Submit CRAN 6.2.0 (#141)

* Increment version number to 6.2.0

* Update NEWS.md and cran-comments.md for 6.2.0

* Add safeguards to pass NoSuggests checks

- added logic to skip adat2eSet() and
  pivotExpressionSet() examples and tests
  if Biobase is not installed in environment
- added rlang to Suggests in DESCRIPTION
  for access to is_installed() function
  for checking if Biobase is installed

Author: scheidec

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: SomaDataIO
 Title: Input/Output 'SomaScan' Data
-Version: 6.1.0.9000
+Version: 6.2.0
 Authors@R: c(
     person(given = "Stu",
            family = "Field",
@@ -41,6 +41,7 @@ Suggests:
     knitr,
     purrr,
     recipes,
+    rlang,
     rmarkdown,
     spelling,
     testthat (>= 3.0.0),

NEWS.md

@@ -1,4 +1,93 @@
-# SomaDataIO (development version)
+# SomaDataIO 6.2.0
+
+### New Functions
+
+* Added `calc_eLOD()` function (#131)
+  - calculates the estimated limit of detection (eLOD)
+    for SeqId columns of an input `soma_adat` or `data.frame`
+
+### Bug Fixes
+
+* Fixed `crayon` bug and `ui_bullet()` issue (#129, #130)
+  - removed `crayon` and `usethis` as dependencies in favor of `cli`
+  - fixed bug in R version 4.4.1 with `ui_bullet()` internal
+    calls within `loadAdatsAsList()` and `write_adat()`
+
+* Fixed bug in `Summary.soma_adat()` operations (#121)
+  - these operations: `min()`, `max()`, `any()`, `range()`, etc.
+    would return the incorrect value due to an `as.matrix()`
+    conversion under the hood
+  - now skips that conversion, trips a warning, and carries on
+  - triggers an error if non-numerics are passed
+    as part of the '...' outside of a `soma_adat`,
+    just like `Summary.data.frame()`
+
+### Function and Object Improvements
+
+* `collapseAdats()` now maintains Cal.Set entries of Col.Meta (#113)
+  - collapsing ADATs can be problematic for the attributes,
+    especially for large numbers of ADATs
+  - `collapseAdats()` now attempts to smartly
+    merge the (potentially numerous elements) Col.Meta
+    attribute in the final object, preserving
+    the "Cal.Set" and "ColCheck" columns in particular
+  - the resulting `Col.Meta` attribute is a combined product
+    of the individual ADAT elements, and the _intersect_ of the
+    analyte features (as is the case for the `rbind()` that is called)
+    
+* Updated checksums and versions for Annotations Excel files (#116)
+  - updated the 7k and 11k file versions and md5sum checksums
+  - now allows `read_annotations()` to load
+    the individual Excel files
+    
+* Updated `lift_master` object to alpha sort columns
+
+### Documentation Updates
+
+* Updated company name, license year, and maintainer (#137)
+  - SomaLogic Operating Co., Inc is now Standard BioTools, Inc.
+  - updated license and copyright year to 2025
+  - updated package maintainer to Caleb Scheidel
+
+* Updated article links in README, intro vignette (#123)
+  - updated links to articles in README and introduction
+    vignette to URLs to pkgdown website rather than
+    `vignette()` code references
+  - added clarification to above documents that articles are
+    available on website only rather than traditional vignettes
+    included with package
+
+* Updates to example documentation
+  - `read_annotations()` example documentation now points to the
+    most recent 11k Excel annotations file
+  - `parseHeader()` example  now prints list elements separately,
+    rather than full object, which slowed website rendering
+
+### Internal :construction:
+
+* Updates to GitHub Action workflows
+  - added `rhub.yaml` configuration file to comply with `rhub` v2
+  - updated macOS version in `pkgdown.yaml` to macOS-14
+  - added write permission to `pkgdown.yaml` file to enable deployment
+  - changed GitHub Action R checks to MacOS and Windows only
+    - `ubuntu` machine was taking too long to build
+
+* Increased package test coverage
+  - added unit tests for `getSomaScanLiftCCC()`,
+    `parseCheck()` and release utilities which
+    were previously untested
+  - increased test coverage for `pivotExpressionSet()`
+
+* Added missing package anchors to .Rd files (#139)
+  - fixed note from remote windows check
+    related to Rd \link{} targets missing
+    package anchors
+    
+* Updated README badge (#109)
+  - now shows 'downloads' per month over total downloads
+
+* Fixed link in DESCRIPTION; master -> main (#107)
+
 
 # SomaDataIO 6.1.0   :partying_face: :champagne:
 

R/adat2eSet.R

@@ -20,7 +20,7 @@
 #' @return A Bioconductor object of class `ExpressionSet`.
 #' @author Stu Field
 #' @references \url{https://bioconductor.org/install/}
-#' @examples
+#' @examplesIf rlang::is_installed("Biobase")
 #' eSet <- adat2eSet(example_data)
 #' class(eSet)
 #' eSet

R/pivotExpressionSet.R

@@ -9,7 +9,7 @@
 #' @return A `tibble` consisting of the long format
 #'   conversion of an `ExpressionSet` object.
 #' @author Stu Field
-#' @examples
+#' @examplesIf rlang::is_installed("Biobase")
 #' # subset into a reduced mini-ADAT object
 #' # 10 samples (rows)
 #' # 5 clinical variables and 3 features (cols)

cran-comments.md

@@ -1,10 +1,10 @@
 
-# Submission 6.1.0
+# Submission 6.2.0
 
 - This is a submission to an existing CRAN package.
 
 - It contains feature upgrades, minor internal bug-fixes,
-  much improved documentation, and expanded vignettes.
+  and improved documentation.
 
 
 ## Reverse Dependencies
@@ -18,28 +18,30 @@
 
 ## R CMD check results
 ```
-0 errors | 0 warnings | 3 notes
+0 errors | 0 warnings | 2 notes
 ```
 
 ### Notes
 
-The following 3 `notes` were displayed during `rhub::check_for_cran()`:
+The following `notes` were displayed during
+`devtools::check(remote = TRUE, manual = TRUE)`:
 
 ```
-* checking HTML version of manual ... NOTE
-Skipping checking math rendering: package 'V8' unavailable
-
-* checking for non-standard things in the check directory ... NOTE
-Found the following files/directories:
-  ''NULL''
-
-* checking for detritus in the temp directory ... NOTE
-Found the following files/directories:
-  'lastMiKTeXException'
+❯ checking CRAN incoming feasibility ... [7s/72s] NOTE
+  Maintainer: ‘Caleb Scheidel <[email protected]>’
+  
+  New maintainer:
+    Caleb Scheidel <[email protected]>
+  Old maintainer(s):
+    Stu Field <[email protected]>
+
+❯ checking installed package size ... NOTE
+    installed size is  6.0Mb
+    sub-directories of 1Mb or more:
+      data      3.8Mb
+      extdata   1.1Mb
 ```
 
-We do not believe these are issues under our control.
-
 
 ## Package Size
 
@@ -49,31 +51,32 @@ We do not believe these are issues under our control.
 ## Example Timings from Win-builder
 
 ```
-name                user    system   elapsed
-Col.Meta            0.28    0.02     0.29    
-SeqId               0.05    0.00     0.04    
-SomaDataIO-package  0.09    0.00     0.09    
-SomaScanObjects     0.25    0.02     0.26    
-adat-helpers        0.05    0.00     0.05    
-adat2eSet           0.31    0.04     0.36    
-addClass            0       0        0    
-cleanNames          0       0        0    
-diffAdats           0.18    0.11     0.30    
-getAnalyteInfo      0.12    0.00     0.13    
-getAnalytes         0.02    0.00     0.01    
-groupGenerics       0.23    0.03     0.27    
-is_intact_attr      0.02    0.00     0.01    
-is_seqFormat        0.02    0.00     0.02    
-lift_adat           0.26    0.00     0.27    
-loadAdatsAsList     1.27    0.02     1.28    
-merge_clin          0.08    0.00     0.08    
-parseHeader         0.46    0.19     0.65    
-pivotExpressionSet  0.06    0.00     0.06    
-read_adat           1.22    0.01     1.23    
-read_annotations    0       0        0    
-rownames            0.01    0.00     0.02    
-soma_adat           0.19    0.00     0.18    
-transform           0       0        0    
-write_adat          0.22    0.03     0.25    
+name	              user	system	elapsed
+Col.Meta	          0.23	0.01	0.25	
+SeqId	              0.03	0.02	0.05	
+SomaDataIO-package	  0.08	0.02	0.10	
+SomaScanObjects	      0.25	0.00	0.25	
+adat-helpers	      0.05	0.00	0.04	
+adat2eSet	          0.31	0.04	0.36	
+addClass	          0	    0	    0 	
+calc_eLOD	          0.01	0.00	0.01	
+cleanNames	          0	    0	    0	
+diffAdats	          0.33	0.00	0.33	
+getAnalyteInfo	      0.11	0.00	0.11	
+getAnalytes	          0.02	0.00	0.01	
+groupGenerics	      0.28	0.00	0.28	
+is_intact_attr	      0	    0 	    0	
+is_seqFormat	      0	    0	    0	
+lift_adat	          0.25	0.02	0.26	
+loadAdatsAsList	      1.36	0.00	1.36	
+merge_clin	          0.08	0.00	0.08	
+parseHeader	          0.08	0.01	0.09	
+pivotExpressionSet	  0.07	0.00	0.06	
+read_adat	          1.22	0.00	1.22	
+read_annotations	  0	    0	    0	
+rownames	          0	    0	    0	
+soma_adat	          0.2 	0.0 	0.2	
+transform	          0	    0	    0	
+write_adat	          0.24	0.01	0.25
 ```
 

inst/WORDLIST

@@ -87,6 +87,7 @@ aliquot
 analyte
 analytes
 barcode
+checksums
 cli
 dplyr
 eLOD
@@ -98,6 +99,7 @@ leftrightarrow
 lifecycle
 lysate
 magrittr
+md
 medNormRef
 nd
 normals

man/adat2eSet.Rd

@@ -1,9 +1,13 @@
 
-suppressPackageStartupMessages(library(Biobase))
+if ( rlang::is_installed("Biobase") ) {
+  suppressPackageStartupMessages(library(Biobase))
+  sub_adat <- example_data[1:10L, c(1:5L, 35:37L)]
+}
+
 
-sub_adat <- example_data[1:10L, c(1:5L, 35:37L)]
 
 test_that("`adat2eSet()` converts `soma_adt` -> eSet correctly", {
+  testthat::skip_if_not_installed("Biobase")
   eSet <- adat2eSet(sub_adat)
   expect_s4_class(eSet, "ExpressionSet")
   expect_true(is.matrix(eSet@assayData$exprs))

man/pivotExpressionSet.Rd

@@ -1,22 +1,27 @@
 
 # Setup -----
-sub_adat <- example_data[1:10, c(1:5, 35:37)]
-long     <- pivotExpressionSet(adat2eSet(sub_adat))
+if ( rlang::is_installed("Biobase") ) {
+  sub_adat <- example_data[1:10, c(1:5, 35:37)]
+  long     <- pivotExpressionSet(adat2eSet(sub_adat))
+}
 
 # Testing ----
 test_that("pivotExpressionSet() returns the correct class and dimensions", {
+  testthat::skip_if_not_installed("Biobase")
   expect_s3_class(long, "tbl_df")
   expect_equal(dim(long), c(30, 29))
 })
 
 test_that("pivotExpressionSet() returns expected metadata columns", {
+  testthat::skip_if_not_installed("Biobase")
   expect_setequal(rownames(sub_adat), long$array_id)
   expect_setequal(getAnalytes(sub_adat), long$feature)
   expect_true(all(names(attributes(sub_adat)$Col.Meta) %in% names(long)))
   expect_true(all(getMeta(sub_adat) %in% names(long)))
 })
 
 test_that("pivotExpressionSet() preserves analyte values", {
+  testthat::skip_if_not_installed("Biobase")
   expect_equal(sub_adat[order(row.names(sub_adat)),]$seq.10000.28,
                subset(long, feature == "seq.10000.28")$value)
 })