[med-svn] [r-bioc-cummerbund] 01/01: Alternate patch for vignettes allowing post-install building
Andreas Tille
tille at debian.org
Sat May 14 22:54:36 UTC 2016
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tille pushed a commit to branch master
in repository r-bioc-cummerbund.
commit 3d85e45bcd1799db24e03f9a12cbf38f6fe567d5
Author: Gordon Ball <gordon at chronitis.net>
Date: Tue May 10 22:46:42 2016 +0200
Alternate patch for vignettes allowing post-install building
---
debian/patches/series | 2 +-
debian/patches/suppress_test_writing_to_usr.patch | 76 -----------------------
debian/patches/vignette-local-files.patch | 31 +++++++++
debian/tests/run-unit-test | 1 +
4 files changed, 33 insertions(+), 77 deletions(-)
diff --git a/debian/patches/series b/debian/patches/series
index c11d124..b6b4fdc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1 @@
-suppress_test_writing_to_usr.patch
+vignette-local-files.patch
diff --git a/debian/patches/suppress_test_writing_to_usr.patch b/debian/patches/suppress_test_writing_to_usr.patch
deleted file mode 100644
index 5f7065b..0000000
--- a/debian/patches/suppress_test_writing_to_usr.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 22 Oct 2014 13:24:34 +0200
-Description: Since it is not allowed to write to /usr
- one part of the vignette was removed. This avoids the following error:
- .
- .
- > cuff <- readCufflinks(dir = myDir, gtfFile = gtfFile,
- + genome = "hg19", rebuild = T)
- Creating database /usr/lib/R/site-library/cummeRbund/extdata/cuffData.db
- Error in sqliteNewConnection(drv, ...) :
- RS-DBI driver: (could not connect to dbname:
- unable to open database file
- )
- Calls: source ... .valueClassTest -> is -> is -> sqliteNewConnection -> .Call
- .
- .
- However, it needs to be verified whether the code that tries to create a
- database in /usr needs to be patched to redirect the database creation
- to /var.
-
---- a/vignettes/cummeRbund-example-workflow.Rnw
-+++ b/vignettes/cummeRbund-example-workflow.Rnw
-@@ -59,30 +59,6 @@ This guide is being released as is, with
-
- \section{Workflow Summary}
-
--\section{Reading cuffdiff output}
--<<loadLib>>=
--library(cummeRbund)
--@
--<<read>>=
--cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund"))
--cuff
--@
--This example uses the 'test' dataset that is included in the cummeRbund package. Importantly, if your current working directory contains the output
--from your cuffdiff analysis, simply calling \Rfunction{cuff<-readCufflinks()} will automatically find the default files and begin parsing your data.
--
--\section{Quality Assessment of data}
--
--\subsection{Evaluating model fit}
--<<model_fit_1,include=FALSE>>=
--d<-dispersionPlot(genes(cuff))
--d
--@
--
--<<label=model_fit_1_plot,fig=TRUE,echo=FALSE>>=
--<<model_fit_1>>
--print(d)
--@
--
- \subsection{Identifying outlier replicates}
- <<rep_boxplot_1,include=FALSE>>=
- pBoxRep<-csBoxplot(genes(cuff),replicates=T)
---- a/vignettes/cummeRbund-manual.Rnw
-+++ b/vignettes/cummeRbund-manual.Rnw
-@@ -248,19 +248,7 @@ To read these files, populate the 'cuffD
- library(cummeRbund)
- @
- %%fileDir<-("../../extdata/")
--<<read,echo=FALSE>>=
--myDir<-system.file("extdata", package="cummeRbund") #You can leave blank if cwd or replace with your own directory path.
--gtfFile<-system.file("extdata/chr1_snippet.gtf",package="cummeRbund") #path to .gtf file used in cuffdiff analysis.
--cuff <- readCufflinks(dir=myDir,gtfFile=gtfFile,genome="hg19",rebuild=T)
--@
--
--<<read2,eval=FALSE>>=
--cuff<-readCufflinks()
--@
--
--<<read3>>=
--cuff
--@
-+% DELETED
-
- Again, by default $dir$ is assumed to be the current working directory and \code{cuff<-readCufflinks()} should work if all appropriate files are in the current working directory. We now also
- recommend that you use both the \Rfunarg{genome} and \Rfunarg{gtfFile} arguments to readCufflinks(). This will allow cummeRbund to archive the transcript structure information located in the .gtf file associated with
diff --git a/debian/patches/vignette-local-files.patch b/debian/patches/vignette-local-files.patch
new file mode 100644
index 0000000..51ced32
--- /dev/null
+++ b/debian/patches/vignette-local-files.patch
@@ -0,0 +1,31 @@
+Description: remove system.file calls in vignettes
+ The makes it possible to test-build the vignettes post-install without
+ them trying to write to the (read-only) library directory, but does
+ require that the extdata folder is copied to the pwd when trying to
+ build the vignettes.
+Author: Gordon Ball <gordon at chronitis.net>
+
+--- a/vignettes/cummeRbund-example-workflow.Rnw
++++ b/vignettes/cummeRbund-example-workflow.Rnw
+@@ -64,7 +64,7 @@
+ library(cummeRbund)
+ @
+ <<read>>=
+-cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund"))
++cuff <- readCufflinks("extdata")
+ cuff
+ @
+ This example uses the 'test' dataset that is included in the cummeRbund package. Importantly, if your current working directory contains the output
+--- a/vignettes/cummeRbund-manual.Rnw
++++ b/vignettes/cummeRbund-manual.Rnw
+@@ -249,8 +249,8 @@
+ @
+ %%fileDir<-("../../extdata/")
+ <<read,echo=FALSE>>=
+-myDir<-system.file("extdata", package="cummeRbund") #You can leave blank if cwd or replace with your own directory path.
+-gtfFile<-system.file("extdata/chr1_snippet.gtf",package="cummeRbund") #path to .gtf file used in cuffdiff analysis.
++myDir<-"extdata" #You can leave blank if cwd or replace with your own directory path.
++gtfFile<-"extdata/chr1_snippet.gtf" #path to .gtf file used in cuffdiff analysis.
+ cuff <- readCufflinks(dir=myDir,gtfFile=gtfFile,genome="hg19",rebuild=T)
+ @
+
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
index 23c37fa..fc4036b 100644
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -6,6 +6,7 @@ if [ "$ADTTMP" = "" ] ; then
ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi
cd $ADTTMP
+cp -r /usr/lib/R/$oname/extdata $ADTTMP
cp /usr/share/doc/$pkg/examples/vignettes/* $ADTTMP
find . -name "*.gz" -exec gunzip \{\} \;
for rnw in `ls *.[rRS]nw` ; do
--
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