Author: tille Date: 2015-10-29 17:58:37 +0000 (Thu, 29 Oct 2015) New Revision: 20325
Added:
trunk/packages/R/r-bioc-000-dependency-scheme/3.2/
trunk/packages/R/r-bioc-000-dependency-scheme/3.2/BioC_3.2-dependency-tree.ditaa
Removed:
trunk/packages/R/r-bioc-000-dependency-scheme/3.2/BioC_3.1-dependency-tree.ditaa
Modified:
trunk/packages/R/r-bioc-000-dependency-scheme/3.2/Makefile
Log:
New BioConductor release 3.2 dependency scheme documentation
Deleted:
trunk/packages/R/r-bioc-000-dependency-scheme/3.2/BioC_3.1-dependency-tree.ditaa
===================================================================
---
trunk/packages/R/r-bioc-000-dependency-scheme/3.1/BioC_3.1-dependency-tree.ditaa
2015-10-26 11:16:42 UTC (rev 20304)
+++
trunk/packages/R/r-bioc-000-dependency-scheme/3.2/BioC_3.1-dependency-tree.ditaa
2015-10-29 17:58:37 UTC (rev 20325)
@@ -1,93 +0,0 @@
-
+------------+
-
| cummerbund |
-
+------------+
-
^
-
|
-
+---+--+
-
| gviz |
-
+------+
-
^
- +-------+
|
- | edger |
+------+-----+
- +-------+
| biovizbase |
- ^
+------+-----+
- |
^
- +---+---+ +------------+ +--------+
|
- | limma | | hilbertvis | | qvalue |
+----------+--------+
- +-------+ +------------+ +--------+
| variantannotation |
- ^
+-------------------+
- :
^ ^
- :
| |
- +------+------+
+------------+----+ +-+---------+
- |cAAA go.db |
| genomicfeatures | | bsgenome |
- +-------------+ +--------------+
+-----------------+ +-----------+
- | altcdfenvs |
^ ^ ^
- +--------------+
| | |
- ^ ^ ^
| +--+-------+--+
- | | |
| | rtracklayer |
- +----------------------------------+ | |
| +-------------+
- | | |
| ^
- | +-----------++ |
+-------------+ |
- | | makecdfenv | |
+-----------+ | +----------+--------+
- | +------------+ |
+-------------------------------->| shortread |<-------|---------------+
genomicalignments |
- | ^ | |
+-----------+ | +-------------------+
- | | | |
| ^ ^
- | | | |
| | |
- | | | |
| +---------+-+ |
- | | +-------------------------+
+------------------------------------->| rsamtools | |
- | | | |
| | +-----------+ |
-+------+-----+ +-------+--+ |
+--+-----+---+ +------------+ +----+----+ | |
-| hypergraph | | affy |<-----------+ | |
biostrings | | annotate | | biomart | | |
-+------------+ +----------+ | |
+------------+ +------------+ +---------+ | |
- ^ ^ ^ ^ | |
^ ^ ^ | |
- | | | | | |
| | | | |
- +---+---+ +----------------+ | ++--------+ | |
| +------+--------+ | +----------+----+ |
- | graph | | preprocesscore | | | affyio | | |
| | annotationdbi |----+ | genomicranges | |
- +-------+ +----------------+ | +---------+ | |
| +---------------+ +---------------+ |
- ^ | | |
| ^ ^ ^ ^ |
- | | | |
| | | | | |
- | +--------+------+ | |
+------------------|-------------+ | | |
|
- | | biocinstaller | | | |
| | | | |
- | +---------------+ | | |
| +----------------------|---------------+ + |
- | | | |
| | | +---------+ |
- | | | |
| | | | |
- | | | |
+---+---+-+ +-+-----------++ |
- | | | | |
xvector | | genomeinfodb | |
- | | | |
+---------+ +--------------+ |
- | | | |
^ ^ |
- | | | |
| | |
- | +----------+ +-+--+--+-+
+---+-----+ | |
- | | multtest |<-------+ biobase | |
iranges +-------------------------+ |
- | +----------+ +---------+
+---------+ |
- | ^
^ |
- | |
| |
- +---------------------------------------------+ |
| |
- | |
| |
- | |
+--+--------+ +--------------+ |
- | |
+----------------->| s4vectors | | biocparallel
+-----------------+
- | | |
+-----------+ +--------------+
- | | |
^
- | | |
|
- | | |
+-------------------------------------------------------+
- | | | |
- +--+--+--+---+-+
+----------+
- | biocgenerics
+------------------------------------------------------------------>| snpstats |
- +--------------+
+----------+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Added:
trunk/packages/R/r-bioc-000-dependency-scheme/3.2/BioC_3.2-dependency-tree.ditaa
===================================================================
---
trunk/packages/R/r-bioc-000-dependency-scheme/3.2/BioC_3.2-dependency-tree.ditaa
(rev 0)
+++
trunk/packages/R/r-bioc-000-dependency-scheme/3.2/BioC_3.2-dependency-tree.ditaa
2015-10-29 17:58:37 UTC (rev 20325)
@@ -0,0 +1,93 @@
+
+------------+
+
| cummerbund |
+
+------------+
+
^
+
|
+
+---+--+
+
| gviz |
+
+------+
+
^
+ +-------+
|
+ | edger |
+------+-----+
+ +-------+
| biovizbase |
+ ^
+------+-----+
+ |
^
+ +---+---+ +------------+ +--------+
|
+ | limma | | hilbertvis | | qvalue |
+----------+--------+
+ +-------+ +------------+ +--------+
| variantannotation |
+ ^
+-------------------+
+ :
^ ^
+ :
| |
+ +------+------+
+------------+----+ +-+---------+
+ |cAAA go.db |
| genomicfeatures | | bsgenome |
+ +-------------+ +--------------+
+-----------------+ +-----------+
+ | altcdfenvs |
^ ^ ^
+ +--------------+
| | |
+ ^ ^ ^
| +--+-------+--+
+ | | |
| | rtracklayer |
+ +----------------------------------+ | |
| +-------------+
+ | | |
| ^
+ | +-----------++ |
+-------------+ |
+ | | makecdfenv | |
+-----------+ | +----------+--------+
+ | +------------+ |
+-------------------------------->| shortread |<-------|---------------+
genomicalignments |
+ | ^ | |
+-----------+ | +-------------------+
+ | | | |
| ^ ^
+ | | | |
| | |
+ | | | |
| +---------+-+ |
+ | | +-------------------------+
+------------------------------------->| rsamtools | |
+ | | | |
| | +-----------+ |
++------+-----+ +-------+--+ |
+--+-----+---+ +------------+ +----+----+ | |
+| hypergraph | | affy |<-----------+ | |
biostrings | | annotate | | biomart | | |
++------------+ +----------+ | |
+------------+ +------------+ +---------+ | |
+ ^ ^ ^ ^ | |
^ ^ ^ | |
+ | | | | | |
| | | | |
+ +---+---+ +----------------+ | ++--------+ | |
| +------+--------+ | +----------+----+ |
+ | graph | | preprocesscore | | | affyio | | |
| | annotationdbi |----+ | genomicranges | |
+ +-------+ +----------------+ | +---------+ | |
| +---------------+ +---------------+ |
+ ^ | | |
| ^ ^ ^ ^ |
+ | | | |
| | | | | |
+ | +--------+------+ | |
+------------------|-------------+ | | |
|
+ | | biocinstaller | | | |
| | | | |
+ | +---------------+ | | |
| +----------------------|---------------+ + |
+ | | | |
| | | +---------+ |
+ | | | |
| | | | |
+ | | | |
+---+---+-+ +-+-----------++ |
+ | | | | |
xvector | | genomeinfodb | |
+ | | | |
+---------+ +--------------+ |
+ | | | |
^ ^ |
+ | | | |
| | |
+ | +----------+ +-+--+--+-+
+---+-----+ | |
+ | | multtest |<-------+ biobase | |
iranges +-------------------------+ |
+ | +----------+ +---------+
+-------+-+ |
+ | ^
^ : |
+ | |
| : |
+ +---------------------------------------------+ |
| : |
+ | |
| v |
+ | |
+--+--------+ +--------------+ |
+ | |
+----------------->| s4vectors | | biocparallel
+-----------------+
+ | | |
+-----------+ +--------------+
+ | | |
^
+ | | |
|
+ | | |
+-------------------------------------------------------+
+ | | | |
+ +--+--+--+---+-+
+----------+
+ | biocgenerics
+------------------------------------------------------------------>| snpstats |
+ +--------------+
+----------+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Modified: trunk/packages/R/r-bioc-000-dependency-scheme/3.2/Makefile
===================================================================
--- trunk/packages/R/r-bioc-000-dependency-scheme/3.1/Makefile 2015-10-26
11:16:42 UTC (rev 20304)
+++ trunk/packages/R/r-bioc-000-dependency-scheme/3.2/Makefile 2015-10-29
17:58:37 UTC (rev 20325)
@@ -1,6 +1,6 @@
#!/usr/bin/make -f
-NAME:=BioC_3.1-dependency-tree
+NAME:=BioC_3.2-dependency-tree
all: png
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