[GenABEL-dev] [Genabel-commits] r1496 - pkg/GenABEL-general/scripts
Maksim Struchalin
m.v.struchalin at mail.ru
Fri Dec 20 09:23:08 CET 2013
Thanks Lennart. That's very usefull.
best,
Maksim
On 20/12/2013 14:58, L.C. Karssen wrote:
> 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, noreply at r-forge.r-project.org wrote:
>> 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='http://cran.xl-mirror.nl')" > install_fresh_R_packages.R
>> +echo "install.packages(\"mvtnorm\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"methods\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"MASS\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"utils\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> echo
>> +echo An R package qvalue is being installed from Bioconductor...
>> +#echo "install.packages(\"qvalue\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "source(\"http://bioconductor.org/biocLite.R\")" >> install_fresh_R_packages.R
>> +echo "biocLite(\"qvalue\")" >> install_fresh_R_packages.R
>> +echo "install.packages(\"genetics\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"haplo.stats\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"hglm\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"PredictABEL\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"VariABEL\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"bigRR\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +R -f install_fresh_R_packages.R
>> +rm -rf install_fresh_R_packages.R
>>
>> -echo "install.packages(\"roxygen2\", repos='http://cran.us.r-project.org')" > install_roxygen_file.R
>> -echo "install.packages(\"mvtnorm\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"methods\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"MASS\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"utils\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"qvalue\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"genetics\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"haplo.stats\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"hglm\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"PredictABEL\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"VariABEL\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"bigRR\", repos='http://cran.us.r-project.org')" >> 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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>> Genabel-commits at lists.r-forge.r-project.org
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>>
>
>
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