Revert "Bioconda utils r 3 3 1 from Ryan with fixed UID"

README.md

@@ -1,3 +1,4 @@
+
 ![](https://raw.githubusercontent.com/bioconda/bioconda-recipes/master/logo/bioconda_monochrome_small.png
  "Bioconda")
 
@@ -37,14 +38,12 @@ prerequisites are assumed:
   recommended.
 - [`docker`](https://www.docker.com/)
 - [`git`](https://git-scm.com/)
-- [`bioconda-utils](https://github.com/bioconda/bioconda-utils)
 
 ### Step 1: Create a new recipe
 
 Fork this repository or create a new branch to work in. Within the new branch,
 [create a recipe](http://conda.pydata.org/docs/building/build.html)
-(`your_package` in this example) in the `recipes` directory. See our
-[guidelines](GUIDELINES.md) for best practices and examples.
+(`your_package` in this example) in the `recipes` directory. See our [guidelines](GUIDELINES.md) for best practices and examples.
 
 ### Step 2: Test the recipe
 
@@ -59,22 +58,19 @@ Bioconductor packages will be built using:
 
     conda build recipes/your_package --channel bioconda --channel r
 
-Then, you can test it using the `bioconda-utils` tools. This should work
-whether on OSX or Linux:
+Then, you can test it in the docker container with:
 
-    bioconda-utils build recipes config.yml --package your_package
+    docker run -v `pwd`:/bioconda-recipes bioconda/bioconda-builder --packages your_package --env-matrix /bioconda-recipes/scripts/env_matrix.yml
 
-Adding the `--docker` flag will build your package using a CentOS 5 Docker
-container to maximize compatibility. This will automatically export your conda
-build directory to the container, so that any packages you build will be
-accessible to your machine even when not running in a Docker container:
+To optionally build for a specific Python version, provide the `CONDA_PY`
+environmental variable. For example, to build specifically for Python 3.4:
 
-    bioconda-utils build recipes config.yml --package your_package --docker
+    docker run -e CONDA_PY=34 -v `pwd`:/bioconda-recipes bioconda/bioconda-builder --packages your_package --env-matrix /bioconda-recipes/scripts/env_matrix.yml
 
 To optionally build and test all packages (if they don't already exist), leave off the
 package name:
 
-    bioconda-utils build recipes config.yml --docker
+    docker run -v `pwd`:/tmp/conda-recipes bioconda/bioconda-builder --env-matrix /bioconda-recipes/scripts/env_matrix.yml
 
 If rebuilding a previously-built package and the version number hasn't changed,
 be sure to increment the build number in `meta.yaml` (the default build number
@@ -117,11 +113,9 @@ For other styles, replace ``?style=flat-square`` with ``?style=flat`` or
 
 ### Building packages for Mac OSX
 **By default, recipes will be built for both Linux and OSX**
-(see "The bioconda build system" section below) upon submitting a pull request.
-Many recipes build cleanly on Linux but not on OSX. The easiest way to find out
-is to let the travis-ci tests try building for both platforms. If it fails on
-OSX but not Linux, the easy fix is to explicitly skip the OSX build using
-a [platform-specific
+(see "The bioconda build system" section below) upon submitting
+a pull request. Many recipes build cleanly on Linux but not on OSX. The easy
+fix is to explicitly skip the OSX build using a [platform-specific
 selector](http://conda.pydata.org/docs/building/meta-yaml.html#skipping-builds)
 on a line in the `meta.yaml` that skips the build, like this:
 
@@ -147,7 +141,7 @@ To test all OSX recipes (skipping those that define `skip: True #[osx]`) use
 the following from the top-level dir:
 
 ```bash
-bioconda-utils build recipes config.yml
+scripts/build-packages.py --repository . --env-matrix scripts/env_matrix.yml
 ```
 
 ### Managing multiple versions of a package
@@ -170,16 +164,25 @@ updated when new releases are made.
 
 ### Other notes
 
-We use the docker container `continuumio/conda_builder_linux` pre-built CentOS
-5 image with compilers installed as part of the standard build. To debug
-a recipe in this container, run it in interactive mode while exporting the
-recipes directory to the `/home/dev/recipes` dir in the container:
+We use a pre-built CentOS 5 image with compilers installed as part of the
+standard build. To build this yourself, you can do:
+
+```bash
+docker login
+(cd scripts && docker build -t bioconda/bioconda-builder .)
+```
 
+Then test a recipe with:
 
 ```bash
-docker run -it --rm -v `pwd`/recipes:/home/dev/recipes continuumio/conda_builder_linux /bin/bash /opt/share/internal_startup.sh
+docker run -v `pwd`:/bioconda-recipes bioconda/bioconda-builder --packages your_package
 ```
 
+If you wish the open a bash shell in the Docker container for manual debugging:
+
+```bash
+docker run -i -t --entrypoint /bin/bash bioconda/bioconda-builder
+```
 
 ## The bioconda build system
 This repository is set up on [Travis CI](https://travis-ci.org) such that on

r-blacklist

@@ -1,21 +1,16 @@
-recipes/bioconductor-summarizedexperiment
-recipes/bioconductor-deseq2
-recipes/bioconductor-xcms
-recipes/bioconductor-genelendatabase
-recipes/bioconductor-camera
 recipes/bcbio-rnaseq
 recipes/bioconductor-affy
 recipes/bioconductor-affyio
 recipes/bioconductor-annotate
 recipes/bioconductor-annotationdbi
 recipes/bioconductor-annotationforge
 recipes/bioconductor-basic4cseq
-#recipes/bioconductor-biobase
-#recipes/bioconductor-biocgenerics
-#recipes/bioconductor-biocinstaller
+recipes/bioconductor-biobase
+recipes/bioconductor-biocgenerics
+recipes/bioconductor-biocinstaller
 recipes/bioconductor-biocparallel
-#recipes/bioconductor-biocstyle
-#recipes/bioconductor-biomart
+recipes/bioconductor-biocstyle
+recipes/bioconductor-biomart
 recipes/bioconductor-biosigner
 recipes/bioconductor-biostrings
 recipes/bioconductor-biovizbase
@@ -130,7 +125,7 @@ recipes/bioconductor-rsubread
 recipes/bioconductor-rtracklayer
 recipes/bioconductor-s4vectors
 recipes/bioconductor-s4vectors/0.8.7
-#recipes/bioconductor-seqlogo
+recipes/bioconductor-seqlogo
 recipes/bioconductor-seqpattern
 recipes/bioconductor-shortread
 recipes/bioconductor-siggenes
@@ -170,7 +165,7 @@ recipes/r-beanplot
 recipes/r-bh
 recipes/r-biasedurn/1.07
 recipes/r-bio3d
-#recipes/r-biom
+recipes/r-biom
 recipes/r-bit
 recipes/r-bit64
 recipes/r-blockmodeling

recipes/bioconductor-affy/meta.yaml

@@ -1,11 +1,12 @@
 package:
   name: bioconductor-affy
-  version: 1.50.0
+  version: 1.48.0
 source:
-  fn: affy_1.50.0.tar.gz
-  url: https://bioarchive.galaxyproject.org/affy_1.50.0.tar.gz
-  md5: aed20ee9653de3ef15868b7e6fd901de
+  fn: affy_1.48.0.tar.gz
+  url: http://bioconductor.org/packages/release/bioc/src/contrib/affy_1.48.0.tar.gz
+  md5: 12e56364b33d2c72547d170ffb7284fc
 build:
+  skip: False
   number: 0
   rpaths:
     - lib/R/lib/

recipes/bioconductor-affyio/meta.yaml

@@ -1,12 +1,12 @@
 package:
   name: bioconductor-affyio
-  version: 1.42.0
+  version: 1.40.0
 source:
-  fn: affyio_1.42.0.tar.gz
-  url: https://bioarchive.galaxyproject.org/affyio_1.42.0.tar.gz
-  md5: aa52c3eacb3401eaf7bdaefea62e6c06
+  fn: affyio_1.40.0.tar.gz
+  url: https://bioarchive.galaxyproject.org/affyio_1.40.0.tar.gz
+  md5: 21a5d31c266ace9f13f448e8fe5eb608
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

recipes/bioconductor-annotate/meta.yaml

@@ -1,12 +1,13 @@
 package:
   name: bioconductor-annotate
-  version: 1.50.0
+  version: 1.48.0
 source:
-  fn: annotate_1.50.0.tar.gz
-  url: https://bioarchive.galaxyproject.org/annotate_1.50.0.tar.gz
-  md5: 917d5e8134e7137218dcb1fd0f6a73f2
+  fn: annotate_1.48.0.tar.gz
+  url: https://bioarchive.galaxyproject.org/annotate_1.48.0.tar.gz
+  md5: f42ea2231d1858f3d0f587cc44562898
 build:
-  number: 0
+  skip: False
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

recipes/bioconductor-annotationdbi/meta.yaml

@@ -1,10 +1,10 @@
 package:
   name: bioconductor-annotationdbi
-  version: 1.34.4
+  version: 1.32.3
 source:
-  fn: AnnotationDbi_1.34.4.tar.gz
-  url: http://bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.34.4.tar.gz
-  md5: 54359883348d6288189afb85be958990
+  fn: AnnotationDbi_1.32.3.tar.gz
+  url: http://bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.32.3.tar.gz
+  md5: f1d5c71bbdaaa0a9c224a4df0a5af4f8
 build:
   number: 0
   rpaths:
@@ -15,15 +15,15 @@ requirements:
     - 'bioconductor-biobase >=1.17.0'
     - 'bioconductor-biocgenerics >=0.15.10'
     - bioconductor-iranges
-    - 'bioconductor-s4vectors >=0.9.25'
+    - bioconductor-s4vectors
     - 'r >=2.7.0'
     - r-dbi
     - r-rsqlite
   run:
     - 'bioconductor-biobase >=1.17.0'
     - 'bioconductor-biocgenerics >=0.15.10'
     - bioconductor-iranges
-    - 'bioconductor-s4vectors >=0.9.25'
+    - bioconductor-s4vectors
     - 'r >=2.7.0'
     - r-dbi
     - r-rsqlite

recipes/bioconductor-annotationforge/build.sh

@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # R refuses to build packages that mark themselves as
@@ -14,4 +13,4 @@ $R CMD INSTALL --build .
 # http://docs.continuum.io/conda/build.html
 # for a list of environment variables that are set during the build
 # process.
-# 
+# 

recipes/bioconductor-annotationforge/meta.yaml

@@ -1,39 +1,43 @@
 package:
   name: bioconductor-annotationforge
-  version: 1.14.2
+  version: 1.12.2
+
 source:
-  fn: AnnotationForge_1.14.2.tar.gz
-  url: http://bioconductor.org/packages/release/bioc/src/contrib/AnnotationForge_1.14.2.tar.gz
-  md5: 7a4ce57b476f58367b8807d2a7e96c04
+  fn: AnnotationForge_1.12.2.tar.gz
+  url: http://bioconductor.org/packages/release/bioc/src/contrib/AnnotationForge_1.12.2.tar.gz
+  md5: 23ec60f94fca10497bbfe1ecf3ab866f
+
 build:
   number: 0
   rpaths:
     - lib/R/lib/
     - lib/
+
 requirements:
   build:
-    - 'bioconductor-annotationdbi >=1.33.14'
+    - 'bioconductor-annotationdbi >=1.31.19'
     - 'bioconductor-biobase >=1.17.0'
     - 'bioconductor-biocgenerics >=0.15.10'
+    - bioconductor-org.hs.eg.db
     - bioconductor-s4vectors
     - 'r >=2.7.0'
     - r-dbi
     - r-rsqlite
-    - r-xml
   run:
-    - 'bioconductor-annotationdbi >=1.33.14'
+    - 'bioconductor-annotationdbi >=1.31.19'
     - 'bioconductor-biobase >=1.17.0'
     - 'bioconductor-biocgenerics >=0.15.10'
+    - bioconductor-org.hs.eg.db
     - bioconductor-s4vectors
     - 'r >=2.7.0'
     - r-dbi
     - r-rsqlite
-    - r-xml
+
 test:
   commands:
     - '$R -e "library(''AnnotationForge'')"'
+
 about:
   home: http://bioconductor.org/packages/release/bioc/html/AnnotationForge.html
   license: Artistic-2.0
-  summary: 'Provides code for generating Annotation packages and their databases.  Packages
-    produced are intended to be used with AnnotationDbi.'
+  summary: 'Provides code for generating Annotation packages and their databases.  Packages produced are intended to be used with AnnotationDbi.'

recipes/bioconductor-biobase/meta.yaml

@@ -1,11 +1,12 @@
 package:
   name: bioconductor-biobase
-  version: 2.32.0
+  version: 2.30.0
 source:
-  fn: Biobase_2.32.0.tar.gz
-  url: https://bioarchive.galaxyproject.org/Biobase_2.32.0.tar.gz
-  md5: acc8c6a85fefcdfd14261c3e3b173e21
+  fn: Biobase_2.30.0.tar.gz
+  url: http://bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.30.0.tar.gz
+  md5: 697d3b5504f899c38a5e6e784ca0e33f
 build:
+  skip: False
   number: 0
   rpaths:
     - lib/R/lib/

recipes/bioconductor-biocgenerics/meta.yaml

@@ -1,11 +1,12 @@
 package:
   name: bioconductor-biocgenerics
-  version: 0.18.0
+  version: 0.16.1
 source:
-  fn: BiocGenerics_0.18.0.tar.gz
-  url: https://bioarchive.galaxyproject.org/BiocGenerics_0.18.0.tar.gz
-  md5: 56dc8110ab4379bb74c72192ee1a74f5
+  fn: BiocGenerics_0.16.1.tar.gz
+  url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz
+  md5: c2148ffd86fc6f1f819c7f68eb2c744f
 build:
+  skip: False
   number: 0
   rpaths:
     - lib/R/lib/

recipes/bioconductor-biocinstaller/meta.yaml

@@ -1,20 +1,22 @@
 package:
   name: bioconductor-biocinstaller
-  version: 1.22.3
+  version: 1.20.1
 source:
-  fn: BiocInstaller_1.22.3.tar.gz
-  url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocInstaller_1.22.3.tar.gz
-  md5: b4547d5fd23d431f2e9ce78a1f619bac
+  fn: BiocInstaller_1.20.1.tar.gz
+  url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocInstaller_1.20.1.tar.gz
+  md5: d6758faae696c9bbed2c5c43fcefdb00
+
 build:
+  skip: False
   number: 0
   rpaths:
     - lib/R/lib/
     - lib/
 requirements:
   build:
-    - 'r >=3.3.0'
+    - 'r >=3.2.0'
   run:
-    - 'r >=3.3.0'
+    - 'r >=3.2.0'
 test:
   commands:
     - '$R -e "library(''BiocInstaller'')"'

recipes/bioconductor-biocparallel/meta.yaml

@@ -1,11 +1,12 @@
 package:
   name: bioconductor-biocparallel
-  version: 1.6.3
+  version: 1.4.3
 source:
-  fn: BiocParallel_1.6.3.tar.gz
-  url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocParallel_1.6.3.tar.gz
-  md5: 932b7149fab8c9a99e79f464c2a5851b
+  fn: BiocParallel_1.4.3.tar.gz
+  url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocParallel_1.4.3.tar.gz
+  md5: 7954a6ae6d148ac6f1179c47fde8d7d4
 build:
+  skip: False
   number: 0
   rpaths:
     - lib/R/lib/

recipes/bioconductor-biocstyle/meta.yaml

@@ -1,10 +1,10 @@
 package:
   name: bioconductor-biocstyle
-  version: 2.0.2
+  version: 1.8.0
 source:
-  fn: BiocStyle_2.0.2.tar.gz
-  url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocStyle_2.0.2.tar.gz
-  md5: 99d9a39af4d6108bc553dcf568520695
+  fn: BiocStyle_1.8.0.tar.gz
+  url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocStyle_1.8.0.tar.gz
+  md5: f8fb61345f5c3044bde6d1f39126f8b8
 build:
   number: 0
   rpaths: