From 32301c2c457495f8c623388ec36e9db885aaaa3b Mon Sep 17 00:00:00 2001 From: Milton Woods Date: Sun, 2 Aug 2026 18:38:31 +1000 Subject: [PATCH 1/2] Update URLs that have moved permanently --- DESCRIPTION | 6 +++--- man/00RNetCDF.Rd | 4 ++-- man/att.copy.nc.Rd | 2 +- man/att.delete.nc.Rd | 2 +- man/att.get.nc.Rd | 2 +- man/att.inq.nc.Rd | 2 +- man/att.put.nc.Rd | 2 +- man/att.rename.nc.Rd | 2 +- man/close.nc.Rd | 2 +- man/create.nc.Rd | 2 +- man/dim.def.nc.Rd | 2 +- man/dim.inq.nc.Rd | 2 +- man/dim.rename.nc.Rd | 2 +- man/file.inq.nc.Rd | 2 +- man/grp.def.nc.Rd | 2 +- man/grp.inq.nc.Rd | 2 +- man/grp.rename.nc.Rd | 2 +- man/open.nc.Rd | 2 +- man/print.nc.Rd | 2 +- man/read.nc.Rd | 2 +- man/sync.nc.Rd | 2 +- man/type.def.nc.Rd | 2 +- man/type.inq.nc.Rd | 2 +- man/utcal.nc.Rd | 6 +++--- man/utinit.nc.Rd | 2 +- man/utinvcal.nc.Rd | 2 +- man/var.def.nc.Rd | 2 +- man/var.get.nc.Rd | 2 +- man/var.inq.nc.Rd | 2 +- man/var.par.nc.Rd | 2 +- man/var.put.nc.Rd | 2 +- man/var.rename.nc.Rd | 2 +- 32 files changed, 37 insertions(+), 37 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9e34e152..de5447f5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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"), @@ -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 diff --git a/man/00RNetCDF.Rd b/man/00RNetCDF.Rd index e72782fa..e0219434 100644 --- a/man/00RNetCDF.Rd +++ b/man/00RNetCDF.Rd @@ -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).} diff --git a/man/att.copy.nc.Rd b/man/att.copy.nc.Rd index 080dfa23..95b307e6 100644 --- a/man/att.copy.nc.Rd +++ b/man/att.copy.nc.Rd @@ -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} diff --git a/man/att.delete.nc.Rd b/man/att.delete.nc.Rd index 9594d136..0dadac68 100644 --- a/man/att.delete.nc.Rd +++ b/man/att.delete.nc.Rd @@ -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} diff --git a/man/att.get.nc.Rd b/man/att.get.nc.Rd index 5b3216ef..09451f6c 100644 --- a/man/att.get.nc.Rd +++ b/man/att.get.nc.Rd @@ -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.} diff --git a/man/att.inq.nc.Rd b/man/att.inq.nc.Rd index 744553ea..b9a5b86b 100644 --- a/man/att.inq.nc.Rd +++ b/man/att.inq.nc.Rd @@ -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} diff --git a/man/att.put.nc.Rd b/man/att.put.nc.Rd index 4da08cc8..9110c70f 100644 --- a/man/att.put.nc.Rd +++ b/man/att.put.nc.Rd @@ -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.} diff --git a/man/att.rename.nc.Rd b/man/att.rename.nc.Rd index 33790925..5b05087a 100644 --- a/man/att.rename.nc.Rd +++ b/man/att.rename.nc.Rd @@ -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} diff --git a/man/close.nc.Rd b/man/close.nc.Rd index 1dacdcf5..fe7b0a91 100644 --- a/man/close.nc.Rd +++ b/man/close.nc.Rd @@ -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} diff --git a/man/create.nc.Rd b/man/create.nc.Rd index 173f7eb6..fee9ac3d 100644 --- a/man/create.nc.Rd +++ b/man/create.nc.Rd @@ -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} diff --git a/man/dim.def.nc.Rd b/man/dim.def.nc.Rd index a5aacac8..84be1512 100644 --- a/man/dim.def.nc.Rd +++ b/man/dim.def.nc.Rd @@ -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} diff --git a/man/dim.inq.nc.Rd b/man/dim.inq.nc.Rd index 0ff28cd4..a253f185 100644 --- a/man/dim.inq.nc.Rd +++ b/man/dim.inq.nc.Rd @@ -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} diff --git a/man/dim.rename.nc.Rd b/man/dim.rename.nc.Rd index 4fe504a3..fac4c11a 100644 --- a/man/dim.rename.nc.Rd +++ b/man/dim.rename.nc.Rd @@ -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} diff --git a/man/file.inq.nc.Rd b/man/file.inq.nc.Rd index e3a7f504..c3b55d87 100644 --- a/man/file.inq.nc.Rd +++ b/man/file.inq.nc.Rd @@ -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} diff --git a/man/grp.def.nc.Rd b/man/grp.def.nc.Rd index d648fff6..d9c8fe35 100644 --- a/man/grp.def.nc.Rd +++ b/man/grp.def.nc.Rd @@ -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} diff --git a/man/grp.inq.nc.Rd b/man/grp.inq.nc.Rd index 973151c0..fd1148eb 100644 --- a/man/grp.inq.nc.Rd +++ b/man/grp.inq.nc.Rd @@ -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} diff --git a/man/grp.rename.nc.Rd b/man/grp.rename.nc.Rd index 3d8421a9..ed3b9431 100644 --- a/man/grp.rename.nc.Rd +++ b/man/grp.rename.nc.Rd @@ -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} diff --git a/man/open.nc.Rd b/man/open.nc.Rd index 0caaa5e1..80fe01bf 100644 --- a/man/open.nc.Rd +++ b/man/open.nc.Rd @@ -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} diff --git a/man/print.nc.Rd b/man/print.nc.Rd index fcee6316..db48f33c 100644 --- a/man/print.nc.Rd +++ b/man/print.nc.Rd @@ -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} diff --git a/man/read.nc.Rd b/man/read.nc.Rd index ccdba707..0b18c184 100644 --- a/man/read.nc.Rd +++ b/man/read.nc.Rd @@ -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} diff --git a/man/sync.nc.Rd b/man/sync.nc.Rd index f4180111..b2b3c8dd 100644 --- a/man/sync.nc.Rd +++ b/man/sync.nc.Rd @@ -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} diff --git a/man/type.def.nc.Rd b/man/type.def.nc.Rd index d0222663..97d41b07 100644 --- a/man/type.def.nc.Rd +++ b/man/type.def.nc.Rd @@ -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} diff --git a/man/type.inq.nc.Rd b/man/type.inq.nc.Rd index bd2b7d19..1321c42f 100644 --- a/man/type.inq.nc.Rd +++ b/man/type.inq.nc.Rd @@ -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} diff --git a/man/utcal.nc.Rd b/man/utcal.nc.Rd index 019d33f8..83a7b320 100644 --- a/man/utcal.nc.Rd +++ b/man/utcal.nc.Rd @@ -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} @@ -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) diff --git a/man/utinit.nc.Rd b/man/utinit.nc.Rd index 4129a046..bde17027 100644 --- a/man/utinit.nc.Rd +++ b/man/utinit.nc.Rd @@ -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} diff --git a/man/utinvcal.nc.Rd b/man/utinvcal.nc.Rd index 03b1aba6..a4e6beb1 100644 --- a/man/utinvcal.nc.Rd +++ b/man/utinvcal.nc.Rd @@ -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} diff --git a/man/var.def.nc.Rd b/man/var.def.nc.Rd index 716278d4..28f46319 100644 --- a/man/var.def.nc.Rd +++ b/man/var.def.nc.Rd @@ -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} diff --git a/man/var.get.nc.Rd b/man/var.get.nc.Rd index 82dde2e4..38238cfb 100644 --- a/man/var.get.nc.Rd +++ b/man/var.get.nc.Rd @@ -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.} diff --git a/man/var.inq.nc.Rd b/man/var.inq.nc.Rd index ff74c0f6..2b29e0e2 100644 --- a/man/var.inq.nc.Rd +++ b/man/var.inq.nc.Rd @@ -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} diff --git a/man/var.par.nc.Rd b/man/var.par.nc.Rd index a0660ddc..acc35b37 100644 --- a/man/var.par.nc.Rd +++ b/man/var.par.nc.Rd @@ -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} diff --git a/man/var.put.nc.Rd b/man/var.put.nc.Rd index 0570d253..cf17ceb3 100644 --- a/man/var.put.nc.Rd +++ b/man/var.put.nc.Rd @@ -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.} diff --git a/man/var.rename.nc.Rd b/man/var.rename.nc.Rd index 5852cb5e..9de581ce 100644 --- a/man/var.rename.nc.Rd +++ b/man/var.rename.nc.Rd @@ -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} From 811a27f4c88fe5e4d7014743ec260de0fc75e5f7 Mon Sep 17 00:00:00 2001 From: Milton Woods Date: Sun, 2 Aug 2026 18:50:44 +1000 Subject: [PATCH 2/2] Try testing mpich on ubuntu-26.04 --- .github/workflows/check-linux-mpi.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check-linux-mpi.yaml b/.github/workflows/check-linux-mpi.yaml index 3ec5cd0f..313b749b 100644 --- a/.github/workflows/check-linux-mpi.yaml +++ b/.github/workflows/check-linux-mpi.yaml @@ -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 }}