From afba459bddd1cf5fdb8a9d1c0347306eb326b1eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Mon, 14 Nov 2016 07:43:32 +0100 Subject: [PATCH 1/8] Add two last R deps for maaslin --- recipes/r-inlinedocs/build.sh | 13 +++++++ recipes/r-inlinedocs/meta.yaml | 64 +++++++++++++++++++++++++++++++ recipes/r-penalized/build.sh | 13 +++++++ recipes/r-penalized/meta.yaml | 70 ++++++++++++++++++++++++++++++++++ 4 files changed, 160 insertions(+) create mode 100644 recipes/r-inlinedocs/build.sh create mode 100644 recipes/r-inlinedocs/meta.yaml create mode 100644 recipes/r-penalized/build.sh create mode 100644 recipes/r-penalized/meta.yaml diff --git a/recipes/r-inlinedocs/build.sh b/recipes/r-inlinedocs/build.sh new file mode 100644 index 0000000000000..0c37df6e8efec --- /dev/null +++ b/recipes/r-inlinedocs/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + +$R CMD INSTALL --build . + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/r-inlinedocs/meta.yaml b/recipes/r-inlinedocs/meta.yaml new file mode 100644 index 0000000000000..51d850a28a456 --- /dev/null +++ b/recipes/r-inlinedocs/meta.yaml @@ -0,0 +1,64 @@ +package: + name: r-inlinedocs + version: "2013.9.3" + +source: + fn: inlinedocs_2013.9.3.tar.gz + url: + - http://cran.r-project.org/src/contrib/inlinedocs_2013.9.3.tar.gz + - http://cran.r-project.org/src/contrib/Archive/inlinedocs/inlinedocs_2013.9.3.tar.gz + md5: 16de1fef5c76f458c06d438fba67791f + +build: + # number: 1 + + # This is required to make R link correctly on Linux. + rpaths: + - lib/R/lib/ + - lib/ + + +requirements: + build: + - r + + run: + - r + +test: + commands: + # You can put additional test commands to be run here. + - $R -e "library('inlinedocs')" + +about: + home: http://inlinedocs.r-forge.r-project.org + license: GPL-2 | GPL-3 + summary: Generates Rd files from R source code with comments. The main features of the default + syntax are that (1) docs are defined in comments near the relevant code, (2) function + argument names are not repeated in comments, and (3) examples are defined in R code, + not comments. It is also easy to define a new syntax. + license_family: GPL3 + +# The original CRAN metadata for this package was: + +# Package: inlinedocs +# Title: Convert inline comments to documentation +# Type: Package +# Version: 2013.9.3 +# Authors@R: c(person("Toby Dylan","Hocking",role=c("aut","cre"), email="toby@sg.cs.titech.ac.jp"), person("Keith","Ponting",role="aut"), person("Thomas","Wutzler",role="aut"), person("Philippe","Grosjean",role="aut"), person("Markus","MAzller",role="aut"), person("R Core Team",role=c("ctb","cph"))) +# Description: Generates Rd files from R source code with comments. The main features of the default syntax are that (1) docs are defined in comments near the relevant code, (2) function argument names are not repeated in comments, and (3) examples are defined in R code, not comments. It is also easy to define a new syntax. +# URL: http://inlinedocs.r-forge.r-project.org +# Depends: methods, utils, R (>= 2.9) +# License: GPL-2 | GPL-3 +# LazyLoad: yes +# Encoding: UTF-8 +# Packaged: 2013-09-03 07:45:07 UTC; toby +# Author: Toby Dylan Hocking [aut, cre], Keith Ponting [aut], Thomas Wutzler [aut], Philippe Grosjean [aut], Markus MAzller [aut], R Core Team [ctb, cph] +# Maintainer: Toby Dylan Hocking +# NeedsCompilation: no +# Repository: CRAN +# Date/Publication: 2013-09-03 13:04:14 + +# See +# http://docs.continuum.io/conda/build.html for +# more information about meta.yaml diff --git a/recipes/r-penalized/build.sh b/recipes/r-penalized/build.sh new file mode 100644 index 0000000000000..0c37df6e8efec --- /dev/null +++ b/recipes/r-penalized/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + +$R CMD INSTALL --build . + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/r-penalized/meta.yaml b/recipes/r-penalized/meta.yaml new file mode 100644 index 0000000000000..829a4c57ab60a --- /dev/null +++ b/recipes/r-penalized/meta.yaml @@ -0,0 +1,70 @@ +package: + name: r-penalized + version: "0.9.47" + +source: + fn: penalized_0.9-47.tar.gz + url: + - https://cran.r-project.org/src/contrib/penalized_0.9-47.tar.gz + md5: '13cf7400f8840317b1bbfc980d3f0333' + +build: + # This is required to make R link correctly on Linux. + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - r + - r-survival + + run: + - r + - r-survival + +test: + commands: + # You can put additional test commands to be run here. + - $R -e "library('penalized')" + + +about: + home: https://cran.r-project.org/web/packages/penalized/index.html + license: GPL-2 + summary: Fitting possibly high dimensional penalized regression models. The penalty structure + can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a + positivity constraint on the regression coefficients. The supported regression models are + linear, logistic and Poisson regression and the Cox Proportional Hazards model. + Cross-validation routines allow optimization of the tuning parameters. + license_family: GPL2 + +# The original CRAN metadata for this package was: + +# Package: penalized +# Version: 0.9-47 +# Date: 2016-05-26 +# Title: L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation +# in GLMs and in the Cox Model +# Author: Jelle Goeman, Rosa Meijer, Nimisha Chaturvedi +# Maintainer: Jelle Goeman +# Depends: R (>= 2.10.0), survival, methods +# Imports: +# Suggests: globaltest +# Description: Fitting possibly high dimensional penalized +# regression models. The penalty structure can be any combination +# of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a +# positivity constraint on the regression coefficients. The +# supported regression models are linear, logistic and Poisson +# regression and the Cox Proportional Hazards model. +# Cross-validation routines allow optimization of the tuning +# parameters. +# License: GPL (>= 2) +# Collate: onattach.R penfit.R breslow.R penalized.R core.R checkinput.R +# cvl.R contrasts.R Brent.R plotpath.R cox.R logit.R linear.R +# poisson.R +# LazyLoad: yes +# Repository: CRAN +# Date/Publication: 2016-05-27 18:08:55 +# Packaged: 2016-05-27 11:43:08 UTC; jjgoeman +# NeedsCompilation: no From 693f254038c0953bfacf369ae50a1c8fdd16d3cd Mon Sep 17 00:00:00 2001 From: Martin Mann Date: Mon, 14 Nov 2016 14:34:35 +0100 Subject: [PATCH 2/8] libgd : fontconfig dep (runtime issue for perl-gd) --- recipes/libgd/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/libgd/meta.yaml b/recipes/libgd/meta.yaml index 30b44b91b6152..19476ddad9380 100644 --- a/recipes/libgd/meta.yaml +++ b/recipes/libgd/meta.yaml @@ -3,7 +3,7 @@ package: version: 2.2.3 build: - number: 1 + number: 2 requirements: build: @@ -14,6 +14,8 @@ requirements: - jpeg - libpng - libtiff + - fontconfig # for libfontconfig.so + run: - libgcc # [not osx] - zlib @@ -21,6 +23,7 @@ requirements: - jpeg - libpng - libtiff + - fontconfig # for libfontconfig.so source: fn: libgd-2.2.3.tar.gz From e06228c07b01aed55c4864f1f3c5daa1b04c9ff3 Mon Sep 17 00:00:00 2001 From: Martin Mann Date: Mon, 14 Nov 2016 15:27:45 +0100 Subject: [PATCH 3/8] jpeg package : license.txt --- recipes/jpeg/license.txt | 1197 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 1197 insertions(+) create mode 100644 recipes/jpeg/license.txt diff --git a/recipes/jpeg/license.txt b/recipes/jpeg/license.txt new file mode 100644 index 0000000000000..31a7308a5eb9b --- /dev/null +++ b/recipes/jpeg/license.txt @@ -0,0 +1,1197 @@ + + + + + + + + + + + + + + + + + + + + + + conda-recipes/license.txt at cce4cb3ea94e5435efcfdc030d6761959c7161f4 · martin-mann/conda-recipes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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The authors make NO WARRANTY or representation, either express or implied,
with respect to this software, its quality, accuracy, merchantability, or
fitness for a particular purpose. This software is provided "AS IS", and you,
its user, assume the entire risk as to its quality and accuracy.
+
This software is copyright (C) 1991-2010, Thomas G. Lane, Guido Vollbeding.
All Rights Reserved except as specified below.
+
Permission is hereby granted to use, copy, modify, and distribute this
software (or portions thereof) for any purpose, without fee, subject to these
conditions:
(1) If any part of the source code for this software is distributed, then this
README file must be included, with this copyright and no-warranty notice
unaltered; and any additions, deletions, or changes to the original files
must be clearly indicated in accompanying documentation.
(2) If only executable code is distributed, then the accompanying
documentation must state that "this software is based in part on the work of
the Independent JPEG Group".
(3) Permission for use of this software is granted only if the user accepts
full responsibility for any undesirable consequences; the authors accept
NO LIABILITY for damages of any kind.
+
These conditions apply to any software derived from or based on the IJG code,
not just to the unmodified library. If you use our work, you ought to
acknowledge us.
+
Permission is NOT granted for the use of any IJG author's name or company name
in advertising or publicity relating to this software or products derived from
it. This software may be referred to only as "the Independent JPEG Group's
software".
+
We specifically permit and encourage the use of this software as the basis of
commercial products, provided that all warranty or liability claims are
assumed by the product vendor.
+
+
ansi2knr.c is included in this distribution by permission of L. Peter Deutsch,
sole proprietor of its copyright holder, Aladdin Enterprises of Menlo Park, CA.
ansi2knr.c is NOT covered by the above copyright and conditions, but instead
by the usual distribution terms of the Free Software Foundation; principally,
that you must include source code if you redistribute it. (See the file
ansi2knr.c for full details.) However, since ansi2knr.c is not needed as part
of any program generated from the IJG code, this does not limit you more than
the foregoing paragraphs do.
+
The Unix configuration script "configure" was produced with GNU Autoconf.
It is copyright by the Free Software Foundation but is freely distributable.
The same holds for its supporting scripts (config.guess, config.sub,
ltmain.sh). Another support script, install-sh, is copyright by X Consortium
but is also freely distributable.
+
The IJG distribution formerly included code to read and write GIF files.
To avoid entanglement with the Unisys LZW patent, GIF reading support has
been removed altogether, and the GIF writer has been simplified to produce
"uncompressed GIFs". This technique does not use the LZW algorithm; the
resulting GIF files are larger than usual, but are readable by all standard
GIF decoders.
+
We are required to state that
"The Graphics Interchange Format(c) is the Copyright property of
CompuServe Incorporated. GIF(sm) is a Service Mark property of
CompuServe Incorporated."
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+ + + + + From 7e04fda0f051bd9d4635a51ce7575b98bd1c7f64 Mon Sep 17 00:00:00 2001 From: Martin Mann Date: Mon, 14 Nov 2016 15:28:23 +0100 Subject: [PATCH 4/8] jpeg : v9 enabled --- recipes/jpeg/build.sh | 955 +++++++++++++++++++++++++++++++++++++ recipes/jpeg/meta.yaml | 1008 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 1963 insertions(+) create mode 100644 recipes/jpeg/build.sh create mode 100644 recipes/jpeg/meta.yaml diff --git a/recipes/jpeg/build.sh b/recipes/jpeg/build.sh new file mode 100644 index 0000000000000..3e11798c11589 --- /dev/null +++ b/recipes/jpeg/build.sh @@ -0,0 +1,955 @@ + + + + + + + + + + + + + + + + + + + + + + conda-recipes/build.sh at cce4cb3ea94e5435efcfdc030d6761959c7161f4 · martin-mann/conda-recipes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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#!/bin/bash
+
./configure --prefix=$PREFIX
make
make install
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+ + + + + diff --git a/recipes/jpeg/meta.yaml b/recipes/jpeg/meta.yaml new file mode 100644 index 0000000000000..8893efa1c9a61 --- /dev/null +++ b/recipes/jpeg/meta.yaml @@ -0,0 +1,1008 @@ + + + + + + + + + + + + + + + + + + + + + + conda-recipes/meta.yaml at cce4cb3ea94e5435efcfdc030d6761959c7161f4 · martin-mann/conda-recipes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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package:
name: jpeg
version: 9b
+
source:
fn: jpegsrc.v9b.tar.gz
url: http://www.ijg.org/files/jpegsrc.v9b.tar.gz
md5: 6a9996ce116ec5c52b4870dbcd6d3ddb
+
build:
number: 0
+
about:
home: http://www.ijg.org/
license: Custom free software license
summary: read/write jpeg COM, EXIF, IPTC medata
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+ + + + + From cac7aaabc6f8973a24fa1653d9892ecf320f9c2d Mon Sep 17 00:00:00 2001 From: Martin Mann Date: Mon, 14 Nov 2016 15:38:01 +0100 Subject: [PATCH 5/8] jpeg: build.sh corrected --- recipes/jpeg/build.sh | 958 +----------------------------------------- 1 file changed, 4 insertions(+), 954 deletions(-) diff --git a/recipes/jpeg/build.sh b/recipes/jpeg/build.sh index 3e11798c11589..94a1d588d5e5c 100644 --- a/recipes/jpeg/build.sh +++ b/recipes/jpeg/build.sh @@ -1,955 +1,5 @@ +#!/bin/bash - - - - - - - - - - - - - - - - - - - - - conda-recipes/build.sh at cce4cb3ea94e5435efcfdc030d6761959c7161f4 · martin-mann/conda-recipes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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- - - - - +./configure --prefix=$PREFIX +make +make install From ac63a046e3c3d20e0d1ec55a9f22739376f702e4 Mon Sep 17 00:00:00 2001 From: Martin Mann Date: Mon, 14 Nov 2016 15:41:03 +0100 Subject: [PATCH 6/8] jpeg : meta corrected --- recipes/jpeg/meta.yaml | 1024 +--------------------------------------- 1 file changed, 16 insertions(+), 1008 deletions(-) diff --git a/recipes/jpeg/meta.yaml b/recipes/jpeg/meta.yaml index 8893efa1c9a61..7d1e0ccfeffd4 100644 --- a/recipes/jpeg/meta.yaml +++ b/recipes/jpeg/meta.yaml @@ -1,1008 +1,16 @@ - - - - - - - - - - - - - - - - - - - - - - conda-recipes/meta.yaml at cce4cb3ea94e5435efcfdc030d6761959c7161f4 · martin-mann/conda-recipes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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package:
name: jpeg
version: 9b
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source:
fn: jpegsrc.v9b.tar.gz
url: http://www.ijg.org/files/jpegsrc.v9b.tar.gz
md5: 6a9996ce116ec5c52b4870dbcd6d3ddb
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build:
number: 0
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about:
home: http://www.ijg.org/
license: Custom free software license
summary: read/write jpeg COM, EXIF, IPTC medata
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- - - - - +package: + name: jpeg + version: 9b + +source: + fn: jpegsrc.v9b.tar.gz + url: http://www.ijg.org/files/jpegsrc.v9b.tar.gz + md5: 6a9996ce116ec5c52b4870dbcd6d3ddb + +build: + number: 0 + +about: + home: http://www.ijg.org/ + license: Custom free software license +summary: read/write jpeg COM, EXIF, IPTC medata From 6b162638f1258c0f5db39430a416ecfadd82066e Mon Sep 17 00:00:00 2001 From: Martin Mann Date: Mon, 14 Nov 2016 15:53:22 +0100 Subject: [PATCH 7/8] libgd: use recent libjpeg 9* --- recipes/libgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/libgd/meta.yaml b/recipes/libgd/meta.yaml index 19476ddad9380..98e35542f7175 100644 --- a/recipes/libgd/meta.yaml +++ b/recipes/libgd/meta.yaml @@ -11,7 +11,7 @@ requirements: - llvm # [osx] - zlib - freetype - - jpeg + - jpeg >=9* # use recent libjpeg - libpng - libtiff - fontconfig # for libfontconfig.so @@ -20,7 +20,7 @@ requirements: - libgcc # [not osx] - zlib - freetype - - jpeg + - jpeg >=9* # use recent libjpeg - libpng - libtiff - fontconfig # for libfontconfig.so From ae9a110f0a0e60646770bc157c3e4de00d027dd2 Mon Sep 17 00:00:00 2001 From: dyusuf Date: Mon, 14 Nov 2016 16:37:14 +0100 Subject: [PATCH 8/8] build pipmir 1.1 --- recipes/pipmir/build.sh | 12 ++++++++++++ recipes/pipmir/meta.yaml | 33 +++++++++++++++++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 recipes/pipmir/build.sh create mode 100644 recipes/pipmir/meta.yaml diff --git a/recipes/pipmir/build.sh b/recipes/pipmir/build.sh new file mode 100644 index 0000000000000..41221ae8c320f --- /dev/null +++ b/recipes/pipmir/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +set -eu -o pipefail + +PKG_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $PKG_HOME +mkdir -p $PREFIX/bin + +cd $SRC_DIR + +cp -r PIPmiR src README $PKG_HOME/. +chmod +x $PKG_HOME/PIPmiR +ln -s $PKG_HOME/PIPmiR $PREFIX/bin/PIPmiR diff --git a/recipes/pipmir/meta.yaml b/recipes/pipmir/meta.yaml new file mode 100644 index 0000000000000..417543b6ff908 --- /dev/null +++ b/recipes/pipmir/meta.yaml @@ -0,0 +1,33 @@ +package: + name: pipmir + version: 1.1 + +source: + fn: PIPmiR_v1_1b_executable.tar.gz + url: https://ohlerlab.mdc-berlin.de/files/duke/PIPmiR/PIPmiR_v1_1b_executable.tar.gz + md5: 4103f0a148e4cc0217c616c1606f11c5 + +build: + skip: True # [not linux] + number: 0 + +requirements: + build: + - java-jdk + - samtools + - viennarna + run: + - java-jdk + - samtools + - viennarna + +test: + commands: + - PIPmiR + +about: + home: https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ + license: 'PIPmiR is provided for academic use only, + if you wish to use it in another setting please contact Uwe Ohler.' + summary: 'We developed the PIPmiR algorithm to identify novel plant miRNA + genes from a combination of deep sequencing data and genomic features.'