From 34e1f225564138f3883072c306d84ca86daa7d5d Mon Sep 17 00:00:00 2001 From: Simon Penel Date: Mon, 27 Apr 2026 16:30:58 +0200 Subject: [PATCH 1/4] Remove oriloc urls to pbil.univ-lyon1.fr --- man/oriloc.Rd | 7 ------- 1 file changed, 7 deletions(-) diff --git a/man/oriloc.Rd b/man/oriloc.Rd index 2adeae3..ef1d261 100644 --- a/man/oriloc.Rd +++ b/man/oriloc.Rd @@ -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}, From 4481d20dfec0fe7022334a76d0f516a83a1e17fa Mon Sep 17 00:00:00 2001 From: Simon Penel Date: Mon, 27 Apr 2026 16:36:14 +0200 Subject: [PATCH 2/4] Remove doclogi urls to pbil.univ-lyon1.fr --- man/EXP.Rd | 4 ---- 1 file changed, 4 deletions(-) diff --git a/man/EXP.Rd b/man/EXP.Rd index 18f8de7..ddb8e63 100644 --- a/man/EXP.Rd +++ b/man/EXP.Rd @@ -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{ From d42f444c1256e353789d392bd2886dba617b9d28 Mon Sep 17 00:00:00 2001 From: Simon Penel Date: Mon, 27 Apr 2026 16:37:23 +0200 Subject: [PATCH 3/4] Remove dead urls --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0a4fffe..28facda 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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"), From 385e0908bb0eabecd67fdd4e140eaf0babe8afed Mon Sep 17 00:00:00 2001 From: Simon Penel Date: Tue, 28 Apr 2026 09:55:48 +0200 Subject: [PATCH 4/4] Fix wrong urls --- man/amb.Rd | 2 +- man/bma.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/man/amb.Rd b/man/amb.Rd index 0f48936..e2210e4 100644 --- a/man/amb.Rd +++ b/man/amb.Rd @@ -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")} } diff --git a/man/bma.Rd b/man/bma.Rd index b6cf48f..a3c4b3c 100644 --- a/man/bma.Rd +++ b/man/bma.Rd @@ -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")} }