[med-svn] r24420 - in trunk/packages/R/r-bioc-000-dependency-scheme: . 3.4

Andreas Tille tille at moszumanska.debian.org
Thu Oct 19 20:20:25 UTC 2017


Author: tille
Date: 2017-10-19 20:20:24 +0000 (Thu, 19 Oct 2017)
New Revision: 24420

Added:
   trunk/packages/R/r-bioc-000-dependency-scheme/3.4/
   trunk/packages/R/r-bioc-000-dependency-scheme/3.4/BioC_3.4-dependency-tree.ditaa
Removed:
   trunk/packages/R/r-bioc-000-dependency-scheme/3.4/BioC_3.3-dependency-tree.ditaa
Modified:
   trunk/packages/R/r-bioc-000-dependency-scheme/3.4/Makefile
Log:
Dependency scheme for version 3.4


Deleted: trunk/packages/R/r-bioc-000-dependency-scheme/3.4/BioC_3.3-dependency-tree.ditaa
===================================================================
--- trunk/packages/R/r-bioc-000-dependency-scheme/3.3/BioC_3.3-dependency-tree.ditaa	2017-10-18 19:32:34 UTC (rev 24389)
+++ trunk/packages/R/r-bioc-000-dependency-scheme/3.4/BioC_3.3-dependency-tree.ditaa	2017-10-19 20:20:24 UTC (rev 24420)
@@ -1,96 +0,0 @@
-    +-------+                                                                                                               +------------+
-    | edger |                                                                                                               | cummerbund |
-    +-------+                                                                                                               +------------+
-        ^	                                                                                                                   ^
-        |	                                                                                                                   |
-    +---+---+   +------------+    +--------+                                                                                   +---+--+
-    | limma |   | hilbertvis |    | qvalue |                                                                                   | gviz |
-    +-------+   +------------+    +--------+                                                                                   +------+
-        ^	                                                                                                                   ^
-        :	                                                                                                                   |
-        :	                                                                    +-----------+                           +------+-----+
- +------+------+                                                                    | ensembldb +-------------------------->| biovizbase |
- |cAAA go.db   |                                                                    +-----------+                           +------+-----+
- +-------------+                                                                          ^                                        ^
-                                                                                          |                                        |
-                                                                                  +-------+-------+                     +----------+--------+
-              +------------------------------------------------------------------>| annotationhub |                     | variantannotation |
-              |                                                                   +---------------+                     +-------------------+
-              |                                                                        ^       ^                            ^          ^
-              |                                                                        |       |                            |          |
-              |                                                                        |       |               +------------+----+   +-+---------+
-              |                                                                        |       |               | genomicfeatures |   |  bsgenome |
- +------------+-----------+       +--------------+                                     |       |               +-----------------+   +-----------+
- | interactivedisplaybase |       |  altcdfenvs  |                                     |       |                     ^        ^       ^
- +------------------------+       +--------------+                                     |       |                     |        |       |
-       ^                             ^  ^    ^                                         |       |                     |     +--+-------+--+
-       |                             |  |    |                                         |       |                     |     | rtracklayer |
-       |    +------------------------+  |    |   +-------------------------------------+       |                     |     +-------------+
-       |    |                           |    |   |                                             |                     |            ^
-       |    |               +-----------++   |   |                                             |       +-------------+            |
-       |    |               | makecdfenv |   |   |                             +-----------+   |       |               +----------+--------+
-       |    |               +------------+   |   |       +-------------------->| shortread |<----------|---------------+ genomicalignments |
-       |    |                         ^      |   |       |                     +-----------+   |       |               +-------------------+
-       |    |                         |      |   |       |                                     |       |                 ^             ^
-       |    |                         |      |   |       |                                     |       |                 |             |
-       |    |                         |      |   |       |                                     |       |       +-----------+--+ +--------+-------------+
-       |    |                         |      +---------------------+     +------------------------------------>|   rsamtools  | | summarizedexperiment |
-       |    |                         |          |       |         |     |                     |       |       +--------------+ +----------------------+
-       |    |                         |          |       |         |     |                     |       |         ^         ^:      ^    ^   ^
-       |    |                         |          |       |         |     |                     |       |         |         |:      :    |   |
-       |    |                         |          |       |         |     |               +=====|=======|=========|=========|:======+    |   |
-       |    |                         |          |       |         |     |               :     |       |         |         |:           |   |
-       |    |                 +-------+--+       |       |      +--+-----+---+  +--------+---+ | +-----+---+     |         |:           |   |
-       |    |                 |   affy   |<-----------+  |      | biostrings |  |  annotate  | | | biomart |     |         |:           |   |
-       |    |                 +----------+       |    |  |      +------------+  +------------+ | +---------+     |         |:           |   |
-       |    |                  ^  ^   ^          |    |  |            ^                  ^     |    ^            |         |:           |   |
-       |    |                  |  |   |          |    |  |            |                  |     |    |            |         |:           |   |
-       |    | +----------------+  |  ++--------+ |    |  |            |               +--+-----+----+-+ +--------+------+  |:           |   |
-       |    | | preprocesscore |  |  | affyio  | |    |  |            |               | annotationdbi | | genomicranges +--|:-----------+   |
-       |    | +----------------+  |  +---------+ |    |  |            |               +---------------+ +---------------+  |:               |
-       |    |                     |              |    |  |            |                 ^        ^        ^  ^             |:               |
-       |    |                     |              |    |  |            |                 |        |        |  |             |:               |
-       |    |                    ++--------------+-+  |  |  +---------|-----------------+        |        |  |             |:               |
-       |    |                    |  biocinstaller  |  |  |  |         |                          |        |  |             |:               |
-       |    |                    +-----------------+  |  |  |         |   +----------------------|--------+  |             |:               |
-       |    |                                         |  |  |         |   |                      |           |             |:               |
-       |    |                                         |  |  |     +---+---+-+                  +-+-----------++            |:               |
-       |    |                                         |  |  |     | xvector |                  | genomeinfodb |            |:               |
-       |    |                                         |  |  |     +---------+                  +--------------+            |:               |
-       |    |                                         |  |  |         ^                               ^                    |:               |
-       |    |                                         |  |  |         |                               |                    |:               |
-       |   ++-----------+       +----------+          |  |  |     +---+-----+                         |                    |:               |
-       |   | hypergraph |       | multtest |          |  |  |     | iranges +-------------------------+                    |:               |
-       |   +------------+       +----------+          |  |  |     +-----+---+                                              |:               |
-       |          ^                  ^                |  |  |         ^ :                                                  |:               |
-       |          |                  |              +-+--+--+-+       | :                                                  |:               |
-       |          |                  +--------------+ biobase +-------|-:--------------------------------------------------|:---------------+
-       |          |                                 +---------+       | v                                                  |v
-       |      +---+---+                                 ^         +---+-------+                                 +----------+---+
-       |      | graph |<-----------------------------+  |  +----->| s4vectors |                                 | biocparallel |
-       |      +-------+                              |  |  |      +-----------+                                 +--------------+
-       |                                             |  |  |                                                       ^                   
-       |                                             |  |  |                                                       |                   
-       |                                             |  |  |   +---------------------------------------------------+                   
-       |                                             |  |  |   |                                                                     
-       |                                          +--+--+--+---+-+                                                                   +----------+
-       +------------------------------------------+ biocgenerics +------------------------------------------------------------------>| snpstats |
-                                                  +--------------+                                                                   +----------+
-
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Copied: trunk/packages/R/r-bioc-000-dependency-scheme/3.4/BioC_3.4-dependency-tree.ditaa (from rev 24389, trunk/packages/R/r-bioc-000-dependency-scheme/3.3/BioC_3.3-dependency-tree.ditaa)
===================================================================
--- trunk/packages/R/r-bioc-000-dependency-scheme/3.4/BioC_3.4-dependency-tree.ditaa	                        (rev 0)
+++ trunk/packages/R/r-bioc-000-dependency-scheme/3.4/BioC_3.4-dependency-tree.ditaa	2017-10-19 20:20:24 UTC (rev 24420)
@@ -0,0 +1,96 @@
+    +-------+                                                                                                               +------------+
+    | edger |                                                                                                               | cummerbund |
+    +-------+                                                                                                               +------------+
+        ^	                                                                                                                   ^
+        |	                                                                                                                   |
+    +---+---+   +------------+    +--------+                                                                                   +---+--+
+    | limma |   | hilbertvis |    | qvalue |                                                                                   | gviz |
+    +-------+   +------------+    +--------+                                                                                   +------+
+        ^	                                                                                                                   ^
+        :	                                                                                                                   |
+        :	                                                                    +-----------+                           +------+-----+
+ +------+------+                                                                    | ensembldb +-------------------------->| biovizbase |
+ |cAAA go.db   |                                                                    +-----------+                           +------+-----+
+ +-------------+                                                                          ^                                        ^
+                                                                                          |                                        |
+                                                                                  +-------+-------+                     +----------+--------+
+              +------------------------------------------------------------------>| annotationhub |                     | variantannotation |
+              |                                                                   +---------------+                     +-------------------+
+              |                                                                        ^       ^                            ^          ^
+              |                                                                        |       |                            |          |
+              |                                                                        |       |               +------------+----+   +-+---------+
+              |                                                                        |       |               | genomicfeatures |   |  bsgenome |
+ +------------+-----------+       +--------------+                                     |       |               +-----------------+   +-----------+
+ | interactivedisplaybase |       |  altcdfenvs  |                                     |       |                     ^        ^       ^
+ +------------------------+       +--------------+                                     |       |                     |        |       |
+       ^                             ^  ^    ^                                         |       |                     |     +--+-------+--+
+       |                             |  |    |                                         |       |                     |     | rtracklayer |
+       |    +------------------------+  |    |   +-------------------------------------+       |                     |     +-------------+
+       |    |                           |    |   |                                             |                     |            ^
+       |    |               +-----------++   |   |                                             |       +-------------+            |
+       |    |               | makecdfenv |   |   |                             +-----------+   |       |               +----------+--------+
+       |    |               +------------+   |   |       +-------------------->| shortread |<----------|---------------+ genomicalignments |
+       |    |                         ^      |   |       |                     +-----------+   |       |               +-------------------+
+       |    |                         |      |   |       |                                     |       |                 ^             ^
+       |    |                         |      |   |       |                                     |       |                 |             |
+       |    |                         |      |   |       |                                     |       |       +-----------+--+ +--------+-------------+
+       |    |                         |      +---------------------+     +------------------------------------>|   rsamtools  | | summarizedexperiment |
+       |    |                         |          |       |         |     |                     |       |       +--------------+ +----------------------+
+       |    |                         |          |       |         |     |                     |       |         ^         ^:      ^    ^   ^
+       |    |                         |          |       |         |     |                     |       |         |         |:      :    |   |
+       |    |                         |          |       |         |     |               +=====|=======|=========|=========|:======+    |   |
+       |    |                         |          |       |         |     |               :     |       |         |         |:           |   |
+       |    |                 +-------+--+       |       |      +--+-----+---+  +--------+---+ | +-----+---+     |         |:           |   |
+       |    |                 |   affy   |<-----------+  |      | biostrings |  |  annotate  | | | biomart |     |         |:           |   |
+       |    |                 +----------+       |    |  |      +------------+  +------------+ | +---------+     |         |:           |   |
+       |    |                  ^  ^   ^          |    |  |            ^                  ^     |    ^            |         |:           |   |
+       |    |                  |  |   |          |    |  |            |                  |     |    |            |         |:           |   |
+       |    | +----------------+  |  ++--------+ |    |  |            |               +--+-----+----+-+ +--------+------+  |:           |   |
+       |    | | preprocesscore |  |  | affyio  | |    |  |            |               | annotationdbi | | genomicranges +--|:-----------+   |
+       |    | +----------------+  |  +---------+ |    |  |            |               +---------------+ +---------------+  |:               |
+       |    |                     |              |    |  |            |                 ^        ^        ^  ^             |:               |
+       |    |                     |              |    |  |            |                 |        |        |  |             |:               |
+       |    |                    ++--------------+-+  |  |  +---------|-----------------+        |        |  |             |:               |
+       |    |                    |  biocinstaller  |  |  |  |         |                          |        |  |             |:               |
+       |    |                    +-----------------+  |  |  |         |   +----------------------|--------+  |             |:               |
+       |    |                                         |  |  |         |   |                      |           |             |:               |
+       |    |                                         |  |  |     +---+---+-+                  +-+-----------++            |:               |
+       |    |                                         |  |  |     | xvector |                  | genomeinfodb |            |:               |
+       |    |                                         |  |  |     +---------+                  +--------------+            |:               |
+       |    |                                         |  |  |         ^                               ^                    |:               |
+       |    |                                         |  |  |         |                               |                    |:               |
+       |   ++-----------+       +----------+          |  |  |     +---+-----+                         |                    |:               |
+       |   | hypergraph |       | multtest |          |  |  |     | iranges +-------------------------+                    |:               |
+       |   +------------+       +----------+          |  |  |     +-----+---+                                              |:               |
+       |          ^                  ^                |  |  |         ^ :                                                  |:               |
+       |          |                  |              +-+--+--+-+       | :                                                  |:               |
+       |          |                  +--------------+ biobase +-------|-:--------------------------------------------------|:---------------+
+       |          |                                 +---------+       | v                                                  |v
+       |      +---+---+                                 ^         +---+-------+                                 +----------+---+
+       |      | graph |<-----------------------------+  |  +----->| s4vectors |                                 | biocparallel |
+       |      +-------+                              |  |  |      +-----------+                                 +--------------+
+       |                                             |  |  |                                                       ^                   
+       |                                             |  |  |                                                       |                   
+       |                                             |  |  |   +---------------------------------------------------+                   
+       |                                             |  |  |   |                                                                     
+       |                                          +--+--+--+---+-+                                                                   +----------+
+       +------------------------------------------+ biocgenerics +------------------------------------------------------------------>| snpstats |
+                                                  +--------------+                                                                   +----------+
+
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Modified: trunk/packages/R/r-bioc-000-dependency-scheme/3.4/Makefile
===================================================================
--- trunk/packages/R/r-bioc-000-dependency-scheme/3.3/Makefile	2017-10-18 19:32:34 UTC (rev 24389)
+++ trunk/packages/R/r-bioc-000-dependency-scheme/3.4/Makefile	2017-10-19 20:20:24 UTC (rev 24420)
@@ -1,6 +1,6 @@
 #!/usr/bin/make -f
 
-NAME:=BioC_3.3-dependency-tree
+NAME:=BioC_3.4-dependency-tree
 
 all: png
 




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