Fails to build with GenomicFeatures 1.64.0

[rekado]

This package fails to build with recent versions of GenomicFeatures:

Error: object ‘makeTxDbFromGRanges’ is not exported by 'namespace:GenomicFeatures'

[mschilli87]

Interesting. What version of GenomicFeatures is that?

v1.24.4 seems to still have it

But maybe it was moved recently? I found this using a quick search.

---

edit: Yep:

CHANGES IN VERSION 1.56.0

NEW FEATURES

o Add getTerminatorSeq(). Same as getPromoterSeq() but > for terminator
  sequences.

SIGNIFICANT USER-VISIBLE CHANGES

o The makeTxDb*() functions and related have moved to > the new txdbmaker
  package. Full list:
    - makeTxDb
    - supportedUCSCtables
    - browseUCSCtrack
    - makeTxDbFromUCSC
    - getChromInfoFromBiomart
    - makeTxDbFromBiomart
    - makeTxDbFromEnsembl
    - makeTxDbFromGRanges
    - makeTxDbFromGFF
    - supportedUCSCFeatureDbTracks
    - supportedUCSCFeatureDbTables
    - UCSCFeatureDbTableSchema
    - makeFeatureDbFromUCSC
    - supportedMiRBaseBuildValues
    - makePackageName
    - makeTxDbPackage
    - makeTxDbPackageFromUCSC
    - makeFDbPackageFromUCSC
    - makeTxDbPackageFromBiomart
  Note that they are still temporarily defined in GenomicFeatures but now
  they just call the corresponding function in txdbmaker. Since this is a
  temporary redirect, the user also gets a warning that tells them to use
  the fully qualified name (e.g. txdbmaker::makeTxDbFromUCSC()) to call
  the function.

[mschilli87]

Should be an easy fix.

[mschilli87]

The breakage was introduced here:

CHANGES IN VERSION 1.64.0

DEPRECATED AND DEFUNCT

o After they got formally deprecated in GenomicFeatures in BioC 3.21 and
  defunct in BioC 3.22, all the functions that went to txdbmaker in
  BioC 3.19 are now gone for good.

o After being defunct in BioC 3.22, microRNAs() is now gone for good.

[mschilli87]

Turns out while the fix will be rather trivial, reproducing this to be able to test the fix before committing it is not that easy: I need an environment with latest BioConductor, which does not support the R version I have. I made a conda env with recent enough R, but bioconda doesn't ship recent enough BioConductor yet. Thus, I need to manually install the entire dependency tree of GenomicFeatures from source. I got it mostly working but now I am hitting a rather cryptic config error for XML. My best guess is that it (now?) requries some CPU features my (ancient) server doesn't support. But maybe it's also just that I missed a dependency in the conda env and I am hitting some ABI incompatibility with a system-wide version. Guix is not available on the server and I am not aware of an easy way to bootstrap it without sudo privileges either. All in all I feel I went down that particular rabbit hole deep enough for what I thought would be a few minutes of active work plus a bit of waiting while stuff installs and tests. I can try on a different system, but I am not sure when I will get to it.

@rekado: Is this urgent for some actual application or just a heads-up that something broke in very new environments and fixing it a bit later (e.g. when bioconda ships an affected version) would suffice?
Otherwise I can attempt a blind fix on a branch if you are setup to test it and verify my fix doesn't miss anything or breaks something else.

[rekado]

@mschilli87 it's not urgent, just something I noticed while preparing a mass CRAN/Bioc update on the Guix r-team branch.

I could give you a Guix pack of an environment containing the dependencies of ciRcus, if that would help, but I'm happy to wait until it's more convenient for you.