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Removing wrong urls in Rd files #21

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Merged
aursiber merged 4 commits into from
Apr 28, 2026
Merged

Removing wrong urls in Rd files #21

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34e1f22
Remove oriloc urls to pbil.univ-lyon1.fr
simonpenel Apr 27, 2026
4481d20
Remove doclogi urls to pbil.univ-lyon1.fr
simonpenel Apr 27, 2026
d42f444
Remove dead urls
simonpenel Apr 27, 2026
385e090
Fix wrong urls
simonpenel Apr 28, 2026
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: seqinr
Title: Biological Sequences Retrieval and Analysis
Version: 4.2-43
Version: 4.2-44
Depends: R (>= 2.10.0)
Imports: ade4,segmented
Authors@R: c(person("Delphine", "Charif", role = "aut"),
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4 changes: 0 additions & 4 deletions man/EXP.Rd
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Expand Up @@ -53,10 +53,6 @@ or \code{sum( freq * EXP$A3 )}. To do the same with the \%*\%
operator you have to explicit the recycling rule as in \code{
drop( freq \%*\% rep(EXP$A, 16))}.
}
\source{
ANALSEQ EXPFILEs for command EXP.\cr
\url{http://pbil.univ-lyon1.fr/software/doclogi/docanals/manuel.html}
}
\references{
\code{citation("seqinr")}
\describe{
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2 changes: 1 addition & 1 deletion man/amb.Rd
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Expand Up @@ -26,7 +26,7 @@ a vector with expanded symbols.
\references{

The nomenclature for incompletely specified bases in nucleic acid sequences
at: \url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC341218/}
at: \url{https://pmc.ncbi.nlm.nih.gov/articles/PMC341218/}

\code{citation("seqinr")}
}
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2 changes: 1 addition & 1 deletion man/bma.Rd
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Expand Up @@ -23,7 +23,7 @@ bma(nucl, warn.non.IUPAC = TRUE, type = c("DNA", "RNA"))
\references{

The nomenclature for incompletely specified bases in nucleic acid sequences
at: \url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC341218/}
at: \url{https://pmc.ncbi.nlm.nih.gov/articles/PMC341218/}

\code{citation("seqinr")}
}
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7 changes: 0 additions & 7 deletions man/oriloc.Rd
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Expand Up @@ -65,13 +65,6 @@ skew in third codon positions.
}
\references{

More illustrated explanations to help understand oriloc outputs
are available there:
\url{https://pbil.univ-lyon1.fr/software/Oriloc/howto.html}.\cr

Examples of oriloc outputs on real sequence data are there:
\url{https://pbil.univ-lyon1.fr/software/Oriloc/index.html}.\cr

The original paper for oriloc:\cr
Frank, A.C., Lobry, J.R. (2000) Oriloc: prediction of replication
boundaries in unannotated bacterial chromosomes. \emph{Bioinformatics},
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