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tille pushed a commit to branch master
in repository r-bioc-000-dependency-scheme.
commit aa64b4f19ddfd8345333aa82d8a980ffe93c1a98
Author: Andreas Tille <tille at debian.org>
Date: Thu Nov 9 11:22:56 2017 +0100
Do not keep several versions - just tag the status to match BioC version
---
2.12/BioC-dependency-tree.ditaa | 70 ----------------
3.0/BioC_3.0-dependency-tree.ditaa | 93 ---------------------
3.0/Makefile | 14 ----
3.1/BioC_3.1-dependency-tree.ditaa | 93 ---------------------
3.1/Makefile | 14 ----
3.1/todo_in_case_of_errors | 2 -
3.2/BioC_3.2-dependency-tree.ditaa | 96 ----------------------
3.2/Makefile | 14 ----
3.2/todo_in_case_of_errors | 2 -
3.3/BioC_3.3-dependency-tree.ditaa | 96 ----------------------
3.3/Makefile | 14 ----
3.4/BioC_3.4-dependency-tree.ditaa | 96 ----------------------
3.4/Makefile | 14 ----
3.5/BioC_3.5-dependency-tree.ditaa | 96 ----------------------
3.5/Makefile | 14 ----
3.6/Makefile | 14 ----
...ndency-tree.ditaa => BioC_dependency-tree.ditaa | 0
2.12/Makefile => Makefile | 2 +-
18 files changed, 1 insertion(+), 743 deletions(-)
diff --git a/2.12/BioC-dependency-tree.ditaa b/2.12/BioC-dependency-tree.ditaa
deleted file mode 100644
index 89664eb..0000000
--- a/2.12/BioC-dependency-tree.ditaa
+++ /dev/null
@@ -1,70 +0,0 @@
- +------------+
- | cummerbund |
- +------------+
- ^ ^
- | |
- +--------+ +-----------+
- | |
- +---+---+ +-----+-------+ +-----------+
- | gviz | | rtracklayer | | shortread |
- +-------+ +-------------+ +-----------+
- ^ ^ ^
- | | |
- +-----+------+ +--+-------------+--+
- +--------------+ | biovizbase |<-------------+ genomicalignments |
- | altcdfenvs | +------------+ +-------------------+
- +--------------+ ^ ^ ^
- ^ ^ ^ | | |
- | | | +-------+-----------+ +-----+----+ |
- +----------------------------------+ | | | variantannotation |<-+ | bsgenome | |
- | | | +-------------------+ | +----------+ |
- | +-----------++ | ^ ^ | ^ |
- | | makecdfenv | | | : | | |
- | +------------+ | +--------+--------+ : +--+------+-+ |
- | ^ | +------------------------------------->| genomicfeatures | : | rsamtools | |
- | | | | +-----------------+ : +-----------+ |
- | | | | ^ ^ : ^ ^ |
- | | | | | | : | | |
- | | +-------------------------+ | +-----------------------------------------------------------+ | |
- | +------+---+ | | | | | : | |
-+------+-----+ | affy | +--+--+--+---+ +----------+ +---------+ | | : | |
-| hypergraph | +----------+ | biostrings | | annotate | | biomart +-----+ | : | |
-+------------+ ^ ^ ^ ^ +------------+ +----------+ +---------+ | : | |
- ^ | | | | ^ ^ ^ | : | |
- | +-----------+ | | +-----------------+ | | | | : | |
- | | | | | | | | | : | |
- +---+---+ +------+---------+ | | | +-----+---+ +------+--------+ | | : | |
- | graph | | preprocesscore | | | | | xvector | | annotationdbi |----+ | : | |
- +-------+ +----------------+ | | | +---------+ +---------------+ | : | |
- ^ | | | ^ ^ ^ ^ | : | |
- | | | | | | | | +---------------+ : | |
- | | | | +------------------|-------------+ | | | : | |
- | +-------------+ | | | | +-------------+ | | +----------------------------+ |
- | | | | | | | | | | : |
- | +------+--------+ +---+-----+ +----+--+-+ +-----+--++ | +------+----+---+ : |
- | | biocinstaller | | affyio | | biobase | | iranges | | | genomicranges | : |
- | +---------------+ +---------+ +---------+ +---------+ | +---------------+ : |
- | ^ ^ | ^ : |
- | | | | | : |
- +---------------------------------------------+ | +-------------------+ | +---------+ : |
- | | | | | : |
- | | | +-------+--+---+ +--------------+ : |
- | | | | genomeinfodb | | biocparallel +--------------------------------------+
- | | | +--------------+ +--------------+ :
- | | | ^ :
- | | | | :
- | | | +-------------------------------------------------------+ :
- | | | | :
- +--+--+--+---+-+ +----+-----+
- | biocgenerics +------------------------------------------------------------------>| snpstats |
- +--------------+ +----------+
-
-
- +-------+
- | edger |
- +-------+
- ^
- |
-+------------+ +--------+ +---+---+
-| hilbertvis | | qvalue | | limma |
-+------------+ +--------+ +-------+
diff --git a/3.0/BioC_3.0-dependency-tree.ditaa b/3.0/BioC_3.0-dependency-tree.ditaa
deleted file mode 100644
index 52878bb..0000000
--- a/3.0/BioC_3.0-dependency-tree.ditaa
+++ /dev/null
@@ -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 | |cAAA annotate | | biomart | | |
-+------------+ +----------+ | | +------------+ +--------------+ +---------+ | |
- ^ ^ ^ ^ | | ^ ^ ^ | |
- | | | | | | | | | | |
- +---+---+ +----------------+ | ++--------+ | | | +------+--------+ | +----------+----+ |
- | graph | | preprocesscore | | | affyio | | | | | annotationdbi |----+ | genomicranges | |
- +-------+ +----------------+ | +---------+ | | | +---------------+ +---------------+ |
- ^ | | | | ^ ^ ^ ^ |
- | | | | | | | | | |
- | | | | +------------------|-------------+ | | | |
- | | | | | | | | | |
- | | | | | | +----------------------|---------------+ + |
- | | | | | | | | +---------+ |
- | | | | | | | | | |
- | | | | | +---+---+-+ +-+-----------++ |
- | | | | | | xvector | | genomeinfodb | |
- | | | | | +---------+ +--------------+ |
- | | | | | ^ ^ |
- | | | | | | | |
- | +---------------+ +-+--+--+-+ +---+-----+ | |
- | | biocinstaller | | biobase | | iranges +-------------------------+ |
- | +---------------+ +---------+ +---------+ |
- | ^ ^ |
- | | | |
- +---------------------------------------------+ | | |
- | | | |
- | | +--+--------+ +--------------+ |
- | | +----------------->| s4vectors | | biocparallel +-----------------+
- | | | +-----------+ +--------------+
- | | | ^
- | | | |
- | | | +-------------------------------------------------------+
- | | | |
- +--+--+--+---+-+ +----------+
- | biocgenerics +------------------------------------------------------------------>| snpstats |
- +--------------+ +----------+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/3.0/Makefile b/3.0/Makefile
deleted file mode 100644
index 76d4eac..0000000
--- a/3.0/Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/make -f
-
-NAME:=BioC_3.0-dependency-tree
-
-all: png
-
-png: $(NAME).png
-
-%.png: %.ditaa
- rm -f $@
- ditaa $^
-
-clean:
- rm -f $(NAME).png
diff --git a/3.1/BioC_3.1-dependency-tree.ditaa b/3.1/BioC_3.1-dependency-tree.ditaa
deleted file mode 100644
index 9d1a20b..0000000
--- a/3.1/BioC_3.1-dependency-tree.ditaa
+++ /dev/null
@@ -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 |
- +--------------+ +----------+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/3.1/Makefile b/3.1/Makefile
deleted file mode 100644
index c03605f..0000000
--- a/3.1/Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/make -f
-
-NAME:=BioC_3.1-dependency-tree
-
-all: png
-
-png: $(NAME).png
-
-%.png: %.ditaa
- rm -f $@
- ditaa $^
-
-clean:
- rm -f $(NAME).png
diff --git a/3.1/todo_in_case_of_errors b/3.1/todo_in_case_of_errors
deleted file mode 100644
index d3cda8e..0000000
--- a/3.1/todo_in_case_of_errors
+++ /dev/null
@@ -1,2 +0,0 @@
-Please send us your sessionInfo() after loading <BioC-Module>. You might also try
-BiocInstaller::biocValid()
diff --git a/3.2/BioC_3.2-dependency-tree.ditaa b/3.2/BioC_3.2-dependency-tree.ditaa
deleted file mode 100644
index 9e97c13..0000000
--- a/3.2/BioC_3.2-dependency-tree.ditaa
+++ /dev/null
@@ -1,96 +0,0 @@
- +------------+
- | cummerbund |
- +------------+
- ^
- |
- +---+--+
- | gviz |
- +------+
- ^
- +-------+ |
- | edger | +------+-----+
- +-------+ | biovizbase |
- ^ +------+-----+
- | ^
- +---+---+ +------------+ +--------+ |
- | limma | | hilbertvis | | qvalue | +----------+--------+
- +-------+ +------------+ +--------+ | variantannotation |
- ^ +-------------------+
- : ^ ^
- : | |
- +------+------+ +------------+----+ +-+---------+
- |cAAA go.db | | genomicfeatures | | bsgenome |
- +-------------+ +--------------+ +-----------------+ +-----------+
- | altcdfenvs | ^ ^ ^
- +--------------+ | | |
- ^ ^ ^ | +--+-------+--+
- | | | | | rtracklayer |
- +----------------------------------+ | | | +-------------+
- | | | | ^
- | +-----------++ | +-------------+ |
- | | makecdfenv | | +-----------+ | +----------+--------+
- | +------------+ | +----------------------->| shortread |<-------|---------------+ genomicalignments |
- | ^ | | +-----------+ | +-------------------+
- | | | | | ^ ^
- | | | | | | |
- | | | | | +-----------+--+ +--------+-------------+
- | | +----------------+ +---------------------------------->| rsamtools | | summarizedexperiment |
- | | | | | | +--------------+ +----------------------+
- | | | | | | ^ ^: ^ ^
- | | | | | | | |: : |
- | | | | | +=============|=========|========|:======+ |
- | | | | | : | | |: |
-+------+-----+ +-------+--+ | +--+-----+---+ +--------+---+ +------+--+ | |: |
-| hypergraph | | affy |<-----------+ | | biostrings | | annotate | | biomart | | |: |
-+------------+ +----------+ | | +------------+ +------------+ +---------+ | |: |
- ^ ^ ^ ^ | | ^ ^ ^ | |: |
- | | | | | | | | | | |: |
- +---+---+ +----------------+ | ++--------+ | | | +--+----------+-+ +--------+------+ |: |
- | graph | | preprocesscore | | | affyio | | | | | annotationdbi | | genomicranges | |: |
- +-------+ +----------------+ | +---------+ | | | +---------------+ +---------------+ |: |
- ^ | | | | ^ ^ ^ ^ |: |
- | | | | | | | | | |: |
- | +--------+------+ | | +---------|-----------------+ | | | |: |
- | | biocinstaller | | | | | | | | |: |
- | +---------------+ | | | | +----------------------|--------+ | |: |
- | | | | | | | | |: |
- | | | | +---+---+-+ +-+-----------++ |: |
- | | | | | xvector | | genomeinfodb | |: |
- | | | | +---------+ +--------------+ |: |
- | | | | ^ ^ |: |
- | | | | | | |: |
- | +----------+ | | | +---+-----+ | |: |
- | | multtest | | | | | iranges +-------------------------+ |: |
- | +----------+ | | | +-----+---+ |: |
- | ^ | | | ^ : |: |
- | | +-+--+--+-+ | : |: |
- | +--------------+ biobase +-------|-:-------------------------------------------------|:-----------+
- | +---------+ | v |v
- | ^ +---+-------+ +---------+----+
- | | +----->| s4vectors | | biocparallel |
- | | | +-----------+ +--------------+
- | | | ^
- | | | |
- | | | +---------------------------------------------------+
- | | | |
- | +-----+--+---+-+ +----------+
- +------------------------------------------+ biocgenerics +------------------------------------------------------------------>| snpstats |
- +--------------+ +----------+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/3.2/Makefile b/3.2/Makefile
deleted file mode 100644
index 70d1a0b..0000000
--- a/3.2/Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/make -f
-
-NAME:=BioC_3.2-dependency-tree
-
-all: png
-
-png: $(NAME).png
-
-%.png: %.ditaa
- rm -f $@
- ditaa $^
-
-clean:
- rm -f $(NAME).png
diff --git a/3.2/todo_in_case_of_errors b/3.2/todo_in_case_of_errors
deleted file mode 100644
index d3cda8e..0000000
--- a/3.2/todo_in_case_of_errors
+++ /dev/null
@@ -1,2 +0,0 @@
-Please send us your sessionInfo() after loading <BioC-Module>. You might also try
-BiocInstaller::biocValid()
diff --git a/3.3/BioC_3.3-dependency-tree.ditaa b/3.3/BioC_3.3-dependency-tree.ditaa
deleted file mode 100644
index eb422fd..0000000
--- a/3.3/BioC_3.3-dependency-tree.ditaa
+++ /dev/null
@@ -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 |
- +--------------+ +----------+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/3.3/Makefile b/3.3/Makefile
deleted file mode 100644
index ab92f9d..0000000
--- a/3.3/Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/make -f
-
-NAME:=BioC_3.3-dependency-tree
-
-all: png
-
-png: $(NAME).png
-
-%.png: %.ditaa
- rm -f $@
- ditaa $^
-
-clean:
- rm -f $(NAME).png
diff --git a/3.4/BioC_3.4-dependency-tree.ditaa b/3.4/BioC_3.4-dependency-tree.ditaa
deleted file mode 100644
index eb422fd..0000000
--- a/3.4/BioC_3.4-dependency-tree.ditaa
+++ /dev/null
@@ -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 |
- +--------------+ +----------+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/3.4/Makefile b/3.4/Makefile
deleted file mode 100644
index cbb89a2..0000000
--- a/3.4/Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/make -f
-
-NAME:=BioC_3.4-dependency-tree
-
-all: png
-
-png: $(NAME).png
-
-%.png: %.ditaa
- rm -f $@
- ditaa $^
-
-clean:
- rm -f $(NAME).png
diff --git a/3.5/BioC_3.5-dependency-tree.ditaa b/3.5/BioC_3.5-dependency-tree.ditaa
deleted file mode 100644
index b0ccb76..0000000
--- a/3.5/BioC_3.5-dependency-tree.ditaa
+++ /dev/null
@@ -1,96 +0,0 @@
- +-------+ +------------+
- | edger | | cummerbund |
- +-------+ +------------+
- ^ ^
- | |
- +---+---+ +------------+ +--------+ +---+--+
- | limma | | hilbertvis | | qvalue | | gviz |
- +-------+ +------------+ +--------+ +------+
- ^ ^
- : |
- : +---------------+ +------+-----+
- +------+------+ | ensembldb +---------------------->| biovizbase |
- |cAAA go.db | +---------------+ +------+-----+
- +-------------+ ^ ^
- | |
- +--------------+ +-------+-------+ +-+----------------+ +----------+--------+
- | protgenerics +------------------------------>| annotationhub |<-----+ annotationfilter | | 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 |
- +--------------+ +----------+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/3.5/Makefile b/3.5/Makefile
deleted file mode 100644
index 82c8cfa..0000000
--- a/3.5/Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/make -f
-
-NAME:=BioC_3.5-dependency-tree
-
-all: png
-
-png: $(NAME).png
-
-%.png: %.ditaa
- rm -f $@
- ditaa $^
-
-clean:
- rm -f $(NAME).png
diff --git a/3.6/Makefile b/3.6/Makefile
deleted file mode 100644
index 95a24cb..0000000
--- a/3.6/Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/make -f
-
-NAME:=BioC_3.6-dependency-tree
-
-all: png
-
-png: $(NAME).png
-
-%.png: %.ditaa
- rm -f $@
- ditaa $^
-
-clean:
- rm -f $(NAME).png
diff --git a/3.6/BioC_3.6-dependency-tree.ditaa b/BioC_dependency-tree.ditaa
similarity index 100%
rename from 3.6/BioC_3.6-dependency-tree.ditaa
rename to BioC_dependency-tree.ditaa
diff --git a/2.12/Makefile b/Makefile
similarity index 80%
rename from 2.12/Makefile
rename to Makefile
index 76d44d0..5c9ce79 100644
--- a/2.12/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
#!/usr/bin/make -f
-NAME:=BioC-dependency-tree
+NAME:=BioC_dependency-tree
all: png
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-000-dependency-scheme.git