[Seqinr-commits] r2095 - in pkg: . data man

[noreply at r-forge.r-project.org]

Author: simonpenel
Date: 2019-09-02 16:26:55 +0200 (Mon, 02 Sep 2019)
New Revision: 2095

Modified:
   pkg/DESCRIPTION
   pkg/data/datalist
   pkg/man/clustal.Rd
   pkg/man/fasta.Rd
   pkg/man/mase.Rd
   pkg/man/msf.Rd
   pkg/man/phylip.Rd
Log:
fix bugs 'Variables with usage in documentation object 'clustal' but not in code' and ' Data files in 'data' directory not in 'datalist'

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2019-08-30 13:28:31 UTC (rev 2094)
+++ pkg/DESCRIPTION	2019-09-02 14:26:55 UTC (rev 2095)
@@ -1,7 +1,7 @@
 Encoding: UTF-8
 Package: seqinr
-Version: 3.4-7
-Date: 2019-08-30
+Version: 3.4-8
+Date: 2019-09-02
 Title: Biological Sequences Retrieval and Analysis
 Authors at R: c(person("Delphine", "Charif", role = "aut"),
              person("Olivier", "Clerc", role = "ctb"),

Modified: pkg/data/datalist
===================================================================
--- pkg/data/datalist	2019-08-30 13:28:31 UTC (rev 2094)
+++ pkg/data/datalist	2019-09-02 14:26:55 UTC (rev 2095)
@@ -12,6 +12,8 @@
 ec999
 fasta
 gs500liz
+gcO2
+gcT
 identifiler
 kaksTorture
 m16j

Modified: pkg/man/clustal.Rd
===================================================================
--- pkg/man/clustal.Rd	2019-08-30 13:28:31 UTC (rev 2094)
+++ pkg/man/clustal.Rd	2019-09-02 14:26:55 UTC (rev 2095)
@@ -3,7 +3,7 @@
      \alias{clustal}
      \title{Example of results obtained after a call to read.alignment}
      \description{This data set gives an example of a protein alignment obtained after a call to the function read.alignment on an alignment file in "clustal" format.}
-     \usage{clustal}
+     \usage{data(clustal)}
      \format{A List of class alignment}
      \source{http://www.clustal.org/}
      \references{

Modified: pkg/man/fasta.Rd
===================================================================
--- pkg/man/fasta.Rd	2019-08-30 13:28:31 UTC (rev 2094)
+++ pkg/man/fasta.Rd	2019-09-02 14:26:55 UTC (rev 2095)
@@ -3,7 +3,7 @@
      \alias{fasta}
      \title{Example of results obtained after a call to read.alignment}
      \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}
+     \usage{data(fasta)}
      \format{A List of class alignment}
      \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.}

Modified: pkg/man/mase.Rd
===================================================================
--- pkg/man/mase.Rd	2019-08-30 13:28:31 UTC (rev 2094)
+++ pkg/man/mase.Rd	2019-09-02 14:26:55 UTC (rev 2095)
@@ -3,7 +3,7 @@
      \alias{mase}
      \title{Example of results obtained after a call to read.alignment}
      \description{This data set gives an example of a protein alignment obtained after a call to the function read.alignment on an alignment file in "mase" format.}
-     \usage{mase}
+     \usage{data(mase)}
      \format{A List of class alignment}
      \source{http://www.clustal.org/}
      \references{Faullcner.D.V. and Jurka,J. (1988) \emph{Multiple sequences alignment editor(MASE).} Trends Biochem. Sa., 13, 321-322.}

Modified: pkg/man/msf.Rd
===================================================================
--- pkg/man/msf.Rd	2019-08-30 13:28:31 UTC (rev 2094)
+++ pkg/man/msf.Rd	2019-09-02 14:26:55 UTC (rev 2095)
@@ -3,7 +3,7 @@
      \alias{msf}
      \title{Example of results obtained after a call to read.alignment}
      \description{This data set gives an example of a protein alignment obtained after a call to the function read.alignment on an alignment file in "msf" format.}
-     \usage{msf}
+     \usage{data(msf)}
      \format{A List of class alignment}
      \source{http://www.ebi.ac.uk/2can/tutorials/formats.html#MSF/}
      \keyword{datasets}

Modified: pkg/man/phylip.Rd
===================================================================
--- pkg/man/phylip.Rd	2019-08-30 13:28:31 UTC (rev 2094)
+++ pkg/man/phylip.Rd	2019-09-02 14:26:55 UTC (rev 2095)
@@ -3,7 +3,7 @@
      \alias{phylip}
      \title{Example of results obtained after a call to read.alignment}
      \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 "phylip" format.}
-     \usage{phylip}
+     \usage{data(phylip)}
      \format{A List of class alignment}
      \source{http://evolution.genetics.washington.edu/phylip.html}
      \references{http://evolution.genetics.washington.edu/phylip.html}