[Seqinr-commits] r1932 - pkg/man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fri Jun 3 19:09:21 CEST 2016 

Author: jeanlobry
Date: 2016-06-03 19:09:21 +0200 (Fri, 03 Jun 2016)
New Revision: 1932

Modified:
   pkg/man/autosocket.Rd
   pkg/man/chargaff.Rd
   pkg/man/choosebank.Rd
   pkg/man/countfreelists.Rd
   pkg/man/countsubseqs.Rd
   pkg/man/fasta.Rd
   pkg/man/getliststate.Rd
   pkg/man/gfrag.Rd
   pkg/man/ghelp.Rd
   pkg/man/isenum.Rd
   pkg/man/knowndbs.Rd
   pkg/man/modifylist.Rd
   pkg/man/oriloc.Rd
   pkg/man/plot.SeqAcnucWeb.Rd
   pkg/man/prettyseq.Rd
   pkg/man/query.Rd
   pkg/man/readfirstrec.Rd
   pkg/man/readsmj.Rd
   pkg/man/residuecount.Rd
   pkg/man/savelist.Rd
   pkg/man/setlistname.Rd
   pkg/man/uco.Rd
Log:
Moving URL pbil.univ-lyon1.fr to doua.prabi.fr

Modified: pkg/man/autosocket.Rd
===================================================================
--- pkg/man/autosocket.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/autosocket.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -12,7 +12,7 @@
 \value{
 An object of class sockconn.
 }
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/chargaff.Rd
===================================================================
--- pkg/man/chargaff.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/chargaff.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -54,7 +54,7 @@
 }
 \references{
 Try \code{example(chargaff)} to mimic figure page 17 in
-\url{http://pbil.univ-lyon1.fr/members/lobry/articles/HDR.pdf}.
+\url{https://pbil.univ-lyon1.fr/members/lobry/articles/HDR.pdf}.
 The red areas correspond to non-allowed values beause the sum
 of the four bases frequencies cannot exceed 100\%.
 The white areas correspond to possible values (more exactly

Modified: pkg/man/choosebank.Rd
===================================================================
--- pkg/man/choosebank.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/choosebank.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -59,8 +59,8 @@
 
 }
 \references{ 
-For more information about the socket communication protocol with ACNUC please get at \url{http://pbil.univ-lyon1.fr/databases/acnuc/remote_acnuc.html}.
-To get the release date and content of all the databases located at the pbil, please look at the following url: \url{http://pbil.univ-lyon1.fr/search/releases.php}\cr
+For more information about the socket communication protocol with ACNUC please get at \url{http://doua.prabi.fr/databases/acnuc/remote_acnuc.html}.
+To get the release date and content of all the databases located at the pbil, please look at the following url: \url{https://pbil.univ-lyon1.fr/search/releases.php}\cr
 Gouy, M., Milleret, F., Mugnier, C., Jacobzone, M., Gautier,C. (1984) ACNUC: a nucleic acid sequence data base and analysis system. 
 \emph{Nucl. Acids Res.}, \bold{12}:121-127.\cr
 Gouy, M., Gautier, C., Attimonelli, M., Lanave, C., Di Paola, G. (1985) 

Modified: pkg/man/countfreelists.Rd
===================================================================
--- pkg/man/countfreelists.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/countfreelists.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -21,7 +21,7 @@
   \item{free}{numeric. The number of free lists}
   \item{annotlines}{vector of strings. Names of annotation lines}
 }
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/countsubseqs.Rd
===================================================================
--- pkg/man/countsubseqs.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/countsubseqs.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -18,7 +18,7 @@
 \value{
 Numeric.
 }
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/fasta.Rd
===================================================================
--- pkg/man/fasta.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/fasta.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -5,6 +5,6 @@
      \description{This data set gives an example of a amino acids alignment obtained after a call to the function read.alignment on an alignment file in "fasta" format.}
      \usage{fasta}
      \format{A List of class alignment}
-     \source{http://pbil.univ-lyon1.fr/help/formats.html/}
+     \source{https://pbil.univ-lyon1.fr/help/formats.html/}
      \references{Pearson W.R. and Lipman D.J. (1988) \emph{Improved tools for biological sequence comparison.}.Proc Natl Acad Sci U S A. 85(8):2444-8.}
      \keyword{datasets}

Modified: pkg/man/getliststate.Rd
===================================================================
--- pkg/man/getliststate.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/getliststate.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -31,7 +31,7 @@
 
 \code{gln} is a shortcut for \code{getliststate(lrank, ...)$name}
 }
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/gfrag.Rd
===================================================================
--- pkg/man/gfrag.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/gfrag.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -21,7 +21,7 @@
 shorter than asked for). NA is returned and a warning is issued in
 case of problem (non existent sequence for instance).
 }
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/ghelp.Rd
===================================================================
--- pkg/man/ghelp.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/ghelp.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -24,7 +24,7 @@
 A vector of string which is returned invisibly and "cated" to the console
 by default.
 }
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/isenum.Rd
===================================================================
--- pkg/man/isenum.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/isenum.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -41,7 +41,7 @@
 }
 
 
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/knowndbs.Rd
===================================================================
--- pkg/man/knowndbs.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/knowndbs.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -31,12 +31,12 @@
 \item{status}{string. "on" means available, "off" means temporarily unavailable}
 \item{info}{string. short description of the database}
 }
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 
 The full list of untagged and tagged databases is here : 
-\url{http://pbil.univ-lyon1.fr/databases/acnuc/banques_raa.php}.
+\url{http://doua.prabi.fr/databases/acnuc/banques_raa.php}.
 
 }
 \author{J.R. Lobry}

Modified: pkg/man/modifylist.Rd
===================================================================
--- pkg/man/modifylist.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/modifylist.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -48,7 +48,7 @@
   \item{socket}{the socket connection that was used}
   
 }
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/oriloc.Rd
===================================================================
--- pkg/man/oriloc.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/oriloc.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -67,10 +67,10 @@
 
 More illustrated explanations to help understand oriloc outputs
 are available there:
-\url{http://pbil.univ-lyon1.fr/software/Oriloc/howto.html}.\cr
+\url{https://pbil.univ-lyon1.fr/software/Oriloc/howto.html}.\cr
 
 Examples of oriloc outputs on real sequence data are there: 
-\url{http://pbil.univ-lyon1.fr/software/Oriloc/index.html}.\cr
+\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

Modified: pkg/man/plot.SeqAcnucWeb.Rd
===================================================================
--- pkg/man/plot.SeqAcnucWeb.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/plot.SeqAcnucWeb.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -18,7 +18,7 @@
 \value{
  An invisible list giving, for each subsequence, its position on the parent sequence.
 }
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/prettyseq.Rd
===================================================================
--- pkg/man/prettyseq.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/prettyseq.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -19,7 +19,7 @@
 \value{
 An invisible vector of string. The output is redirected to the console.
 }
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/query.Rd
===================================================================
--- pkg/man/query.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/query.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -23,7 +23,7 @@
 The query language defines several selection criteria and operations between 
 lists of elements matching criteria. It creates mainly lists of sequences, but 
 also lists of species (or, more generally, taxa) and of keywords.
-See \url{http://pbil.univ-lyon1.fr/databases/acnuc/cfonctions.html#QUERYLANGUAGE}
+See \url{http://doua.prabi.fr/databases/acnuc/cfonctions.html#QUERYLANGUAGE}
 for the last update of the description of the query language.\cr
 
 Selection criteria (no space before the = sign) are: 
@@ -81,7 +81,7 @@
 }
 \references{ 
 To get the release date and content of all the databases located at the pbil, please look at 
-the following url: \url{http://pbil.univ-lyon1.fr/search/releases.php}\cr
+the following url: \url{http://doua.prabi.fr/search/releases}\cr
 Gouy, M., Milleret, F., Mugnier, C., Jacobzone, M., Gautier,C. (1984) ACNUC: a nucleic acid sequence data base and analysis system. 
 \emph{Nucl. Acids Res.}, \bold{12}:121-127.\cr
 Gouy, M., Gautier, C., Attimonelli, M., Lanave, C., Di Paola, G. (1985) 

Modified: pkg/man/readfirstrec.Rd
===================================================================
--- pkg/man/readfirstrec.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/readfirstrec.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -39,7 +39,7 @@
 }
 \references{
   See ACNUC physical structure at 
-  \url{http://pbil.univ-lyon1.fr/databases/acnuc/structure.html}.\cr
+  \url{http://doua.prabi.fr/databases/acnuc/structure.html}.\cr
   
   \code{citation("seqinr")}
 }

Modified: pkg/man/readsmj.Rd
===================================================================
--- pkg/man/readsmj.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/readsmj.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -30,7 +30,7 @@
 }
 \references{
   See ACNUC physical structure at:
-  \url{http://pbil.univ-lyon1.fr/databases/acnuc/structure.html}.\cr
+  \url{http://doua.prabi.fr/databases/acnuc/structure.html}.\cr
   
   \code{citation("seqinr")}
 }

Modified: pkg/man/residuecount.Rd
===================================================================
--- pkg/man/residuecount.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/residuecount.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -18,7 +18,7 @@
 NA in case of problem.
 }
 
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/savelist.Rd
===================================================================
--- pkg/man/savelist.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/savelist.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -23,7 +23,7 @@
 \value{
 none.
 }
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/setlistname.Rd
===================================================================
--- pkg/man/setlistname.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/setlistname.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -23,7 +23,7 @@
   \item{4}{no list of rank \code{lrank} exists.}
 }
 
-\references{ \url{http://pbil.univ-lyon1.fr/databases/acnuc.html}
+\references{ \url{http://doua.prabi.fr/databases/acnuc.html}
 
 \code{citation("seqinr")}
 }

Modified: pkg/man/uco.Rd
===================================================================
--- pkg/man/uco.Rd	2016-06-03 16:29:25 UTC (rev 1931)
+++ pkg/man/uco.Rd	2016-06-03 17:09:21 UTC (rev 1932)
@@ -79,7 +79,7 @@
 
 Charif, D., Thioulouse, J., Lobry, J.R., Perrière, G. (2005) Online 
 Synonymous Codon Usage Analyses with the ade4 and seqinR packages. 
-\emph{Bioinformatics}, \bold{21}:545-547. \url{http://pbil.univ-lyon1.fr/members/lobry/repro/bioinfo04/}.\cr
+\emph{Bioinformatics}, \bold{21}:545-547. \url{https://pbil.univ-lyon1.fr/members/lobry/repro/bioinfo04/}.\cr
 
 Suzuki, H., Brown, C.J., Forney, L.J., Top, E. (2008)
 Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria.

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