From 391eb6c32f4c50af191b5f8355352d7980afdc01 Mon Sep 17 00:00:00 2001
From: Danielle Callan <dmleake92@gmail.com>
Date: Fri, 21 Nov 2025 12:16:48 -0500
Subject: [PATCH 1/2] update docs, deps, version

---
 DESCRIPTION                | 12 ++++++------
 R/microbiomeData-package.R |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ec72e80..bae533d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: microbiomeData
 Title: Curated Data from MicrobiomeDB.org
-Version: 1.0.5
+Version: 1.0.7
 Authors@R: 
     c(person(given = "Danielle",
            family = "Callan",
@@ -9,26 +9,26 @@ Authors@R:
 biocViews: 
 Imports:
     S4Vectors,
-    microbiomeComputations,
-    veupathUtils
+    microbiomeComputations (>= 5.1.7),
+    mbioUtils (>= 0.1.0)
 Extends:
     MicrobiomeDB
 Remotes:
     microbiomeDB/microbiomeComputations,
     microbiomeDB/MicrobiomeDB,
-    microbiomeDB/veupathUtils
+    microbiomeDB/mbioUtils
 URL: https://github.com/microbiomeDB/microbiomeData, https://microbiomedb.github.io/microbiomeData/
 BugReports: https://github.com/microbiomeDB/microbiomeData/issues
 Description: An R package containing all of the curated datasets from MicrobiomeDB.org.
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Depends: 
     R (>= 2.10),
-    MicrobiomeDB
+    MicrobiomeDB (>= 1.1.2)
 License: Apache License (>= 2)
 LazyData: true
 LazyDataCompression: xz
diff --git a/R/microbiomeData-package.R b/R/microbiomeData-package.R
index 9149534..5481a02 100644
--- a/R/microbiomeData-package.R
+++ b/R/microbiomeData-package.R
@@ -3,5 +3,5 @@
 
 ## usethis namespace: start
 ## usethis namespace: end
-#' @import veupathUtils
+#' @import mbioUtils
 #' @import data.table
\ No newline at end of file

From 89ff6c2b6d22c6767ca623130220d46b32826879 Mon Sep 17 00:00:00 2001
From: Danielle Callan <dmleake92@gmail.com>
Date: Fri, 21 Nov 2025 12:54:38 -0500
Subject: [PATCH 2/2] update readme for potential installation struggles

---
 README.md | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/README.md b/README.md
index 8d6fb26..c2b2cfa 100644
--- a/README.md
+++ b/README.md
@@ -17,6 +17,43 @@ Use the R package [remotes](https://cran.r-project.org/web/packages/remotes/inde
 remotes::install_github('microbiomeDB/microbiomeData')
 ```
 
+### Troubleshooting Installation Issues
+
+#### Maaslin2 Installation
+
+If you encounter difficulties installing `Maaslin2` try installing from GitHub directly:
+
+```R
+remotes::install_github("biobakery/Maaslin2")
+```
+
+#### SpiecEasi and gfortran on macOS
+
+If you encounter errors related to `gfortran` when installing `SpiecEasi`, particularly errors like:
+
+```
+ld: library 'emutls_w' not found
+ld: warning: search path '/opt/gfortran/lib' not found
+```
+
+This typically occurs when gfortran is installed via Homebrew but R expects it in a different location. The recommended solution is to install the official gfortran from the R project:
+
+1. Download and install gfortran from: https://github.com/R-macos/gcc-14-branch/releases
+2. Restart R and try installing again
+
+Alternatively, if you have gfortran installed via Homebrew (`/opt/homebrew/bin/gfortran`), you may need to create symlinks or set appropriate environment variables.
+
+### Important: Dependency Change (v1.0.7+)
+
+Starting with version 1.0.7, this package depends on `mbioUtils` instead of `veupathUtils`. If you're updating from an older version and encounter issues, you may need to:
+
+```R
+# Remove old installation
+remove.packages(c("microbiomeData", "MicrobiomeDB", "microbiomeComputations", "veupathUtils"))
+# Reinstall fresh
+remotes::install_github('microbiomeDB/microbiomeData')
+```
+
 ## Usage
 This package contains all of the curated datasets from MicrobiomeDB.org. It is an extension to the [MicrobiomeDB R package](https://github.com/microbiomeDB/MicrobiomeDB) which can be used to analyze and visualize these data. That package is installed and attached with this one.