Fails to print deprecated package names

ChangqingW commented 1 month ago

When I ran BiocCheck::BiocCheck in the console, it finds deprecated packages but fails to print out their names, leaving a very confusing message like the following:

> BiocCheck::BiocCheck('~/FLAMES')
─ BiocCheckVersion: 1.40.0
─ BiocVersion: 3.19
─ Package: FLAMES
─ PackageVersion: 1.11.0
─ sourceDir: /home/q/FLAMES
─ installDir: /tmp/Rtmp2K0NzR/fileb70dc7d74255d
─ BiocCheckDir: /home/q/FLAMES.BiocCheck
─ platform: unix
─ isTarBall: FALSE

* Installing package...
* Checking for deprecated package usage...
    * ERROR: Package dependency in the DESCRIPTION is 'Deprecated'.
      Update your package to not rely on the following:
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...

> sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Arch Linux

Matrix products: default
BLAS:   /usr/lib/libblas.so.3.12.0
LAPACK: /usr/lib/liblapack.so.3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Australia/Melbourne
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocCheck_1.40.0 roxygen2_7.3.2

This also happens to our Github Action set up by biocthis::use_github_action

ChangqingW commented 1 month ago

I got the package name from debug(BiocCheck:::checkDeprecatedPackages), but not sure why this is not printed to the console

Browse[1]> allDeprecated[logVec]
[1] "zlibbioc"

lshep commented 1 month ago

There is a directory similar to when running R CMD check that normally is nameOfPackage.BiocCheck. Normally in this directory there is a more detail explanations of notes/warnings/errors

LiNk-NY commented 1 month ago

@ChangqingW

Note that you should be using Bioc-devel and consequently, the devel version of BiocCheck, especially if you're developing a package. I have updated BiocCheck to include the first 3 lines of errant code. See version 1.41.13.

Best, Marcel

Bioconductor / BiocCheck

Fails to print deprecated package names #217