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<div class="moz-cite-prefix">Thanks Lennart. That's very usefull.<br>
best,<br>
Maksim<br>
<br>
On 20/12/2013 14:58, L.C. Karssen wrote:<br>
</div>
<blockquote cite="mid:52B3F891.8000301@karssen.org" type="cite">
<pre wrap="">Hi Maksim,
Thanks for making this comprehensive script. Once I've got the new
Jenkins server up I will also incorporate it in there.
One suggestion: Instead of having all these lines like:
echo "install.packages(\"pkg", repos='http.url')" > install.R
you can try the following (a so-called HERE document):
repo="http.url" # Making a variable seems handy
cat <<EOF > install.R
install.packages("pkg", repos="$repo")
install.packages("pkg2", repos="$repo")
etc.
EOF
The idea behind a HERE document is that you continue adding to it until
you reached fixed string (EOF in this case, but you can use any string
you want).
Saves you a lot of typing and quotes.
Best,
Lennart.
On 20-12-13 04:56, <a class="moz-txt-link-abbreviated" href="mailto:noreply@r-forge.r-project.org">noreply@r-forge.r-project.org</a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Author: maksim
Date: 2013-12-20 04:56:16 +0100 (Fri, 20 Dec 2013)
New Revision: 1496
Modified:
pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
Log:
Some bugs fixed. The R package qvalue is installed from Bioconductor now because CRAN deleted it from its repository. Now the ready GenABEL distributive is in the GenABEL_DISTRIBUTIVE_IS_HERE directory after the script finished. You should check out all the warning messages in output before using the distributive.
Modified: pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
===================================================================
--- pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh 2013-12-20 03:09:34 UTC (rev 1495)
+++ pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh 2013-12-20 03:56:16 UTC (rev 1496)
@@ -4,19 +4,15 @@
-echo
echo Remove GenABEL_version_for_submission...
-echo
rm -rf $installation_dir
echo
echo Create GenABEL_version_for_submission...
-echo
mkdir GenABEL_version_for_submission
cd GenABEL_version_for_submission
echo
echo Extract packages from r-forge...
-echo
svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/filevector
svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/DatABEL
svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/MetABEL
@@ -29,31 +25,33 @@
echo
echo Install the freshest R packages from CRAN repository...
+
+echo "install.packages(\"roxygen2\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" > install_fresh_R_packages.R
+echo "install.packages(\"mvtnorm\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" >> install_fresh_R_packages.R
+echo "install.packages(\"methods\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" >> install_fresh_R_packages.R
+echo "install.packages(\"MASS\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" >> install_fresh_R_packages.R
+echo "install.packages(\"utils\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" >> install_fresh_R_packages.R
echo
+echo An R package qvalue is being installed from Bioconductor...
+#echo "install.packages(\"qvalue\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" >> install_fresh_R_packages.R
+echo "source(\<a class="moz-txt-link-rfc2396E" href="http://bioconductor.org/biocLite.R\">"http://bioconductor.org/biocLite.R\"</a>)" >> install_fresh_R_packages.R
+echo "biocLite(\"qvalue\")" >> install_fresh_R_packages.R
+echo "install.packages(\"genetics\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" >> install_fresh_R_packages.R
+echo "install.packages(\"haplo.stats\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" >> install_fresh_R_packages.R
+echo "install.packages(\"hglm\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" >> install_fresh_R_packages.R
+echo "install.packages(\"PredictABEL\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" >> install_fresh_R_packages.R
+echo "install.packages(\"VariABEL\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" >> install_fresh_R_packages.R
+echo "install.packages(\"bigRR\", repos='<a class="moz-txt-link-freetext" href="http://cran.xl-mirror.nl">http://cran.xl-mirror.nl</a>')" >> install_fresh_R_packages.R
+R -f install_fresh_R_packages.R
+rm -rf install_fresh_R_packages.R
-echo "install.packages(\"roxygen2\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" > install_roxygen_file.R
-echo "install.packages(\"mvtnorm\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" >> install_roxygen_file.R
-echo "install.packages(\"methods\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" >> install_roxygen_file.R
-echo "install.packages(\"MASS\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" >> install_roxygen_file.R
-echo "install.packages(\"utils\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" >> install_roxygen_file.R
-echo "install.packages(\"qvalue\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" >> install_roxygen_file.R
-echo "install.packages(\"genetics\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" >> install_roxygen_file.R
-echo "install.packages(\"haplo.stats\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" >> install_roxygen_file.R
-echo "install.packages(\"hglm\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" >> install_roxygen_file.R
-echo "install.packages(\"PredictABEL\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" >> install_roxygen_file.R
-echo "install.packages(\"VariABEL\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" >> install_roxygen_file.R
-echo "install.packages(\"bigRR\", repos='<a class="moz-txt-link-freetext" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>')" >> install_roxygen_file.R
-R -f install_roxygen_file.R
-rm -rf install_roxygen_file.R
-
echo
echo Build and install packages...
-echo
R CMD build DatABEL
R CMD INSTALL DatABEL_*
@@ -72,8 +70,6 @@
PATH="$PATH:$probabel_src_location"
echo Search ProbABEL executive files in $probabel_src_location
-R CMD build MixABEL
-R CMD INSTALL MixABEL_*
cd GenABEL.data
rm -rf inst R
@@ -86,10 +82,9 @@
echo
echo Build, check and install GenABEL...
-echo
# clean up the dev-version for distrib
cd GenABEL
-rm cleanup* configure* *.R
+rm -rf cleanup* configure* *.R
cd src
cp DAlib/*.c* .
cp DAlib/*.h* .
@@ -110,22 +105,42 @@
# end cleanup
R CMD check GenABEL
-R CMD INSTALL GenABEL
+R CMD build GenABEL
+R CMD INSTALL GenABEL_*
+
+
+
+R CMD build MixABEL
+R CMD INSTALL MixABEL_*
+
+
echo
echo Build the tutorial...
-echo
# build the tutorial
cd GenABEL_general
make
cd ..
+
+if [ -f GenABEL_general/GenABEL-tutorial.pdf ];
+then
cp GenABEL_general/GenABEL-tutorial.pdf GenABEL/inst/doc/.
-# end build the tutorial
-
echo
echo Build the working version of GenABEL...
-echo
R CMD build GenABEL
+mkdir GenABEL_DISTRIBUTIVE_IS_HERE
+cp GenABEL_*gz GenABEL_DISTRIBUTIVE_IS_HERE
+echo "The distributive of GenABEL is in $installation_dir/GenABEL_DISTRIBUTIVE_IS_HERE directory. Check out that there were no errors/warnings during running this script."
+echo "GenABEL building DONE!"
+else
+ echo "ERROR: File GenABEL_general/GenABEL-tutorial.pdf does not exist. It should have been generated after runing a make command in the GenABEL_general directory. Something did not work out."
+ echo "Making GenABEL_general/GenABEL-tutorial.pdf was the last step in building GenABEL. Figure out what has happned, create GenABEL_general/GenABEL-tutorial.pdf by running the command make in the GenABEL_general dir, copy it in GenABEL/inst/doc/ and run R CMD build GenABEL."
+fi
+
+
+# end build the tutorial
+
+
# and do not forget to run R CMD check --as-cran!
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<pre wrap="">
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