From d00788f0de838ce81369afcf4e53f9798a70af7a Mon Sep 17 00:00:00 2001 From: Leonardo Ramirez-Lopez Date: Tue, 19 Jul 2022 14:23:20 +0200 Subject: [PATCH 1/9] Update DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ee5f8e3..77b4c1a 100644 --- 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] (), From d10bfb251721e6e18768233a675d1ed6f5dd9cb1 Mon Sep 17 00:00:00 2001 From: Leonardo Ramirez-Lopez Date: Tue, 19 Jul 2022 14:23:22 +0200 Subject: [PATCH 2/9] Update AAA.R --- R/AAA.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/AAA.R b/R/AAA.R index d4f92e9..fad797d 100644 --- 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( From 9aa55232a86ddc966984c556fd462ba868821d66 Mon Sep 17 00:00:00 2001 From: Leonardo Ramirez-Lopez Date: Tue, 19 Jul 2022 14:23:24 +0200 Subject: [PATCH 3/9] Update README.md --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index b3a90e7..3e202a5 100644 --- a/README.md +++ b/README.md @@ -13,8 +13,7 @@ _Antoine Stevens & Leo Ramirez-Lopez_ _Last update: 18.07.2022_ -_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. From 0282507f67e894bcb0d71516618ae781b7144137 Mon Sep 17 00:00:00 2001 From: Leonardo Ramirez-Lopez Date: Tue, 23 Aug 2022 19:34:10 +0200 Subject: [PATCH 4/9] fix(read non-UTF IDs properly) in some cases the conversion to UTF was converting all the IDs to NA --- R/read_nircal.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/read_nircal.R b/R/read_nircal.R index f762f7e..499773a 100644 --- 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 +401,8 @@ 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 <- ids[-c(1, length(ids))] ids <- substr(x = ids, start = regexpr("/", ids) + 1, stop = 100000) flush(connection) From b6315745154146da1066ec74fad6bd0447944929 Mon Sep 17 00:00:00 2001 From: Leonardo Ramirez-Lopez Date: Tue, 30 Aug 2022 15:15:45 +0200 Subject: [PATCH 5/9] fix(iconv() to enc2utf8()): do not generate NAs --- R/read_nircal.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/read_nircal.R b/R/read_nircal.R index 499773a..c588dce 100644 --- a/R/read_nircal.R +++ b/R/read_nircal.R @@ -402,7 +402,8 @@ get_nircal_ids <- function(connection, from, to) { ) ids <- strsplit(ids, "\n", useBytes = TRUE)[[1]] - ids <- iconv(ids, to = "UTF-8", sub = NA) + # 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) From 71f9ab82acd5726181270387a56afc35e5b58e42 Mon Sep 17 00:00:00 2001 From: Leonardo Ramirez-Lopez Date: Tue, 30 Aug 2022 18:28:55 +0200 Subject: [PATCH 6/9] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3e202a5..2376f93 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@

Misc. Functions for Processing and Sample Selection of Spectroscopic Data

_Antoine Stevens & Leo Ramirez-Lopez_ -_Last update: 18.07.2022_ +_Last update: 30.08.2022_ _This version: 0.2.6 - chicago -_ From 5d69e31f1e8ca8148c7d7403822081033e68e6bf Mon Sep 17 00:00:00 2001 From: Leonardo Ramirez-Lopez Date: Tue, 30 Aug 2022 18:45:56 +0200 Subject: [PATCH 7/9] Update my-comments.md --- my-comments.md | 78 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) diff --git a/my-comments.md b/my-comments.md index 84620a7..59ece95 100644 --- 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 = "ramirez.lopez.leo@gmail.com") +``` +- "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 From e628e165dde6ae7df8c8c34955381eaddbea8551 Mon Sep 17 00:00:00 2001 From: Leo Date: Tue, 30 Aug 2022 19:16:55 +0200 Subject: [PATCH 8/9] fix(options to HTML5) --- R/prospectr.R | 2 +- man/prospectr-package.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/prospectr.R b/R/prospectr.R index 0da3871..268d1de 100644 --- a/R/prospectr.R +++ b/R/prospectr.R @@ -17,7 +17,7 @@ #' \ifelse{html}{\out{Stable lifecycle}}{\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/man/prospectr-package.Rd b/man/prospectr-package.Rd index d0b553b..f4a29ec 100644 --- a/man/prospectr-package.Rd +++ b/man/prospectr-package.Rd @@ -9,7 +9,7 @@ \ifelse{html}{\out{Stable lifecycle}}{\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 \code{R} functions useful for pre-processing spectral data well as for selecting representaive samples/spectra. From 4facdcd057b0807da8f38df9075af9202d2e2286 Mon Sep 17 00:00:00 2001 From: Leonardo Ramirez-Lopez Date: Tue, 30 Aug 2022 19:28:47 +0200 Subject: [PATCH 9/9] Update NEWS.md --- NEWS.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/NEWS.md b/NEWS.md index fd9eccd..8980f3c 100644 --- 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 ===============