Merge pull request #47 from l-ramirez-lopez/v0.2.6

V0.2.6
l-ramirez-lopez · Aug 31, 2022 · 9e8cf86 · 9e8cf86
2 parents 64a402c + f96bdbf
commit 9e8cf86
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: prospectr
 Type: Package
 Title: Miscellaneous Functions for Processing 
        and Sample Selection of Spectroscopic Data
-Version: 0.2.5
+Version: 0.2.6
 Date: 2022-07-18
 Author: 
     Antoine Stevens [aut, cre] (<https://orcid.org/0000-0002-1588-7519>), 

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,17 @@
 # `prospectr`
 
+
+`prospectr` 0.2.6
+===============
+
+### Improvements and fixes
+
+* `read_nircal()`: non-utf characters in sample IDs are properly handled (before
+some IDs were wrongly converted into NAs).Non-UTF8 characters are now converted 
+to their corresponding codes.
+
+* Documentation is now compatible with HTML5.
+
 `prospectr` 0.2.5
 ===============
 

diff --git a/R/AAA.R b/R/AAA.R
@@ -10,7 +10,7 @@
     "\033[34m",
     pkg, " version ",
     prospectr_v,
-    " -- \033[39m'antilla'"
+    " -- \033[39m'chicago'"
   )
 
   mss2 <- paste0(

diff --git a/R/prospectr.R b/R/prospectr.R
@@ -17,7 +17,7 @@
 #' \ifelse{html}{\out{<a href='https://www.tidyverse.org/lifecycle/#stable'><img src='figures/lifecycle-stable.svg' alt='Stable lifecycle'></a>}}{\strong{Stable}}
 #'
 #' Misc functions for spectral data
-#' \if{html}{\figure{logo.png}{options: align='right' alt='logo' width='120'}}
+#' \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}}
 #'
 #' This package implements a number of `R` functions useful for
 #' pre-processing spectral data well as for selecting representaive samples/spectra.

diff --git a/R/read_nircal.R b/R/read_nircal.R
@@ -138,7 +138,7 @@ read_nircal <- function(file,
   }
 
   rawcoords <- get_nircal_indices(x = nircalraw)
-
+  
   ids <- get_nircal_ids(connection = con, from = rawcoords$values_s[5], to = rawcoords$values_s2)
   nd <- length(ids)
 
@@ -401,8 +401,9 @@ get_nircal_ids <- function(connection, from, to) {
     "character"
   )
 
-  ids <- iconv(ids, to = "UTF-8", sub = NA)
   ids <- strsplit(ids, "\n", useBytes = TRUE)[[1]]
+  # ids <- iconv(ids, to = "UTF-8", sub = NA)
+  ids <- enc2utf8(ids)
   ids <- ids[-c(1, length(ids))]
   ids <- substr(x = ids, start = regexpr("/", ids) + 1, stop = 100000)
   flush(connection)

diff --git a/README.md b/README.md
@@ -11,10 +11,9 @@
 <em><p align="left"> Misc. Functions for Processing and Sample Selection of Spectroscopic Data </p></em>
 _Antoine Stevens & Leo Ramirez-Lopez_
 
-_Last update: 18.07.2022_
+_Last update: 30.08.2022_
 
-_This version: 0.2.5 - antilla -_ (this version fixes a bug in the 
-`kenStone()` function)
+_This version: 0.2.6 - chicago -_ 
 
 `prospectr` is becoming more and more used in spectroscopic applications, which 
 is evidenced by the number of scientific publications citing the package. 

diff --git a/man/prospectr-package.Rd b/man/prospectr-package.Rd
diff --git a/my-comments.md b/my-comments.md
@@ -1,4 +1,82 @@
 # prospectr
+# version 0.2.6 - chicago
+
+# submission message:
+Dear CRAN maintainers,
+I am submitting my package "prospectr" to CRAN. This version accounts for 
+problems found in Rd files auto-generated with roxygen2 7.1.2 (not compatible 
+with HTML5). The new Rd files are now compatible with HTML5 (as Rd files 
+are generated with roxygen2_7.2.0 ). 
+Prior to this submission, this tarball has been checked with in the winbuilder service. Apart from that it has been also submitted to extensive tests in rhub.
+A first submission of this version failed (for "r-devel-linux-x86_64-debian-gcc"), 
+therefore following platforms were tested for a second submission using Rhub: 
+- Debian Linux, R-devel, GCC ASAN/UBSAN
+- Debian Linux, R-devel, GCC, no long double
+- Debian Linux, R-devel, clang, ISO-8859-15 locale
+- Debian Linux, R-devel, GCC
+For this second submission the package passed all the tests in the above platforms. 
+Reverse dependencies have also been checked. 
+Best regards,
+Leonardo
+
+
+## Package was built using: 
+```
+devtools::build(
+  pkg = ".",
+  path = NULL,
+  binary = FALSE,
+  vignettes = TRUE,
+  manual = TRUE,
+  args = NULL,
+  quiet = FALSE
+)
+```
+
+# R win builder checks for release of `prospectr 0.2.6` (`chicago`) 30.08.2022 
+passed all the checks without notes.
+
+# Rhub checks for release of `prospectr 0.2.6` (`chicago`) 30.08.2022
+The checks were conducted in the following platforms through rhub:
+
+```
+rhub::check(paste0(gsub("/prospectr$", "/", getwd()), "prospectr_0.2.6.tar.gz"), 
+            platform = c("fedora-gcc-devel"), 
+            email = "[email protected]")
+```
+- "linux-x86_64-rocker-gcc-san"
+
+- "fedora-gcc-devel"  NOTE
+  installed size is  6.6Mb
+  sub-directories of 1Mb or more:
+    data   1.9Mb
+    libs   3.9Mb
+
+- "windows-x86_64-devel" OK
+
+- "macos-highsierra-release-cran" OK
+
+- "windows-x86_64-release" OK
+
+
+- "ubuntu-gcc-release" NOTE
+  installed size is  6.8Mb
+  sub-directories of 1Mb or more:
+    data   1.9Mb
+    libs   4.0Mb
+
+
+- "solaris-x86-patched-ods" checking package dependencies (2.7s)
+   Package suggested but not available: ‘testthat’
+
+   The suggested packages are required for a complete check.
+   Checking can be attempted without them by setting the environment
+   variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
+
+   See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+   manual.
+
+
 
 # version 0.2.5 - antilla