updating cran comments and news

NEWS.md

@@ -4,10 +4,23 @@
 DONE:
 -->
 
-# datelife 0.6.5
-  - data: 
-    - updated `opentree_chronograms` object. It now has 253 chronograms from Open Tree of Life and uses "xz" compression. 
-  - examples: 
+# datelife v0.6.6
+  - when congruification fails, return `NA` and produce a warning on functions that use `geiger::congruify.phylo()`:
+    - `congruify_and_mrca_phylo()`
+    - `extract_calibrations_phylo()`
+    - `congruify_and_check()`
+  - changes to `congruify_and_mrca_multiPhylo()`:
+    - filters out results of `congruify_and_mrca_phylo()` that do not inherit `data.frame`; usually this happens when congruification fails
+    - correctly assigns congruified `phy` as attribute
+  - `use_calibrations_bladj.matchedCalibrations()` correctly uses `calibrations` argument
+  - `get_ott_children()` has error handling for when OpenTree APIs might be down, or there is no internet connection
+  - varius fixes to `make_datelife_query()` _et al._ functions
+  - added a new vignette for making datelife query functions (allows testing various functionalities)
+
+# datelife v0.6.5
+  - data:
+    - updated `opentree_chronograms` object. It now has 253 chronograms from Open Tree of Life and uses "xz" compression.
+  - examples:
     - set to not test examples
   - functions:
     - added functions `matrix_to_table` and `matrices_to_table` that go from a matrix of patristic distances to a table of taxon name pairs and respective node ages.
@@ -18,7 +31,7 @@ DONE:
     - `use_calibrations_bladj` takes an output of `congruify_and_mrca` functions.
   - added function method `congruify_and_mrca`
 
-# datelife 0.6.1
+# datelife v0.6.1
   - Functions:
     - `get_otol_chronograms` was updated and renamed to `get_opentree_chronograms`
     - Update `match_all_calibrations`
@@ -29,26 +42,26 @@ DONE:
   - Vignettes: added case study vignette
   - Description: added `BiocManager` package to imports
 
-# datelife 0.6.0
+# datelife v0.6.0
 
   - Dependencies: Bioconductor packages are used conditionally
   - Package website with `pkgdown`
   - documentation: expanded for all functions
   - examples and function files are written to tempdir()
   - function rename: `get_biggest_phylo` to `get_biggest_multiphylo`
 
-# datelife 0.5.0
+# datelife v0.5.0
 
   - functions:
     - `datelife_query_check` is deprecated
     - `use_each_calibration` renamed to `use_calibrations_each`
     - plotting functions have been moved to `datelifeplot` package
 
-# datelife 0.3.1
+# datelife v0.3.1
 
   - Now muscle or mafft can be used for alignment of BOLD sequences
 
-# datelife 0.2.19
+# datelife v0.2.19
 
   - MrBayes and TreePL as dating methods
   - Fully ultrametric summary chronograms and datelife() outputs

cran-comments.md

@@ -1,66 +1,47 @@
-## New submission v 0.6.5
-This is a new submission where I have:
+## New submission v0.6.6
+This is mainly a maintainace submission where I have:
 
-* compressed database with "xz" compression, so the package size is now under 5 Mb
-* started the process of moving database object and functions used to create it to its own package
+* fixed an error from an example coming up on Linux platforms
+* fixed a couple bugs
 
-### Test environments:
+Thanks!
 
-- MacOS, Platform: x86_64-apple-darwin17.0 (64-bit)
-  - R 4.2.0, local `devtools::check()`
-  - R 4.1.1, `rhub::check_for_cran(platforms = "macos-highsierra-release-cran")`
-- Windows, Platform x86_64-w64-mingw32 (64-bit)
-  - R 4.2.0, `devtools::check_win_release()`
-  - R Under development (2022-03-23 r81968 ucrt)
-  - `rhub::check_for_cran(platforms = "windows-x86_64-release")`
-- Linux, Platform: x86_64-pc-linux-gnu (64-bit)
-  - R 4.2.0 release
-  - R 4.3 Under development (2022-06-08 r82470)
+Luna Sanchez
 
-### Results
-0 errors ✔ | 0 warnings ✔ | 3 notes ✖
+
+## Test environments:
+
+* local OS X install, R 4.2.0
+* macOS Big Sur 10.16, x86_64-apple-darwin17.0, R 4.2.2
+* Ubuntu 20.04.5, x86_64-pc-linux-gnu (github actions), R 4.2.2
+* Windows Server x64 (build 20348), x86_64-w64-mingw32 (github actions), R 4.2.2
+* Fedora Linux, R-devel, clang, gfortran
+* Ubuntu Linux 20.04.1 LTS, R-release, GCC
+* Windows Server 2022, R-devel, 64 bit
+* Debian Linux, R-release, GCC
+
+
+## R CMD check results
+
+0 errors ✔ | 0 warnings ✔ | 2 notes ✖
 
 * Note 1
 
 ```
 ❯ checking package dependencies ... NOTE
   Packages suggested but not available for checking: 'msa', 'Biostrings'
 
-  Imports includes 21 non-default packages.
+  Imports includes 22 non-default packages.
   Importing from so many packages makes the package vulnerable to any
   of them becoming unavailable.  Move as many as possible to Suggests
   and use conditionally.
 ```
 **Comments**: <br/>
-All the packages imported are needed for the datelife workflow.
 
-* Note 2
+All the packages imported are needed for the datelife workflow.
 
-```
-Possibly misspelled words in DESCRIPTION:
-  Ané (26:53)
-  BLADJ (32:15)
-  Britton (33:6)
-  Criscuolo (24:18)
-  DateLife (21:62)
-  Huelsenbeck (33:71)
-  O'Meara (35:9)
-  PATHd (32:79)
-  Ronquist (34:9)
-  SDM (23:67)
-  Schenk (29:50)
-  al (24:31, 26:60, 31:19, 32:30, 33:17)
-  chronogram (22:55)
-  chronograms (19:43, 23:14, 25:26)
-  congruification (30:76)
-  et (24:28, 26:57, 31:16, 32:27, 33:14)
-  mrBayes (33:62)
-  treePL (34:69)
-```
-**Comments**: <br/>
-None of these word are misspelled
 
-* Note 3
+* Note 2
 
 ```
 Found the following (possibly) invalid DOIs:
@@ -70,4 +51,5 @@ Found the following (possibly) invalid DOIs:
     Message: 503
 ```
 **Comments**: <br/>
+
 The DOI is functional