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mjwoods merged 2 commits into from
Aug 2, 2026
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Update URLs that have permanently moved #168

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Update URLs that have moved permanently
mjwoods Aug 2, 2026
811a27f
Try testing mpich on ubuntu-26.04
mjwoods Aug 2, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/check-linux-mpi.yaml
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Expand Up @@ -19,7 +19,7 @@ jobs:
matrix:
config:
- {os: ubuntu-latest, r: 'release', mpi: 'openmpi'}
- {os: ubuntu-latest, r: 'release', mpi: 'mpich'}
- {os: ubuntu-26.04, r: 'release', mpi: 'mpich'}

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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6 changes: 3 additions & 3 deletions DESCRIPTION
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@@ -1,6 +1,6 @@
Package: RNetCDF
Version: 2.11-2
Date: 2026-07-19
Date: 2026-08-02
Title: Interface to 'NetCDF' Datasets
Authors@R: c(person("Pavel", "Michna", role = "aut",
email = "rnetcdf-devel@bluewin.ch"),
Expand All @@ -16,7 +16,7 @@ Description: An interface to the 'NetCDF' file formats designed by Unidata
of time units are enabled by 'UDUNITS' version 2, also from Unidata.
License: GPL (>= 2) | file LICENSE
URL: https://github.com/mjwoods/RNetCDF
https://www.unidata.ucar.edu/software/netcdf/
https://www.unidata.ucar.edu/software/udunits/
https://www.unidata.ucar.edu/software/netcdf
https://www.unidata.ucar.edu/software/udunits
BugReports: https://github.com/mjwoods/RNetCDF/issues
NeedsCompilation: yes
4 changes: 2 additions & 2 deletions man/00RNetCDF.Rd
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Expand Up @@ -81,9 +81,9 @@ In addition to the external types, NetCDF4 supports user-defined types. See \cod
}

\references{
\url{https://www.unidata.ucar.edu/software/netcdf/}
\url{https://www.unidata.ucar.edu/software/netcdf}

\url{https://www.unidata.ucar.edu/software/udunits/}
\url{https://www.unidata.ucar.edu/software/udunits}
}

\note{When installing RNetCDF from source code, the netcdf4 library and header files must be installed on the system. Calendar functions will only be enabled in RNetCDF if the udunits2 library and header files are detected during the build process. Parallel file access requires a netcdf4 library built with MPI support along with an MPI interface package installed in R (e.g. pbdMPI or Rmpi).}
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2 changes: 1 addition & 1 deletion man/att.copy.nc.Rd
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Expand Up @@ -21,7 +21,7 @@
Valid attribute ID numbers range from 0 to the number of attributes minus 1. The number of attributes of a file, group, or variable can be found using the relevant inquiry function (\code{\link[RNetCDF]{file.inq.nc}}, \code{\link[RNetCDF]{grp.inq.nc}}, or \code{\link[RNetCDF]{var.inq.nc}}).
}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/att.delete.nc.Rd
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Expand Up @@ -19,7 +19,7 @@
Valid attribute ID numbers range from 0 to the number of attributes minus 1. The number of attributes of a file, group, or variable can be found using the relevant inquiry function (\code{\link[RNetCDF]{file.inq.nc}}, \code{\link[RNetCDF]{grp.inq.nc}}, or \code{\link[RNetCDF]{var.inq.nc}}).
}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/att.get.nc.Rd
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Expand Up @@ -35,7 +35,7 @@ Valid attribute ID numbers range from 0 to the number of attributes minus 1. The

\details{This function returns the value of the attribute.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\note{\code{NC_BYTE} is always interpreted as signed.}

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2 changes: 1 addition & 1 deletion man/att.inq.nc.Rd
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Expand Up @@ -29,7 +29,7 @@
Valid attribute ID numbers range from 0 to the number of attributes minus 1. The number of attributes of a file, group, or variable can be found using the relevant inquiry function (\code{\link[RNetCDF]{file.inq.nc}}, \code{\link[RNetCDF]{grp.inq.nc}}, or \code{\link[RNetCDF]{var.inq.nc}}).
}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/att.put.nc.Rd
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Expand Up @@ -23,7 +23,7 @@ Text represented by R type \code{character} can be written to NetCDF types \code
R \code{numeric} and \code{integer} variables can be written to NetCDF numeric types. The NetCDF library handles type conversions, but conversions of values outside the range of a type will result in an error. Due to the lack of native support for 64-bit integers in R, this function accepts \code{\link[bit64:bit64-package]{integer64}} vectors.
}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\note{\code{NC_BYTE} is always interpreted as signed.}

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2 changes: 1 addition & 1 deletion man/att.rename.nc.Rd
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Expand Up @@ -19,7 +19,7 @@

Valid attribute ID numbers range from 0 to the number of attributes minus 1. The number of attributes of a file, group, or variable can be found using the relevant inquiry function (\code{\link[RNetCDF]{file.inq.nc}}, \code{\link[RNetCDF]{grp.inq.nc}}, or \code{\link[RNetCDF]{var.inq.nc}}).}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/close.nc.Rd
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Expand Up @@ -15,7 +15,7 @@

\details{This function closes an open NetCDF dataset. After an open NetCDF dataset is closed, its NetCDF ID may be reassigned to the next NetCDF dataset that is opened or created. Therefore, the passed object (\code{ncfile}) should be deleted by the user after calling this function.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/create.nc.Rd
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Expand Up @@ -37,7 +37,7 @@ The file format is specified by the \code{format} argument, which may take the f
}
}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/dim.def.nc.Rd
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Expand Up @@ -19,7 +19,7 @@

\details{This function creates a new NetCDF dimension. There is a suggested limit (100) to the number of dimensions. Ordinarily, the name and length of a dimension are fixed when the dimension is first defined. The name may be changed later, but the length of a dimension (other than the unlimited dimension) cannot be changed without copying all the data to a new NetCDF dataset with a redefined dimension length. A NetCDF dimension in an open NetCDF dataset is referred to by a small integer called a dimension ID. In the C interface, dimension IDs are 0, 1, 2, ..., in the order in which the dimensions were defined. At most one unlimited length dimension may be defined for each NetCDF dataset.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/dim.inq.nc.Rd
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Expand Up @@ -23,7 +23,7 @@

\details{This function returns information about a NetCDF dimension. Information about a dimension include its name, its ID, its length and a flag if it is the unlimited dimension of this NetCDF dataset, if any. The length of the unlimited dimension, if any, is the number of records written so far.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/dim.rename.nc.Rd
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Expand Up @@ -16,7 +16,7 @@

\details{This function renames an existing dimension in a NetCDF dataset open for writing. A dimension cannot be renamed to have the same name as another dimension.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/file.inq.nc.Rd
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Expand Up @@ -22,7 +22,7 @@
\item{libvers}{Version string of the NetCDF library in the current R session.}
}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/grp.def.nc.Rd
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Expand Up @@ -19,7 +19,7 @@

Most NetCDF object types, including groups, variables and global attributes, are visible only in the group where they are defined. However, dimensions are visible in their groups and all child groups.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/grp.inq.nc.Rd
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Expand Up @@ -30,7 +30,7 @@

\details{This function provides information about the structure of a NetCDF group or dataset. The results allow programs to explore a dataset without prior knowledge of the contents.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/grp.rename.nc.Rd
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Expand Up @@ -16,7 +16,7 @@

\details{This function renames an existing group in a dataset of \code{"netcdf4"} format that is open for writing. A group cannot be renamed to have the same name as another group, type or variable in the parent group.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/open.nc.Rd
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Expand Up @@ -27,7 +27,7 @@

\details{This function opens an existing NetCDF dataset for access. By default, the dataset is opened read-only. If \code{write=TRUE}, then the dataset can be changed. This includes appending or changing data, adding dimensions, variables, and attributes.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/print.nc.Rd
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Expand Up @@ -18,7 +18,7 @@
The output of this function is similar to the \code{ncdump -h} command supplied with the NetCDF C library. One important difference is that array dimensions are shown by \code{print.nc} in the order used by R, where the leftmost subscript varies fastest.
}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/read.nc.Rd
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Expand Up @@ -23,7 +23,7 @@
Groups in the dataset may optionally be read recursively and returned as nested lists. Each list has the name of the corresponding group in the dataset.
}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/sync.nc.Rd
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Expand Up @@ -14,7 +14,7 @@

\details{This function offers a way to synchronize the disk copy of a NetCDF dataset with in-memory buffers. There are two reasons one might want to synchronize after writes: To minimize data loss in case of abnormal termination, or to make data available to other processes for reading immediately after it is written.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/type.def.nc.Rd
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Expand Up @@ -39,7 +39,7 @@ Several varieties of data type are supported, as specified by argument \code{cla
\code{type.def.nc} may be repeated to insert additional members of an \code{"enum"} type or fields of a \code{"compound"} type. However, the size of a \code{"compound"} type is calculated from the fields specified when it is first defined, and later insertion of fields will only succeed if there is sufficient free space after the last field. Existing fields/members cannot be modified, and types cannot be removed from a dataset.
}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/type.inq.nc.Rd
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Expand Up @@ -33,7 +33,7 @@

\details{This function obtains information about a NetCDF data type, which could be builtin or user-defined. The items in the return list depend on the class of the NetCDF type.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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6 changes: 3 additions & 3 deletions man/utcal.nc.Rd
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Expand Up @@ -27,9 +27,9 @@ Conversions involving alternative calendars are not supported by UDUNITS, but th

\seealso{\code{\link{utinvcal.nc}}}

\references{\url{https://www.unidata.ucar.edu/software/udunits/}
\references{\url{https://www.unidata.ucar.edu/software/udunits}

\url{http://cfconventions.org}}
\url{https://cfconventions.org}}

\author{Pavel Michna, Milton Woods}

Expand Down Expand Up @@ -69,7 +69,7 @@ if (inherits(try(utcal.nc("seconds since 1970-01-01", 0)), "try-error")) {
att.put.nc(nc, "NC_GLOBAL", "references", "NC_CHAR",
"https://www.unidata.ucar.edu/software/udunits")
att.put.nc(nc, "NC_GLOBAL", "comment", "NC_CHAR",
"Uses attributes recommended by http://cfconventions.org")
"Uses attributes recommended by https://cfconventions.org")

# Define time coordinate and attributes:
dim.def.nc(nc, "time", nt)
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2 changes: 1 addition & 1 deletion man/utinit.nc.Rd
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Expand Up @@ -17,7 +17,7 @@
UDUNITS2 obtains a unit system by reading an XML file. The file name is given by argument \code{path}, if it is a non-empty character string. Otherwise, the file name is taken from environment variable \code{UDUNITS2_XML_PATH}, if it is a non-empty character string. By default, the file name is set to an XML file distributed with RNetCDF.
}

\references{\url{https://www.unidata.ucar.edu/software/udunits/}}
\references{\url{https://www.unidata.ucar.edu/software/udunits}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/utinvcal.nc.Rd
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Expand Up @@ -24,7 +24,7 @@ A vector of POSIXct values is also accepted as input. These are converted to the

\seealso{\code{\link{utcal.nc}}}

\references{\url{https://www.unidata.ucar.edu/software/udunits/}}
\references{\url{https://www.unidata.ucar.edu/software/udunits}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/var.def.nc.Rd
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Expand Up @@ -38,7 +38,7 @@ A NetCDF variable in an open NetCDF dataset is referred to by a small integer ca

Attributes may be associated with a variable to specify such properties as units.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/var.get.nc.Rd
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Expand Up @@ -74,7 +74,7 @@ Arrays of type \code{character} drop the fastest-varying dimension of the corres
The arguments marked for \code{"netcdf4"} format refer to the chunk cache used for reading and writing variables. Default cache settings are defined by the NetCDF library, and they can be adjusted for each variable to improve performance in some applications.
}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\note{\code{NC_BYTE} is always interpreted as signed.}

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2 changes: 1 addition & 1 deletion man/var.inq.nc.Rd
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Expand Up @@ -38,7 +38,7 @@

\details{This function returns information about a NetCDF variable, including its name, ID, type, number of dimensions, a vector of the dimension IDs, and the number of attributes.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/var.par.nc.Rd
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Expand Up @@ -20,7 +20,7 @@ All netCDF metadata writing operations are collective - all creation of groups,

Note that when the file format is \code{"classic"} or \code{"offset64"}, the change always applies to all variables in the file, even if a single variable is specified in argument \code{variable}.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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2 changes: 1 addition & 1 deletion man/var.put.nc.Rd
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Expand Up @@ -57,7 +57,7 @@ Awkwardness arises mainly from one thing: NetCDF data are written with the last
The arguments marked for \code{"netcdf4"} format refer to the chunk cache used for reading and writing variables. Default cache settings are defined by the NetCDF library, and they can be adjusted for each variable to improve performance in some applications.
}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\note{\code{NC_BYTE} is always interpreted as signed. For best performance, it is recommended that the definition of dimensions, variables and attributes is completed before variables are read or written.}

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2 changes: 1 addition & 1 deletion man/var.rename.nc.Rd
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Expand Up @@ -16,7 +16,7 @@

\details{This function renames an existing variable in a NetCDF dataset open for writing. A variable cannot be renamed to have the same name as another variable.}

\references{\url{https://www.unidata.ucar.edu/software/netcdf/}}
\references{\url{https://www.unidata.ucar.edu/software/netcdf}}

\author{Pavel Michna, Milton Woods}

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