Merge branch 'master' into develop

dankelley · Mar 27, 2021 · 24e3a81 · 24e3a81
2 parents 4ff810a + fd5602d
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diff --git a/.gitignore b/.gitignore
@@ -40,5 +40,3 @@ dan[0-9]*
 ar_index_global_prof.rda
 argo_bio-profile_index.rda
 Rplots.pdf
-
-docs
diff --git a/R/oce.R b/R/oce.R
@@ -1704,7 +1704,8 @@ oce.write.table <- function (x, file="", ...)
 #' @references
 #' 1. Sverdrup, H U, Martin W Johnson, and Richard H Fleming. The Oceans,
 #' Their Physics, Chemistry, and General Biology. New York: Prentice-Hall, 1942.
-#' \url{http://ark.cdlib.org/ark:/13030/kt167nb66r}
+## \url{https://ark.cdlib.org/ark:/13030/kt167nb66r}
+#' \url{https://publishing.cdlib.org/ucpressebooks/view?docId=kt167nb66r}
 #'
 #' 2.Locarnini, R. A., A. V. Mishonov, J. I. Antonov, T. P. Boyer,
 #' H. E. Garcia, O. K. Baranova, M. M. Zweng, D. R. Johnson, and

diff --git a/R/topo.R b/R/topo.R
@@ -224,21 +224,22 @@ setMethod(f="subset",
 #' name specifies the data request, if a file of that name is not already
 #' present on the local file system.  The return value is the name of the data
 #' file, and its typical use is as the filename for a call to [read.topo()].
-#' Given the rules on file naming, subsequent calls to `download.topo()`
+#' Given the rules on file naming, subsequent calls to `download.topo`
 #' with identical parameters will simply return the name of the cached file,
 #' assuming the user has not deleted it in the meantime.
 #'
 #' The specified longitude and latitude limits are rounded to 2 digits
 #' (corresponding to a footprint of approximately 1km), and these are used
 #' in the server request. If the resultant request would generate under
-#' 1 row or column in the result, [download.topo] generates an
+#' 1 row or column in the result, `download.topo` generates an
 #' error message and stops.
 #'
 #' @section Historical note relating to NOAA server changes:
-#' In May of 2020, [download.topo()] stopped working, evidently owing
+#' In May of 2020, `download.topo` stopped working, evidently owing
 #' to changes in the NOAA server API, which had been inferred by reverse
-#' engineering a NOAA data-request website. Luckily, \code{marmap::getNOAA.bathy()}
-#' was found to be working at that time, and so [download.topo()] was revised based on
+#' engineering a NOAA data-request website. However, the
+#' `marmap` function `getNOAA.bathy`
+#' was found to be working at that time, and so `download.topo` was revised based on
 #' that function.  The problem of keeping up with changing data-server APIs should
 #' be easier in the future, since NOAA has made the API public.
 #'

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,8 +1,7 @@
 # Resubmission of 1.4-0 (rejected at pretest stage)
 
-This resubmission addresses a pretest problems relating to (a) the tarball
-exceeding 5e6 bytes and (b) an unlinkable reference to a function in the marmap
-package.  I have trimmed the tarball and changed the link{} to code{}.
+This resubmission addresses a pretest problem relating to an unlinkable
+reference to a function in the marmap package that I had missed before.
 
 # Tests
 

diff --git a/docs/articles/adp.html b/docs/articles/adp.html
diff --git a/docs/articles/adp_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/adp_files/accessible-code-block-0.0.1/empty-anchor.js
diff --git a/...dp_files/header-attrs-2.1/header-attrs.js → ...dp_files/header-attrs-2.7/header-attrs.js b/...dp_files/header-attrs-2.1/header-attrs.js → ...dp_files/header-attrs-2.7/header-attrs.js
diff --git a/docs/articles/ctd_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/ctd_files/accessible-code-block-0.0.1/empty-anchor.js
diff --git a/...dp_files/header-attrs-2.3/header-attrs.js → ...td_files/header-attrs-2.7/header-attrs.js b/...dp_files/header-attrs-2.3/header-attrs.js → ...td_files/header-attrs-2.7/header-attrs.js
diff --git a/docs/articles/flags_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/flags_files/accessible-code-block-0.0.1/empty-anchor.js
diff --git a/...td_files/header-attrs-2.1/header-attrs.js → ...gs_files/header-attrs-2.7/header-attrs.js b/...td_files/header-attrs-2.1/header-attrs.js → ...gs_files/header-attrs-2.7/header-attrs.js
diff --git a/docs/articles/map_projections_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/map_projections_files/accessible-code-block-0.0.1/empty-anchor.js
diff --git a/docs/articles/map_projections_files/header-attrs-2.1/header-attrs.js b/docs/articles/map_projections_files/header-attrs-2.1/header-attrs.js
diff --git a/docs/articles/map_projections_files/header-attrs-2.3/header-attrs.js b/docs/articles/map_projections_files/header-attrs-2.3/header-attrs.js
diff --git a/...td_files/header-attrs-2.3/header-attrs.js → ...ns_files/header-attrs-2.7/header-attrs.js b/...td_files/header-attrs-2.3/header-attrs.js → ...ns_files/header-attrs-2.7/header-attrs.js
diff --git a/docs/articles/oce_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/oce_files/accessible-code-block-0.0.1/empty-anchor.js
diff --git a/docs/articles/oce_files/header-attrs-2.1/header-attrs.js b/docs/articles/oce_files/header-attrs-2.1/header-attrs.js
diff --git a/docs/articles/oce_files/header-attrs-2.3/header-attrs.js b/docs/articles/oce_files/header-attrs-2.3/header-attrs.js
diff --git a/...gs_files/header-attrs-2.1/header-attrs.js → ...ce_files/header-attrs-2.7/header-attrs.js b/...gs_files/header-attrs-2.1/header-attrs.js → ...ce_files/header-attrs-2.7/header-attrs.js