R packrat snapshot: upgrading package gives "stale" errors - r

Question

I'm using packrat to freeze all versions of dependencies for an application. Sometimes I run into troubles with "staleness".
For instance, today I upgraded one package to a newer version. I did this by launching R in the packrat-managed project:
% R --quiet
Packrat mode on. Using library in directory:
- "~/git/myapp/app/packrat/lib"
> install.packages('MyPackage')
Installing package into ‘/Users/kwilliams/git/myapp/app/packrat/lib/x86_64-apple-darwin17.7.0/3.5.3’
(as ‘lib’ is unspecified)
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3537k 100 3537k 0 0 5530k 0 --:--:-- --:--:-- --:--:-- 5527k
* installing *source* package ‘MyPackage’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MyPackage)
The downloaded source packages are in
‘/private/var/folders/zp/hj5hqfw970z0_78mrb_802lm0001z9/T/RtmpzfYDUz/downloaded_packages’
However, when I try to generate a new snapshot file, nothing happens:
> packrat::snapshot()
Snapshot written to '/Users/kwilliams/git/myapp/app/packrat/packrat.lock'
(The file is no different than before - the old version of MyPackage is still listed.)
I verified that the new version was indeed installed, and try the snapshot again:
> packageVersion('MyPackage')
[1] ‘7.4’
> packrat::snapshot()
The following packages are stale:
_
MyPackage 7.4
These packages must be updated by calling packrat::restore() before
snapshotting. If you are sure you want the installed versions of these
packages to be snapshotted, call packrat::snapshot() again with
ignore.stale=TRUE.
--
Snapshot operation was cancelled, no changes were made.
Huh? Not sure why the different results between the two times.
status() does seem to know the situation correctly:
> packrat::status()
The following packages are out of sync between packrat and your current library:
packrat library
MyPackage 7.3.1-22287 7.4
Use packrat::snapshot() to set packrat to use the current library, or use
packrat::restore() to reset the library to the last snapshot.
I figure I'll force it, so I add ignore.stale=TRUE:
> packrat::snapshot(ignore.stale=TRUE)
Upgrading these packages already present in packrat:
from to
MyPackage 7.3.1-22287 7.4
Fetching sources for MyPackage (7.4) ... FAILED
Error in snapshotSources(project, activeRepos(project), allRecordsFlat) :
Errors occurred when fetching source files:
Error in getSourceForPkgRecord(pkgRecord, sourceDir, availablePkgs, repos) :
Could not find sources for MyPackage (7.4).
Bummer. Might this have something to do with the fact that this is a locally-created package, installed from a local CRAN-alike? This would be a packrat bug, because (as noted above) install.packages() can find the source package just fine.
So I think there are two potential packrat bugs here:
Inability to snapshot the newly installed package
Inability to download source for the package
FWIW, I think the first problem is identical to the situation here: https://groups.google.com/forum/#!topic/packrat-discuss/HvD45u6w4Zg, in which Kevin Ushey (author/maintainer of packrat) says "it's possible that the logic around 'stale' packages can just go away."

Answer 1

Here are the workarounds I'm using to get back on my way:
As mentioned above, use ignore.stale=TRUE to force the snapshot even when it thinks things are stale.
Copy the source package manually to packrat/src/MyPackage/.
Now it succeeds:
> packrat::snapshot(ignore.stale=TRUE)
Upgrading these packages already present in packrat:
from to
MyPackage 7.3.1-22287 7.4
Snapshot written to '/Users/kwilliams/git/myapp/app/packrat/packrat.lock'
The packrat/packrat.lock file has been updated correctly:
% git diff
diff --git a/app/packrat/packrat.lock b/app/packrat/packrat.lock
index 6c17020..f717d29 100644
--- a/app/packrat/packrat.lock
+++ b/app/packrat/packrat.lock
## -30,9 +30,9 ## Hash: 9772da3bc51603a19a2b75f008fd63e3
Package: MyPackage
Source: source
-Version: 7.3.1-22287
+Version: 7.4
SourcePath: lib/MyPackage
-Hash: 4fe20417f5711b3c7c90a4efe3bb4bc7
+Hash: 880a308537e8de571106893e839386f6
...