l-ramirez-lopez · l-ramirez-lopez · May 29, 2026 · May 29, 2026 · May 29, 2026 · May 29, 2026
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -29,3 +29,7 @@
 ^CODE_OF_CONDUCT\.md$
 ^vignettes/.*_files$
 
+vignettes/.quarto/
+vignettes/*_cache/
+vignettes/*_files/
+
diff --git a/.gitignore b/.gitignore
@@ -28,4 +28,8 @@ vignettes/*_files/
 docs
 /doc/
 /Meta/
-Makevars.omp
+Makevars.omp
+
+vignettes/.quarto/
+vignettes/*_cache/
+vignettes/*_files/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: resemble
 Type: Package
 Title: Similarity Retrieval and Local Learning for Spectral Chemometrics
 Version: 3.0.1
-Date: 2026-04-21
+Date: 2026-06-18
 Authors@R: c(
   person(given = "Leonardo",
          family = "Ramirez-Lopez",
@@ -23,9 +23,11 @@ Description:
     spectral data sets, including memory-based learning (MBL), optimal subset
     search and selection, and retrieval-based modelling with model libraries.
     Supports local learning, optimisation of spectral libraries, and
-    ensemble prediction from precomputed models.
-    Most of these functions are based on the methods presented in 
-    Ramirez-Lopez et al. (2013) <doi:10.1016/j.geoderma.2012.12.014>.
+    ensemble prediction from precomputed models. Most of these functions are
+    based on the methods presented in Ramirez-Lopez et al. (2013)
+    <doi:10.1016/j.geoderma.2012.12.014>, Ramirez-Lopez et al. (2026a)
+    <doi:10.1016/j.aca.2026.345682>, and Ramirez-Lopez et al. (2026b)
+    <doi:10.1016/j.aca.2026.345651>.
 License: MIT + file LICENSE
 URL: https://l-ramirez-lopez.github.io/resemble/, https://github.com/l-ramirez-lopez/resemble
 Depends:
@@ -52,7 +54,7 @@ VignetteBuilder: quarto
 NeedsCompilation: yes
 LazyData: true
 Repository: CRAN
-RoxygenNote: 7.3.3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 Config/VersionName: tarragona
+Config/roxygen2/version: 8.0.0
diff --git a/NAMESPACE b/NAMESPACE
@@ -9,6 +9,7 @@ S3method(plot,ortho_projection)
 S3method(predict,gesearch)
 S3method(predict,liblex)
 S3method(predict,ortho_projection)
+S3method(predict,plsr)
 S3method(predict,resemble_model)
 S3method(print,diss_correlation)
 S3method(print,diss_method)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+# `resemble 3.0.1 (tarragona)`
+===============
+
+## Fixes
+
+- Fixed: An error was thrown when passing a categorical variable as side info in `diss_evaluate()`.
+
+- Vignettes appear now in the right order in CRAN.
+
 # `resemble 3.0.0 (vertex)`
 ===============
 

diff --git a/R/AAA.R b/R/AAA.R
@@ -1,3 +1,10 @@
+.onLoad <- function(lib, pkg) {
+  n <- suppressWarnings(as.integer(Sys.getenv("OMP_NUM_THREADS", unset = NA_character_)))
+  if (!is.na(n) && n >= 1L) {
+    resemble_set_omp_threads(n)
+  }
+}
+
 .onAttach <- function(lib, pkg) {
   pkg_v <- pkg_info()
 

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1150,3 +1150,9 @@ ith_pred_cpp <- function(plslib, xscale, Xu, dxrxu = NULL) {
     .Call(`_resemble_ith_pred_cpp`, plslib, xscale, Xu, dxrxu)
 }
 
+#' @keywords internal
+#' @noRd
+resemble_set_omp_threads <- function(n) {
+    invisible(.Call(`_resemble_resemble_set_omp_threads`, n))
+}
+
diff --git a/R/diss_evaluate.R b/R/diss_evaluate.R
@@ -110,18 +110,22 @@ diss_evaluate <- function(diss, side_info) {
         call. = FALSE
       )
     }
-    side_info <- as.factor(side_info)
-    if (nlevels(side_info) < 2L) {
+    side_info_cat <- as.factor(side_info[, 1])  
+    if (nlevels(side_info_cat) < 2L) {
       stop(
         "'side_info' must have at least two categories.",
         call. = FALSE
       )
     }
-    get_eval <- .eval_categorical
+    get_eval <- function(y, indices_closest) 
+      .eval_categorical(as.matrix(as.factor(y[, 1])), indices_closest)
   } else {
     get_eval <- .eval_continuous
   }
 
+
+
+
   if (any(colSums(!is.na(side_info)) < 4L)) {
     stop(
       "Each 'side_info' variable must have at least 4 non-missing values.",

diff --git a/R/gesearch.R b/R/gesearch.R
@@ -196,11 +196,13 @@
 #' of selectivity ratio plot. Chemometrics and Intelligent Laboratory Systems
 #' 95:35-48.
 #' 
-#' Ramirez-Lopez, L., Viscarra Rossel, R., Behrens, T., Orellano, C.,
-#' Perez-Fernandez, E., Kooijman, L., Wadoux, A. M. J.-C., Breure, T.,
-#' Summerauer, L., Safanelli, J. L., & Plans, M. (2026a). When spectral
-#' libraries are too complex to search: Evolutionary subset selection for
-#' domain-adaptive calibration. \emph{Analytica Chimica Acta}, under review.
+#' Ramirez-Lopez, L., Viscarra Rossel, R., Orellano, C.,
+#' Kooijman, L., Perez-Fernandez, E., Wadoux, A. M. J.-C.,
+#' Plans, M., Breure, T., Summerauer, L., Safanelli, J. L.,
+#' Behrens, T., & Boqué, R. (2026a). When spectral libraries
+#' are too complex to search: Evolutionary subset selection for
+#' domain-adaptive calibration. \emph{Analytica Chimica Acta},
+#' 1412, 345651. \doi{10.1016/j.aca.2026.345651}
 #'
 #' @seealso
 #' \code{\link{fit_pls}}, \code{\link{gesearch_control}}, \code{\link{mbl}}
@@ -995,8 +997,7 @@ gesearch.default <- function(
 
 
 #' @aliases gesearch
-#' @importFrom stats quantile complete.cases diffinv na.pass model.extract 
-#' model.frame model.matrix
+#' @importFrom stats quantile complete.cases diffinv na.pass model.extract model.frame model.matrix
 #' @export
 gesearch.formula <- function(
     formula,

diff --git a/R/liblex.R b/R/liblex.R
@@ -277,8 +277,8 @@
 #' Ramirez-Lopez, L., Metz, M., Lesnoff, M., Orellano, C.,
 #' Perez-Fernandez, E., Plans, M., Breure, T., Behrens, T.,
 #' Viscarra Rossel, R., & Peng, Y. (2026b). Rethinking local spectral
-#' modelling: From per-query refitting to model libraries. 
-#' \emph{Analytica Chimica Acta}, under review.
+#' modelling: From per-query refitting to model libraries.
+#' \emph{Analytica Chimica Acta}, 345682. \doi{10.1016/j.aca.2026.345682}
 #'
 #' Rajalahti, T., Arneberg, R., Berven, F.S., Myhr, K.M., Ulvik, R.J., 
 #' Kvalheim, O.M. (2009). Biomarker discovery in mass spectral profiles by 

diff --git a/R/local_helpers.R b/R/local_helpers.R
@@ -1038,6 +1038,7 @@ get_plsr <- function(
 #' @author Leonardo Ramirez-Lopez
 #' @keywords internal
 #' @noRd
+#' @export
 predict.plsr <- function(object, newdata, ncomp = NULL, ...) {
   if (!inherits(object, "plsr")) {
     stop("'object' must be of class 'plsr'", call. = FALSE)

diff --git a/R/resemble.R b/R/resemble.R
@@ -75,17 +75,20 @@
 #' @title Overview of the functions in the resemble package
 #' @references
 #'
-#' Ramirez-Lopez, L., Viscarra Rossel, R., Behrens, T., Orellano, C.,
-#' Perez-Fernandez, E., Kooijman, L., Wadoux, A. M. J.-C., Breure, T.,
-#' Summerauer, L., Safanelli, J. L., & Plans, M. (2026a). When spectral
-#' libraries are too complex to search: Evolutionary subset selection for
-#' domain-adaptive calibration. \emph{Analytica Chimica Acta}, under review.
+#' 
+#' Ramirez-Lopez, L., Viscarra Rossel, R., Orellano, C.,
+#' Kooijman, L., Perez-Fernandez, E., Wadoux, A. M. J.-C.,
+#' Plans, M., Breure, T., Summerauer, L., Safanelli, J. L.,
+#' Behrens, T., & Boqué, R. (2026a). When spectral libraries
+#' are too complex to search: Evolutionary subset selection for
+#' domain-adaptive calibration. \emph{Analytica Chimica Acta},
+#' 1412, 345651. \doi{10.1016/j.aca.2026.345651}
 #' 
 #' Ramirez-Lopez, L., Metz, M., Lesnoff, M., Orellano, C.,
 #' Perez-Fernandez, E., Plans, M., Breure, T., Behrens, T.,
 #' Viscarra Rossel, R., & Peng, Y. (2026b). Rethinking local spectral
-#' modelling: From per-query refitting to model libraries. 
-#' \emph{Analytica Chimica Acta}, under review.
+#' modelling: From per-query refitting to model libraries.
+#' \emph{Analytica Chimica Acta}, 345682. \doi{10.1016/j.aca.2026.345682}
 #' 
 #' Ramirez-Lopez, L., Behrens, T., Schmidt, K., Stevens, A., Dematte, J.A.M.,
 #' Scholten, T. (2013a). The spectrum-based learner: A new local approach for

diff --git a/README.md b/README.md
@@ -14,9 +14,9 @@ status](https://www.r-pkg.org/badges/version/resemble?v=2.png)](https://CRAN.R-p
 
 <!-- badges: end -->
 
-*Last update: 2026-04-21*
+*Last update: 2026-06-18*
 
-Version: 3.0.0 – vortex
+Version: 3.0.1 – tarragona
 
 <em>
 <p align="right">
@@ -261,6 +261,24 @@ citation(package = "resemble")
 
 ## News: Memory-based learning and `resemble`
 
+- **2026.04:** [Greenberg et al.,
+  2026](https://doi.org/10.1016/j.geoderma.2026.117829)  
+  used `resemble` for MBL-PLSR modelling of portable X-ray fluorescence
+  (pXRF) spectra, showing improved soil property predictions relative to
+  global PLSR across in-situ and ex-situ measurement settings.
+
+- **2026.05:** [Ramirez-Lopez et al.,
+  2026](https://doi.org/10.1016/j.aca.2026.345682) introduced `liblex`,
+  a retrieval-gated modelling framework that converts spectral libraries
+  into libraries of precomputed local experts for scalable memory-based
+  learning. For this, `resemble` was used.
+
+- **2026.05:** [Ramirez-Lopez et al.,
+  2026](https://doi.org/10.1016/j.aca.2026.345651) introduced
+  `gesearch`, an evolutionary subset-selection method for identifying
+  target-domain-relevant samples from complex spectral libraries. For
+  this, `resemble` was used.
+
 - **2026.05:** [van Leeuwen et al.,
   2026](https://doi.org/10.1016/j.geoderma.2026.117804)  
   used `resemble` for principal component Mahalanobis nearest-neighbour

diff --git a/README.qmd b/README.qmd
@@ -279,6 +279,14 @@ citation(package = "resemble")
 
 ## News: Memory-based learning and `resemble`
 
+* **2026.04:** [Greenberg et al., 2026](https://doi.org/10.1016/j.geoderma.2026.117829)  
+  used `resemble` for MBL-PLSR modelling of portable X-ray fluorescence (pXRF) spectra, showing improved soil property predictions relative to global PLSR across in-situ and ex-situ measurement settings.
+
+* **2026.05:** [Ramirez-Lopez et al., 2026](https://doi.org/10.1016/j.aca.2026.345682)
+  introduced `liblex`, a retrieval-gated modelling framework that converts spectral libraries into libraries of precomputed local experts for scalable memory-based learning. For this, `resemble` was used.
+
+* **2026.05:** [Ramirez-Lopez et al., 2026](https://doi.org/10.1016/j.aca.2026.345651)
+  introduced `gesearch`, an evolutionary subset-selection method for identifying target-domain-relevant samples from complex spectral libraries. For this, `resemble` was used.
 
 * **2026.05:** [van Leeuwen et al., 2026](https://doi.org/10.1016/j.geoderma.2026.117804)  
   used `resemble` for principal component Mahalanobis nearest-neighbour search to extract spectrally similar samples from the KSSL library for MIR model calibration in Dutch soils.

diff --git a/man/gesearch.Rd b/man/gesearch.Rd
diff --git a/man/liblex.Rd b/man/liblex.Rd
diff --git a/man/mbl.Rd b/man/mbl.Rd
diff --git a/man/resemble-package.Rd b/man/resemble-package.Rd
diff --git a/my-comments.md b/my-comments.md
@@ -1,3 +1,53 @@
+# version 3.0.1
+
+Dear CRAN maintainers,
+
+This is a resubmission of resemble 3.0.1. The previous submission was held up
+by two NOTEs about CPU/elapsed time ratio in tests and vignettes. Both have
+been resolved by capping OpenMP threads via `OMP_THREAD_LIMIT` and
+`OMP_NUM_THREADS` in `tests/testthat/setup.R` and in the affected vignette
+setup chunks.
+
+## Test environments
+- Ubuntu 24.04, R 4.5.3 (local)
+- winbuilder R-release: 0 errors, 0 warnings, 0 notes
+- winbuilder R-oldrelease: 0 errors, 0 warnings, 0 notes
+- winbuilder R-devel: likely false positive ERROR — known incompatibility
+  between Rcpp 1.1.1 and R 4.6.0 RC (R_NamespaceRegistry removed from R API),
+  affecting all Rcpp-dependent packages. See:
+  https://github.com/RcppCore/Rcpp/issues/1473
+  Debian R-devel passes with Status: OK.
+
+Best regards,
+Leo
+
+The package was tested locally:
+
+devtools::check(
+    args = "--as-cran",
+    env_vars = c(
+        `_R_CHECK_CRAN_INCOMING_` = "true",
+        `_R_CHECK_CRAN_INCOMING_REMOTE_` = "true"
+    )
+)
+
+❯ checking compilation flags used ... NOTE
+  Compilation used the following non-portable flag(s):
+    ‘-mno-omit-leaf-frame-pointer’
+
+0 errors ✔ | 0 warnings ✔ | 1 note ✖
+
+The package was built using:
+
+devtools::install()
+
+devtools::build(
+  vignettes = TRUE,
+  manual = TRUE,
+  clean_doc = FALSE
+)
+
+
 # version 3.0.0
 
 Dear CRAN maintainers,

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