updated environment and docker files

Dockerfile

@@ -25,4 +25,4 @@ RUN conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
     conda env create -f conda/environment-dev.yaml
 
-ENTRYPOINT ["/bin/local/miniconda/envs/recetox-aplcms/bin/R", "-e", "devtools::test()"]
+ENTRYPOINT ["/bin/local/miniconda/envs/recetox-aplcms-dev/bin/R", "-e", "devtools::test()"]

conda/environment-build.yaml

@@ -7,24 +7,4 @@ dependencies:
   - anaconda-client
   - conda-build
   - conda-verify
-  - r-base >=3.5
-  - r-mass
-  - r-rgl
-  - bioconductor-mzR
-  - r-splines2
-  - r-doparallel
-  - r-foreach
-  - r-iterators
-  - r-snow
-  - r-gbm
-  - r-e1071
-  - r-randomForest
-  - r-rocr
-  - r-rocs
-  - r-rcpp
-  - r-arrow
-  - r-dplyr
-  - r-tidyr
-  - r-stringr
-  - r-datacomparer
-  - r-tibble
+  - r-base =4.2

conda/environment-dev.yaml

@@ -1,33 +1,25 @@
-name: recetox-aplcms
+name: recetox-aplcms-dev
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - r-base >= 3.5
-  - r-pkgload <= 1.2.4
-  - r-devtools
-  - r-biocmanager
+  - r-base =4.2
   - r-mass
   - r-rgl
   - bioconductor-mzR
   - r-splines2
   - r-doparallel
   - r-foreach
-  - r-iterators
   - r-snow
-  - r-gbm
-  - r-e1071
-  - r-randomForest
-  - r-rocr
-  - r-rocs
   - r-rcpp
-  - r-arrow <= 8.0.0
+  - r-arrow >=7.0.0,<10.0.0
   - r-dplyr
   - r-tidyr
   - r-stringr
-  - r-datacomparer
   - r-tibble
+  # - r-pkgload <=1.2.4
+  - r-devtools 
   - r-languageserver
   - r-jsonlite
   - r-styler

conda/environment.yaml

@@ -0,0 +1,21 @@
+name: recetox-aplcms
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - r-base =4.2
+  - r-mass
+  - r-rgl
+  - bioconductor-mzR
+  - r-splines2
+  - r-doparallel
+  - r-foreach
+  - r-snow
+  - r-rcpp
+  - r-arrow >=7.0.0,<10.0.0
+  - r-dplyr
+  - r-tidyr
+  - r-stringr
+  - r-tibble
+

conda/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "recetox-aplcms" %}
-{% set version = "0.9.4" %}
-{% set github = "https://github.com/RECETOX/recetox-aplcms" %}
+{% set version = "0.10.0" %}
+{% set github = "https://github.com/RECETOX" %}
 
 package:
   name: "r-{{ name|lower }}"
@@ -13,72 +13,65 @@ build:
   number: 0
   noarch: generic
   rpaths:
-    - lib/
     - lib/R/lib/
-  script: R CMD INSTALL --build .
-
-
+    - lib/
+  script_env:
+    - RGL_USE_NULL=TRUE # avoid warning at test-time
+  script: R CMD INSTALL --build . 
+
 requirements:
   host:
-    - r-base >=3.5
+    - r-base =4.2
     - r-mass
     - r-rgl
     - bioconductor-mzR
     - r-splines2
     - r-doparallel
     - r-foreach
-    - r-iterators
     - r-snow
-    - r-gbm
-    - r-e1071
-    - r-randomForest
-    - r-rocr
-    - r-rocs
     - r-rcpp
+    - r-arrow >=7.0.0,<10.0.0
     - r-dplyr
     - r-tidyr
     - r-stringr
-    - r-microbenchmark
+    - r-tibble
 
   run:
-    - r-base >=3.5
-    - r-devtools
-    - r-biocmanager
+    - r-base =4.2
     - r-mass
     - r-rgl
     - bioconductor-mzR
     - r-splines2
     - r-doparallel
     - r-foreach
-    - r-iterators
     - r-snow
-    - r-gbm
-    - r-e1071
-    - r-randomForest
-    - r-rocr
-    - r-rocs
     - r-rcpp
-    - r-arrow <= 8.0.0
+    - r-arrow >=7.0.0,<10.0.0
     - r-dplyr
     - r-tidyr
     - r-stringr
     - r-tibble
 
 test:
   commands:
-    - $R -e "library(recetox.aplcms)"
+    - $R -e "library('recetox.aplcms')"
 
 about:
   home: "{{ github }}"
-  license: GPL2.0
+  license: GPL-2.0
+  license_file: LICENSE
   summary: apLCMS is a software which generates a feature table from a batch of LC/MS spectra. A modified fork of the original apLCMS by Tianwei Yu.
 
 extra:
   maintainers:
-    - RECETOX/conda
+    - hechth
+    - martenson
+    - maximskorik
   identifiers:
     - doi:10.1093/bioinformatics/btp291
     - doi:10.1186/1471-2105-11-559
     - doi:10.1021/pr301053d
     - doi:10.1093/bioinformatics/btu430
     - doi:10.1038/s41598-020-70850-0
+  container:
+    extended-base: True