(brook)

Remove hacks.mk as being superceded.

On Darwin, gegl v0.4.22 links against Apple's OpenCL (see gegl/meson.build).
Presumably the hacks in hacks.mk are no longer necessary.  In any case,
the package builds and can be used by gimp without it.

(brook)

Update the module extension on Darwin.

gegl v0.4.22 now uses .dylib as the extension for modules on Darwin.
Consequently, it is no longer necessary to rename the files post-install.
It is, however, necessary to use different extensions for more of PLIST.

(brook)

Update the module extension for Darwin.

Babl v0.1.74 now uses .dylib as the extension for modules on Darwin.
Consequently, it is no longer necessary to rename the files post-install,
but it is necessary to use different extensions for more of PLIST.

(brook)

Fix broken PLIST on Darwin.

Apparently the installed location for gimp-debug-tool differs for Darwin
versus other platforms.  The Makefile included logic to define the location,
but was not used in PLIST.  This just adds the appropriate substitution
into PLIST.

(brook)

Remove a stray commented out .include line left over from earlier testing.

(brook)

Fix build breakage on Darwin.

Darwin uses a different extension (.dylib) than other Unixes (.so) for
shared libraries that applications must link against.  However, Gnome
applications expect plugins to use the same extension (.so) on all platforms,
including Darwin.  Consequently, on Darwin some shared libraries must be
renamed, both on the filesystem and internally, and others must use the
correct extension in PLIST.  This is partially mentioned in PR #54824, but
that missed the need for internal renaming of the libraries.  It also
introduced a dependency on the Apple OpenCL framework, which does not seem
to be necessary.

Finally, all the references to Apple-specific OpenCL code must be removed;
previously only some of them were.

(brook)

Correctly fix the build breakage on Darwin.

The previous patch removed use of --version-script on Darwin and converted
the shared library extensions to the Darwin standard of .dylib.  The former
is necessary, but the latter was not quite correct.  A distinction must be
made between shared libraries provided by the package for linking of
applications and shared libraries provided by the package for dynamic loading
by Gnome applications.  Gnome applications expect that plugins will use the
.so extension on all Unix platforms, including Darwin.  Thus, a subset of the
shared libraries must be renamed, both on the filesystem and internally.
This is partly mentioned in PR #54824, although that is for graphics/gegl
not tnis package.

(brook)

Fix build breakage on Darwin.

MacOS uses the .dylib extension for shared libraries and dyld does not
understand the --version-script option.

(brook)

Fix breakage on Darwin.

MacOS does not provide /usr/include, but it sneaks into some command lines
and causes errors.  Be explicit about the path to glib2 to avoid this.

(brook)

Fix build on Darwin.

During the build, help2man runs pango-view but does not include
LD_LIBRARY_PATH in the environment.  That is needed on Darwin to run
uninstalled programs.  This adds a wrapper so that LD_LIBRARY_PATH
can be defined appropriately.

(brook)

gdk-pixbuf2: Fix build on certain Darwin configurations.

During the build, newly compiled applications are run and require libraries also
within the build area.  At least on Darwin, these must be accessed via
LD_LIBRARY_PATH, which must be added to the meson build files to be included in
the appropriate commands.

(brook)

Add a missing dependency on devel/R-BH.

(brook)

Add a missing dependency on graphics/R-latticeExtra.

(brook)

Add missing dependency on devel/R-R6.

(brook)

Add missing dependencies on devel/R-BH and devel/R-R6.

(brook)

Add missing dependency on devel/R-R6.

(brook)

Add missing dependency on devel/R-R6.

(brook)

Add missing dependency on textproc/libxml2.

(brook)

Add missing dependencies on devel/R-BH and devel/R-R6.

(brook)

Add a missing dependency on graphics/R-gridExtra.

(brook)

Add a missing dependency on devel/R-R6.

(brook)

Add a missing dependency on devel/R-R6.

(brook)

doc/pkgsrc.*: regen

(brook)