I forgot to mention that the BLOSUM and PAM substitution matrices have
also moved from Biostrings to the new pwalign package.
37 software packages were affected by this move (see list below). All of
them have been fixed. If you maintain one of them, please resync your
GitHub repo with the repo at git.bioconductor.org.
Let me know if you have any questions.
Cheers,
H.
List of software packages that were affected by the Biostrings/pwalign
split (in alphabetical order):
amplican
ChIPpeakAnno
ClustIRR
CNEr
crisprShiny
DECIPHER
DominoEffect
enhancerHomologSearch
girafe
GUIDEseq
hiReadsProcessor
HTSeqGenie
idpr
IMMAN
iPAC
IsoformSwitchAnalyzeR
LinTInd
MethTargetedNGS
methylscaper
motifbreakR
msa
MSA2dist
openPrimeR
QSutils
QuartPAC
R453Plus1Toolbox
Rcpi
RSVSim
sangeranalyseR
sangerseqR
scanMiR
ShortRead
SPLINTER
StructuralVariantAnnotation
svaNUMT
TFBSTools
XNAString
On 4/24/24 09:52, Hervé Pagès wrote:
>
> Hi developers,
>
> pairwiseAlignement() and stringDist() have recently moved from
> Biostrings to the new pwalign package. This is causing a number of
> failures today on the 3.19 report. Since yesterday I've been actively
> repairing packages affected by this by pushing fixes to
> git.bioconductor.org. Most packages are now fixed but this won't
> reflect before tomorrow's report.
>
> Later in the day I'll send emails to the maintainers of packages that
> I have touched and ask them to resync their GitHub repos with
> git.bioconductor.org.
>
> Sorry for the inconvenience.
>
> Let me know if you have any questions.
>
> Best,
>
> H.
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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