Check whether to load databases after sync mode check

example_projects/project-upgrade/rproject.toml

@@ -4,7 +4,8 @@
 name = "project-upgrade"
 r_version = "4.4"
 repositories = [
-    {alias = "PPM", url = "https://packagemanager.posit.co/cran/2024-12-22"}
+    {alias = "PPM", url = "https://packagemanager.posit.co/cran/2025-04-12"},
+    {alias = "PPM-old", url = "https://packagemanager.posit.co/cran/2025-04-01"}
 ]
 
 dependencies = [

example_projects/project-upgrade/rv.lock

@@ -3,79 +3,59 @@
 version = 1
 r_version = "4.4"
 
-[[packages]]
-name = "MASS"
-version = "7.3-60.2"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
-path = "4.4.0/Recommended"
-force_source = false
-dependencies = []
-
-[[packages]]
-name = "Matrix"
-version = "1.6-5"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
-path = "4.4.0/Recommended"
-force_source = false
-dependencies = [
-    "lattice",
-]
-
 [[packages]]
 name = "R6"
-version = "2.5.1"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+version = "2.6.1"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "RColorBrewer"
 version = "1.1-3"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "cli"
-version = "3.6.2"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+version = "3.6.4"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "colorspace"
-version = "2.1-0"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+version = "2.1-1"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "fansi"
 version = "1.0.6"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "farver"
-version = "2.1.1"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+version = "2.1.2"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "ggplot2"
-version = "3.4.4"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+version = "3.5.1"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = [
     "cli",
     "glue",
     "gtable",
     "isoband",
     "lifecycle",
-    "MASS",
-    "mgcv",
     "rlang",
     "scales",
     "tibble",
@@ -85,15 +65,15 @@ dependencies = [
 
 [[packages]]
 name = "glue"
-version = "1.7.0"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+version = "1.8.0"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "gtable"
-version = "0.3.4"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+version = "0.3.6"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = [
     "cli",
@@ -105,29 +85,21 @@ dependencies = [
 [[packages]]
 name = "isoband"
 version = "0.2.7"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "labeling"
 version = "0.4.3"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
-force_source = false
-dependencies = []
-
-[[packages]]
-name = "lattice"
-version = "0.22-5"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
-path = "4.4.0/Recommended"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "lifecycle"
 version = "1.0.4"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = [
     "cli",
@@ -138,48 +110,26 @@ dependencies = [
 [[packages]]
 name = "magrittr"
 version = "2.0.3"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
-[[packages]]
-name = "mgcv"
-version = "1.9-1"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
-path = "4.4.0/Recommended"
-force_source = false
-dependencies = [
-    "nlme",
-    "Matrix",
-]
-
 [[packages]]
 name = "munsell"
-version = "0.5.0"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+version = "0.5.1"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = [
     "colorspace",
 ]
 
-[[packages]]
-name = "nlme"
-version = "3.1-164"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
-path = "4.4.0/Recommended"
-force_source = false
-dependencies = [
-    "lattice",
-]
-
 [[packages]]
 name = "pillar"
-version = "1.9.0"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+version = "1.10.1"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = [
     "cli",
-    "fansi",
     "glue",
     "lifecycle",
     "rlang",
@@ -190,21 +140,21 @@ dependencies = [
 [[packages]]
 name = "pkgconfig"
 version = "2.0.3"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "rlang"
-version = "1.1.3"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+version = "1.1.5"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "scales"
 version = "1.3.0"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = [
     "cli",
@@ -222,7 +172,7 @@ dependencies = [
 [[packages]]
 name = "tibble"
 version = "3.2.1"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = [
     "fansi",
@@ -237,14 +187,14 @@ dependencies = [
 [[packages]]
 name = "utf8"
 version = "1.2.4"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "vctrs"
 version = "0.6.5"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = [
     "cli",
@@ -256,13 +206,13 @@ dependencies = [
 [[packages]]
 name = "viridisLite"
 version = "0.4.2"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []
 
 [[packages]]
 name = "withr"
-version = "3.0.0"
-source = { repository = "https://packagemanager.posit.co/cran/2024-02-22" }
+version = "3.0.2"
+source = { repository = "https://packagemanager.posit.co/cran/2025-04-01" }
 force_source = false
 dependencies = []

src/activate.rs

@@ -97,8 +97,7 @@ fn scripts_as_paths(is_home: bool) -> (PathBuf, PathBuf) {
 
 fn write_activate_file(dir: impl AsRef<Path>, is_home: bool) -> Result<(), ActivateError> {
     let template = ACTIVATE_FILE_TEMPLATE.to_string();
-    let global_wd_content = if is_home
-    {
+    let global_wd_content = if is_home {
         r#"
         owd <- getwd()
         setwd("~")

src/lockfile.rs

@@ -481,6 +481,16 @@ impl Lockfile {
         true
     }
 
+    pub fn contains_resolved_dep(&self, dep: &ResolvedDependency) -> bool {
+        self.packages
+            .iter()
+            .find(|lock_pkg| {
+                lock_pkg.name == dep.name.as_ref()
+                    && lock_pkg.version == dep.version.as_ref().original
+            })
+            .is_some()
+    }
+
     /// Gets a set of all the package names listed in the lockfile
     pub fn package_names(&self) -> HashSet<&str> {
         let mut out = HashSet::new();

src/main.rs

@@ -123,16 +123,24 @@ pub enum MigrateSubcommand {
     },
 }
 
-#[derive(Debug, Clone)]
-enum SyncMode {
+#[derive(Debug, Clone, PartialEq)]
+enum ResolveMode {
     Default,
     FullUpgrade,
     // TODO: PartialUpgrade -- allow user to specify packages to upgrade
 }
 
 /// Resolve dependencies for the project. If there are any unmet dependencies, they will be printed
 /// to stderr and the cli will exit.
-fn resolve_dependencies(context: &CliContext) -> Vec<ResolvedDependency> {
+fn resolve_dependencies<'a>(
+    context: &'a CliContext,
+    resolve_mode: &ResolveMode,
+) -> Vec<ResolvedDependency<'a>> {
+    let lockfile = match resolve_mode {
+        ResolveMode::Default => &context.lockfile,
+        ResolveMode::FullUpgrade => &None,
+    };
+
     let mut resolver = Resolver::new(
         &context.project_dir,
         &context.databases,
@@ -143,8 +151,9 @@ fn resolve_dependencies(context: &CliContext) -> Vec<ResolvedDependency> {
             .map(|x| x.url())
             .collect(),
         &context.r_version,
-        context.lockfile.as_ref(),
+        lockfile.as_ref(),
     );
+
     if context.show_progress_bar {
         resolver.show_progress_bar();
     }
@@ -164,24 +173,46 @@ fn resolve_dependencies(context: &CliContext) -> Vec<ResolvedDependency> {
         ::std::process::exit(1)
     }
 
-    resolution.found
+    // If upgrade and there is a lockfile, we want to adjust the resolved dependencies s.t. if the resolved dep has the same
+    // name and version in the lockfile, we say that it was resolved from the lockfile
+    let resolved = if resolve_mode == &ResolveMode::FullUpgrade && context.lockfile.is_some() {
+        resolution
+            .found
+            .into_iter()
+            .map(|mut dep| {
+                dep.from_lockfile = context
+                    .lockfile
+                    .as_ref()
+                    .unwrap()
+                    .contains_resolved_dep(&dep);
+                dep
+            })
+            .collect::<Vec<_>>()
+    } else {
+        resolution.found
+    };
+
+    resolved
 }
 
 fn _sync(
     mut context: CliContext,
     dry_run: bool,
     has_logs_enabled: bool,
-    sync_mode: SyncMode,
+    resolve_mode: ResolveMode,
 ) -> Result<()> {
     if !has_logs_enabled {
         context.show_progress_bar();
     }
-    context.load_databases_if_needed()?;
-    match sync_mode {
-        SyncMode::Default => (),
-        SyncMode::FullUpgrade => context.lockfile = None,
+
+    // If the sync mode is an upgrade, we want to load the databases even if all packages are contained in the lockfile
+    // because we ignore the lockfile during initial resolution
+    match resolve_mode {
+        ResolveMode::Default => context.load_databases_if_needed()?,
+        ResolveMode::FullUpgrade => context.load_databases()?,
     }
-    let resolved = resolve_dependencies(&context);
+
+    let resolved = resolve_dependencies(&context, &resolve_mode);
 
     match timeit!(
         if dry_run {
@@ -312,16 +343,21 @@ fn try_main() -> Result<()> {
         }
         Command::Plan { upgrade } => {
             let upgrade = if upgrade {
-                SyncMode::FullUpgrade
+                ResolveMode::FullUpgrade
             } else {
-                SyncMode::Default
+                ResolveMode::Default
             };
             let context = CliContext::new(&cli.config_file)?;
             _sync(context, true, cli.verbose.is_present(), upgrade)?;
         }
         Command::Sync => {
             let context = CliContext::new(&cli.config_file)?;
-            _sync(context, false, cli.verbose.is_present(), SyncMode::Default)?;
+            _sync(
+                context,
+                false,
+                cli.verbose.is_present(),
+                ResolveMode::Default,
+            )?;
         }
         Command::Add {
             packages,
@@ -349,7 +385,7 @@ fn try_main() -> Result<()> {
                 context,
                 dry_run,
                 cli.verbose.is_present(),
-                SyncMode::Default,
+                ResolveMode::Default,
             )?;
         }
         Command::Upgrade { dry_run } => {
@@ -358,7 +394,7 @@ fn try_main() -> Result<()> {
                 context,
                 dry_run,
                 cli.verbose.is_present(),
-                SyncMode::FullUpgrade,
+                ResolveMode::FullUpgrade,
             )?;
         }
         Command::Info {
@@ -396,7 +432,7 @@ fn try_main() -> Result<()> {
             let info = CacheInfo::new(
                 &context.config,
                 &context.cache,
-                resolve_dependencies(&context),
+                resolve_dependencies(&context, &ResolveMode::Default),
             );
             if json {
                 println!(
@@ -451,7 +487,7 @@ fn try_main() -> Result<()> {
         Command::Summary { json } => {
             let mut context = CliContext::new(&cli.config_file)?;
             context.load_databases()?;
-            let resolved = resolve_dependencies(&context);
+            let resolved = resolve_dependencies(&context, &ResolveMode::Default);
             let summary = ProjectSummary::new(
                 &context.library,
                 &resolved,

src/resolver/dependency.rs

@@ -27,7 +27,7 @@ pub struct ResolvedDependency<'d> {
     pub(crate) kind: PackageType,
     pub(crate) installation_status: InstallationStatus,
     pub(crate) path: Option<Cow<'d, str>>,
-    pub(crate) from_lockfile: bool,
+    pub from_lockfile: bool,
     pub(crate) from_remote: bool,
     // Remotes are only for local/git deps so the values will always be owned
     pub(crate) remotes: HashMap<String, (Option<String>, PackageRemote)>,