Indeed. The wrong set of repos was used for the count:
db <- available.packages(repos=BiocManager::repositories(version="3.13"))
deps <- tools::package_dependencies("netDx", db, recursive=TRUE,
reverse=FALSE, which="strong")
lengths(deps)
# netDx
# 200
Fixed now:
Hi Shraddha,
Note that the badge on the landing page is using this formula (~ from
the `biocViews` package):
```r
db <- available.packages(repos = BiocManager::repositories())
deps <- tools::package_dependencies("netDx", db, recursive = TRUE,
reverse = FALSE, which = "strong")
lengths(deps)
#'
Hi Augustin,
Please don't rely on JAVA_HOME to detect Java. The JDK installer on
Windows doesn't set this variable so you shouldn't expect it to be set
on the user's machine. AFAIK the other Bioconductor packages that depend
on Java don't use their own code to detect Java. Instead I believe
That should be fixable. The build system needs to have a correct setting
for JAVA_HOME. But you have
clearly nonportable code in .onLoad in paxtoolsr.R -- system("which java")
... this should not be
necessary at all, just import rJava.
On Mon, Oct 18, 2021 at 12:29 PM Augustin Luna wrote:
> I
I have the following error:
"error: JAVA_HOME cannot be determined from the Registry"
for this package:
https://bioconductor.org/checkResults/devel/bioc-LATEST/paxtoolsr/riesling1-install.html
I have been given assurances that Java is present but given this
error, I am not so sure and I am
Hi all,
Despite moving rarely-used packages to Suggests and eliminating some (e.g.
TCGAutils), the number of dependencies is still listed as 200 for our
package netDx.
https://www.bioconductor.org/packages/devel/bioc/html/netDx.html#since
Is there anything else we can do to cut down on
For clarification:
The release 3.14 branch has not yet been created. Please continue to update
master/devel branch.
Next week when the release occurs the core team will automatically create the
RELEASE_3_14 branch on git.bioconductor.org but until that time the only branch
accessible is
The deadline for fixing packages in preparation for the release is this Friday
October 22nd. All packages should be installing, building, and checking without
ERROR in the Bioconductor build report. While you can continue to push changes
past this date, this ensures all changes are reflected
