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0001-r-packages-skeleton-cran-diffs-at-3.4.0-time.patch
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diff -urN r-packages-new/r-bh/meta.yaml r-packages-new.fixed/r-bh/meta.yaml
--- r-packages-new/r-bh/meta.yaml 2017-06-14 17:05:00.000000000 +0100
+++ r-packages-new.fixed/r-bh/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -66,7 +66,7 @@
''range'' ''scope_exit'' ''smart_ptr'' ''spirit'' ''tuple'' ''type_traits'' ''typeof''
''unordered'' ''utility'' ''uuid''.'
- license_family: OTHER
+ license_family: BSD
# The original CRAN metadata for this package was:
diff -urN r-packages-new/r-bitops/meta.yaml r-packages-new.fixed/r-bitops/meta.yaml
--- r-packages-new/r-bitops/meta.yaml 2017-06-14 17:05:30.000000000 +0100
+++ r-packages-new.fixed/r-bitops/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-boot/meta.yaml r-packages-new.fixed/r-boot/meta.yaml
--- r-packages-new/r-boot/meta.yaml 2017-06-14 17:05:32.000000000 +0100
+++ r-packages-new.fixed/r-boot/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -54,7 +54,7 @@
summary: Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their
Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written
by Angelo Canty for S.
- license_family: MIT
+ license_family: Public-Domain
# The original CRAN metadata for this package was:
diff -urN r-packages-new/r-bradleyterry2/meta.yaml r-packages-new.fixed/r-bradleyterry2/meta.yaml
--- r-packages-new/r-bradleyterry2/meta.yaml 2017-06-14 17:05:34.000000000 +0100
+++ r-packages-new.fixed/r-bradleyterry2/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-brew/meta.yaml r-packages-new.fixed/r-brew/meta.yaml
--- r-packages-new/r-brew/meta.yaml 2017-06-14 17:05:35.000000000 +0100
+++ r-packages-new.fixed/r-brew/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-brglm/meta.yaml r-packages-new.fixed/r-brglm/meta.yaml
--- r-packages-new/r-brglm/meta.yaml 2017-06-14 17:05:37.000000000 +0100
+++ r-packages-new.fixed/r-brglm/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-cairo/meta.yaml r-packages-new.fixed/r-cairo/meta.yaml
--- r-packages-new/r-cairo/meta.yaml 2017-06-14 17:05:41.000000000 +0100
+++ r-packages-new.fixed/r-cairo/meta.yaml 2017-06-14 15:23:27.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 1
# This is required to make R link correctly on Linux.
rpaths:
@@ -32,12 +32,17 @@
requirements:
build:
- r-base
+ - pkg-config # [not win]
+ - cairo 1.14.* # [not win]
+ - libpng >=1.6.27,<1.7 # [not win]
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
run:
- r-base
+ - cairo 1.14.* # [not win]
+ - libpng >=1.6.27,<1.7 # [not win]
- {{native}}gcc-libs # [win]
- libgcc # [not win]
diff -urN r-packages-new/r-catools/meta.yaml r-packages-new.fixed/r-catools/meta.yaml
--- r-packages-new/r-catools/meta.yaml 2017-06-14 17:05:46.000000000 +0100
+++ r-packages-new.fixed/r-catools/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-curl/meta.yaml r-packages-new.fixed/r-curl/meta.yaml
--- r-packages-new/r-curl/meta.yaml 2017-06-14 17:06:08.000000000 +0100
+++ r-packages-new.fixed/r-curl/meta.yaml 2017-06-14 15:24:21.000000000 +0100
@@ -32,12 +32,14 @@
requirements:
build:
- r-base
+ - {{native}}curl
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
run:
- r-base
+ - {{native}}curl
- {{native}}gcc-libs # [win]
- libgcc # [not win]
diff -urN r-packages-new/r-data.table/build.sh r-packages-new.fixed/r-data.table/build.sh
--- r-packages-new/r-data.table/build.sh 2017-06-14 17:06:12.000000000 +0100
+++ r-packages-new.fixed/r-data.table/build.sh 2017-06-14 15:20:53.000000000 +0100
@@ -7,6 +7,11 @@
$R CMD INSTALL --build .
# Add more build steps here, if they are necessary.
+# The build for data.table moves data.table.so to datatable.so, but doesn't
+# change the install name, which confuses the conda-build post build stuff.
+if [ $(uname) = "Darwin" ]; then
+ install_name_tool -id datatable.so $PREFIX/lib/R/library/data.table/libs/datatable.so
+fi
# See
# http://docs.continuum.io/conda/build.html
diff -urN r-packages-new/r-dichromat/meta.yaml r-packages-new.fixed/r-dichromat/meta.yaml
--- r-packages-new/r-dichromat/meta.yaml 2017-06-14 17:06:21.000000000 +0100
+++ r-packages-new.fixed/r-dichromat/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-domc/meta.yaml r-packages-new.fixed/r-domc/meta.yaml
--- r-packages-new/r-domc/meta.yaml 2017-06-14 17:06:24.000000000 +0100
+++ r-packages-new.fixed/r-domc/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -28,6 +28,7 @@
- lib/R/lib/
- lib/
+ skip: true # [win]
requirements:
build:
diff -urN r-packages-new/r-feather/build.sh r-packages-new.fixed/r-feather/build.sh
--- r-packages-new/r-feather/build.sh 2017-06-14 17:06:38.000000000 +0100
+++ r-packages-new.fixed/r-feather/build.sh 2017-06-14 15:20:53.000000000 +0100
@@ -4,6 +4,11 @@
mv DESCRIPTION DESCRIPTION.old
grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+# conda-build sets this to 10.7 at present, and that changes
+# the behaviour of clang++ such that <cstdint> is not found.
+if [[ ${MACOSX_DEPLOYMENT_TARGET} == 10.7 ]]; then
+ export MACOSX_DEPLOYMENT_TARGET=10.9
+fi
$R CMD INSTALL --build .
# Add more build steps here, if they are necessary.
diff -urN r-packages-new/r-fracdiff/meta.yaml r-packages-new.fixed/r-fracdiff/meta.yaml
--- r-packages-new/r-fracdiff/meta.yaml 2017-06-14 17:06:52.000000000 +0100
+++ r-packages-new.fixed/r-fracdiff/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-git2r/meta.yaml r-packages-new.fixed/r-git2r/meta.yaml
--- r-packages-new/r-git2r/meta.yaml 2017-06-14 17:07:07.000000000 +0100
+++ r-packages-new.fixed/r-git2r/meta.yaml 2017-06-14 15:25:00.000000000 +0100
@@ -32,12 +32,14 @@
requirements:
build:
- r-base
+ - {{native}}openssl
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
run:
- r-base
+ - {{native}}openssl
- {{native}}gcc-libs # [win]
- libgcc # [not win]
diff -urN r-packages-new/r-gsl/build.sh r-packages-new.fixed/r-gsl/build.sh
--- r-packages-new/r-gsl/build.sh 2017-06-14 17:07:16.000000000 +0100
+++ r-packages-new.fixed/r-gsl/build.sh 2017-06-14 15:20:53.000000000 +0100
@@ -4,6 +4,12 @@
mv DESCRIPTION DESCRIPTION.old
grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+export CFLAGS="$(gsl-config --cflags)"
+export LDFLAGS="$(gsl-config --libs)"
+
+# For whatever reason, it can't link to gsl correctly without this on OS X.
+export DYLD_FALLBACK_LIBRARY_PATH=$PREFIX/lib
+
$R CMD INSTALL --build .
# Add more build steps here, if they are necessary.
diff -urN r-packages-new/r-highr/meta.yaml r-packages-new.fixed/r-highr/meta.yaml
--- r-packages-new/r-highr/meta.yaml 2017-06-14 17:07:29.000000000 +0100
+++ r-packages-new.fixed/r-highr/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -54,7 +54,7 @@
summary: Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML
output. Source code of other languages is supported via Andre Simon's highlight
package (http://www.andre-simon.de).
- license_family: GPL
+ license_family: GPL3
# The original CRAN metadata for this package was:
diff -urN r-packages-new/r-htmlwidgets/meta.yaml r-packages-new.fixed/r-htmlwidgets/meta.yaml
--- r-packages-new/r-htmlwidgets/meta.yaml 2017-06-14 17:07:38.000000000 +0100
+++ r-packages-new.fixed/r-htmlwidgets/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 1
# This is required to make R link correctly on Linux.
rpaths:
@@ -41,6 +41,8 @@
- r-htmltools >=0.3
- r-jsonlite >=0.9.16
- r-yaml
+ - pandoc >=1.19.2 # [not linux]
+ - pandoc >=1.15.0 # [linux]
test:
commands:
diff -urN r-packages-new/r-igraph/bld.bat r-packages-new.fixed/r-igraph/bld.bat
--- r-packages-new/r-igraph/bld.bat 2017-06-14 17:07:46.000000000 +0100
+++ r-packages-new.fixed/r-igraph/bld.bat 2017-06-14 15:20:53.000000000 +0100
@@ -1,3 +1,12 @@
+@rem :: Prevent interpretation of /**/ as an absolute Windows path.
+set MSYS2_ARG_CONV_EXCL=-DIGRAPH_THREAD_LOCAL
+
+@rem :: Prevent interpretation of \? as escaped character.
+@rem :: (where I'm not sure which character ? represents)
+set PREFIXS=%PREFIX:\=/%
+set LIB_XML=%PREFIXS%/Library/mingw-w64
+set LIB_GMP=%PREFIXS%/Library/mingw-w64
+
"%R%" CMD INSTALL --build .
if errorlevel 1 exit 1
diff -urN r-packages-new/r-igraph/meta.yaml r-packages-new.fixed/r-igraph/meta.yaml
--- r-packages-new/r-igraph/meta.yaml 2017-06-14 17:07:46.000000000 +0100
+++ r-packages-new.fixed/r-igraph/meta.yaml 2017-06-14 15:25:56.000000000 +0100
@@ -36,13 +36,16 @@
- r-nmf
- r-irlba
- r-magrittr
+ - {{native}}gmp
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
+ - {{native}}libxml2 # [win]
run:
- r-base
- - r-matrix
+ - {{native}}gmp
+ - {{native}}libxml2 # [win] - r-matrix
- r-nmf
- r-irlba
- r-magrittr
diff -urN r-packages-new/r-jpeg/meta.yaml r-packages-new.fixed/r-jpeg/meta.yaml
--- r-packages-new/r-jpeg/meta.yaml 2017-06-14 17:07:56.000000000 +0100
+++ r-packages-new.fixed/r-jpeg/meta.yaml 2017-06-14 15:59:11.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 3
# This is required to make R link correctly on Linux.
rpaths:
@@ -32,15 +32,15 @@
requirements:
build:
- r-base
+ - {{native}}libjpeg-turbo # [win]
+ - jpeg 9* # [not win]
+ run:
+ - {{native}}libjpeg-turbo # [win]
+ - jpeg 9* # [not win]
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
- run:
- - r-base
- - {{native}}gcc-libs # [win]
- - libgcc # [not win]
-
test:
commands:
# You can put additional test commands to be run here.
diff -urN r-packages-new/r-kernsmooth/meta.yaml r-packages-new.fixed/r-kernsmooth/meta.yaml
--- r-packages-new/r-kernsmooth/meta.yaml 2017-06-14 17:08:00.000000000 +0100
+++ r-packages-new.fixed/r-kernsmooth/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -59,7 +59,7 @@
summary: 'Functions for kernel smoothing (and density estimation) corresponding to the book: Wand,
M.P. and Jones, M.C. (1995) "Kernel Smoothing".'
- license_family: MIT
+ license_family: Public-Domain
# The original CRAN metadata for this package was:
diff -urN r-packages-new/r-knitr/meta.yaml r-packages-new.fixed/r-knitr/meta.yaml
--- r-packages-new/r-knitr/meta.yaml 2017-06-14 17:08:02.000000000 +0100
+++ r-packages-new.fixed/r-knitr/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -65,7 +65,7 @@
license: GPL
summary: Provides a general-purpose tool for dynamic report generation in R using Literate
Programming techniques.
- license_family: GPL
+ license_family: GPL3
# The original CRAN metadata for this package was:
diff -urN r-packages-new/r-labeling/meta.yaml r-packages-new.fixed/r-labeling/meta.yaml
--- r-packages-new/r-labeling/meta.yaml 2017-06-14 17:08:05.000000000 +0100
+++ r-packages-new.fixed/r-labeling/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-magrittr/meta.yaml r-packages-new.fixed/r-magrittr/meta.yaml
--- r-packages-new/r-magrittr/meta.yaml 2017-06-14 17:08:31.000000000 +0100
+++ r-packages-new.fixed/r-magrittr/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-minqa/meta.yaml r-packages-new.fixed/r-minqa/meta.yaml
--- r-packages-new/r-minqa/meta.yaml 2017-06-14 17:08:56.000000000 +0100
+++ r-packages-new.fixed/r-minqa/meta.yaml 2017-06-14 16:00:18.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-mlmrev/meta.yaml r-packages-new.fixed/r-mlmrev/meta.yaml
--- r-packages-new/r-mlmrev/meta.yaml 2017-06-14 17:08:58.000000000 +0100
+++ r-packages-new.fixed/r-mlmrev/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-nloptr/build.sh r-packages-new.fixed/r-nloptr/build.sh
--- r-packages-new/r-nloptr/build.sh 2017-06-14 17:09:15.000000000 +0100
+++ r-packages-new.fixed/r-nloptr/build.sh 2017-06-14 15:20:53.000000000 +0100
@@ -4,7 +4,8 @@
mv DESCRIPTION DESCRIPTION.old
grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
-$R CMD INSTALL --build .
+export DYLD_FALLBACK_LIBRARY_PATH=$PREFIX/lib
+$R CMD INSTALL --build --configure-args="--with-nlopt-cflags=-I${PREFIX}/include --with-nlopt-libs=\"-L${PREFIX}/lib -lnlopt_cxx\"" .
# Add more build steps here, if they are necessary.
diff -urN r-packages-new/r-nloptr/meta.yaml r-packages-new.fixed/r-nloptr/meta.yaml
--- r-packages-new/r-nloptr/meta.yaml 2017-06-14 17:09:15.000000000 +0100
+++ r-packages-new.fixed/r-nloptr/meta.yaml 2017-06-14 16:03:26.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
@@ -34,10 +34,13 @@
- r-base
- posix # [win]
- {{native}}toolchain # [win]
+ - {{native}}nlopt # [win]
+ - nlopt-static # [not win]
- gcc # [not win]
run:
- r-base
+ - {{native}}nlopt # [win]
- {{native}}gcc-libs # [win]
- libgcc # [not win]
diff -urN r-packages-new/r-nycflights13/meta.yaml r-packages-new.fixed/r-nycflights13/meta.yaml
--- r-packages-new/r-nycflights13/meta.yaml 2017-06-14 17:09:24.000000000 +0100
+++ r-packages-new.fixed/r-nycflights13/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -55,7 +55,7 @@
license: CC0
summary: Airline on-time data for all flights departing NYC in 2013. Also includes useful 'metadata'
on airlines, airports, weather, and planes.
- license_family: OTHER
+ license_family: Public-Domain
# The original CRAN metadata for this package was:
diff -urN r-packages-new/r-pbdzmq/meta.yaml r-packages-new.fixed/r-pbdzmq/meta.yaml
--- r-packages-new/r-pbdzmq/meta.yaml 2017-06-14 17:09:33.000000000 +0100
+++ r-packages-new.fixed/r-pbdzmq/meta.yaml 2017-06-14 16:11:37.000000000 +0100
@@ -29,10 +29,15 @@
- lib/
# Suggests: pbdRPC
+# unlike r-rzmq, this package pre-bakes a whole set of Windows
+# Makefiles, and so it doesn't depend on our shared
+# m2-mingw-w64-zeromq package. This is beyond horrible.
requirements:
build:
- r-base
- r-r6
+ - pkg-config # [not win]
+ - zeromq 4.1.* # [not win]
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
@@ -42,6 +47,7 @@
- r-r6
- {{native}}gcc-libs # [win]
- libgcc # [not win]
+ - zeromq 4.1.* # [not win]
test:
commands:
diff -urN r-packages-new/r-perm/meta.yaml r-packages-new.fixed/r-perm/meta.yaml
--- r-packages-new/r-perm/meta.yaml 2017-06-14 17:09:38.000000000 +0100
+++ r-packages-new.fixed/r-perm/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -52,7 +52,7 @@
home: https://CRAN.R-project.org/package=perm
license: GPL
summary: Perform Exact or Asymptotic permutation tests
- license_family: GPL
+ license_family: GPL3
# The original CRAN metadata for this package was:
diff -urN r-packages-new/r-pki/meta.yaml r-packages-new.fixed/r-pki/meta.yaml
--- r-packages-new/r-pki/meta.yaml 2017-06-14 17:09:41.000000000 +0100
+++ r-packages-new.fixed/r-pki/meta.yaml 2017-06-14 16:14:02.000000000 +0100
@@ -15,9 +15,9 @@
sha256: 2fcca38b387ecaae6bbfea795f175adb06a21d653c7fceb972fbeb4826410cf6
- # patches:
+ patches:
# List any patch files here
- # - fix.patch
+ - 0001-Win32-Determine-LOCAL_SOFT.patch
build:
# If this is a new build for the same version, increment the build number.
@@ -34,12 +34,14 @@
- r-base
- r-base64enc
- posix # [win]
+ - {{native}}openssl
- {{native}}toolchain # [win]
- gcc # [not win]
run:
- r-base
- r-base64enc
+ - {{native}}openssl
- {{native}}gcc-libs # [win]
- libgcc # [not win]
diff -urN r-packages-new/r-png/meta.yaml r-packages-new.fixed/r-png/meta.yaml
--- r-packages-new/r-png/meta.yaml 2017-06-14 17:09:49.000000000 +0100
+++ r-packages-new.fixed/r-png/meta.yaml 2017-06-14 16:37:38.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 3
# This is required to make R link correctly on Linux.
rpaths:
@@ -35,11 +35,17 @@
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
+ - {{native}}libpng # [win]
+ - libpng >=1.6.27,<1.7 # [not win]
+ - {{native}}zlib
run:
- r-base
- {{native}}gcc-libs # [win]
- libgcc # [not win]
+ - {{native}}libpng # [win]
+ - libpng >=1.6.27,<1.7 # [not win]
+ - {{native}}zlib
test:
commands:
diff -urN r-packages-new/r-profilemodel/meta.yaml r-packages-new.fixed/r-profilemodel/meta.yaml
--- r-packages-new/r-profilemodel/meta.yaml 2017-06-14 17:09:56.000000000 +0100
+++ r-packages-new.fixed/r-profilemodel/meta.yaml 2017-06-14 15:20:53.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-quadprog/meta.yaml r-packages-new.fixed/r-quadprog/meta.yaml
--- r-packages-new/r-quadprog/meta.yaml 2017-06-14 17:10:06.000000000 +0100
+++ r-packages-new.fixed/r-quadprog/meta.yaml 2017-06-14 15:20:59.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-rcolorbrewer/meta.yaml r-packages-new.fixed/r-rcolorbrewer/meta.yaml
--- r-packages-new/r-rcolorbrewer/meta.yaml 2017-06-14 17:10:26.000000000 +0100
+++ r-packages-new.fixed/r-rcolorbrewer/meta.yaml 2017-06-14 15:20:59.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 3
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-rcpp/meta.yaml r-packages-new.fixed/r-rcpp/meta.yaml
--- r-packages-new/r-rcpp/meta.yaml 2017-06-14 17:10:28.000000000 +0100
+++ r-packages-new.fixed/r-rcpp/meta.yaml 2017-06-14 15:20:59.000000000 +0100
@@ -15,9 +15,9 @@
sha256: bd8cae275bb45cf98f3e3c6e1b5189bdd9c02e74b25241419ed3e4851d859c7f
- # patches:
- # List any patch files here
- # - fix.patch
+ patches:
+ - 0001-Add-CXX1XSTD-to-PKG_CPPFLAGS.patch
+ - 0002-macOS-When-target-lt-10.9-libstdc-supports-only-some.patch
build:
# If this is a new build for the same version, increment the build number.
diff -urN r-packages-new/r-rcurl/meta.yaml r-packages-new.fixed/r-rcurl/meta.yaml
--- r-packages-new/r-rcurl/meta.yaml 2017-06-14 17:10:35.000000000 +0100
+++ r-packages-new.fixed/r-rcurl/meta.yaml 2017-06-14 16:48:12.000000000 +0100
@@ -36,12 +36,14 @@
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
+ - {{native}}curl # [not osx]
run:
- r-base
- r-bitops
- {{native}}gcc-libs # [win]
- libgcc # [not win]
+ - {{native}}curl # [not osx]
test:
commands:
diff -urN r-packages-new/r-rjava/meta.yaml r-packages-new.fixed/r-rjava/meta.yaml
--- r-packages-new/r-rjava/meta.yaml 2017-06-14 17:10:49.000000000 +0100
+++ r-packages-new.fixed/r-rjava/meta.yaml 2017-06-14 15:21:00.000000000 +0100
@@ -15,9 +15,8 @@
sha256: dada5e031414da54eb80b9024d51866c20b92d41d68da65789fe0130bc54bd8a
- # patches:
- # List any patch files here
- # - fix.patch
+ patches:
+ - 0001-Improve-lib-jvm.-so-dylib-dll-loading.patch
build:
# If this is a new build for the same version, increment the build number.
@@ -33,6 +32,7 @@
build:
- r-base
- posix # [win]
+ - {{posix}}curl # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
diff -urN r-packages-new/r-rjsonio/meta.yaml r-packages-new.fixed/r-rjsonio/meta.yaml
--- r-packages-new/r-rjsonio/meta.yaml 2017-06-14 17:10:52.000000000 +0100
+++ r-packages-new.fixed/r-rjsonio/meta.yaml 2017-06-14 15:21:00.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-rmarkdown/meta.yaml r-packages-new.fixed/r-rmarkdown/meta.yaml
--- r-packages-new/r-rmarkdown/meta.yaml 2017-06-14 17:10:56.000000000 +0100
+++ r-packages-new.fixed/r-rmarkdown/meta.yaml 2017-06-14 15:21:00.000000000 +0100
@@ -51,6 +51,8 @@
- r-knitr >=1.14
- r-rprojroot
- r-yaml >=2.1.5
+ - pandoc >=1.19.2 # [not linux]
+ - pandoc >=1.15.0 # [linux]
test:
commands:
diff -urN r-packages-new/r-rodbc/meta.yaml r-packages-new.fixed/r-rodbc/meta.yaml
--- r-packages-new/r-rodbc/meta.yaml 2017-06-14 17:11:04.000000000 +0100
+++ r-packages-new.fixed/r-rodbc/meta.yaml 2017-06-14 16:48:52.000000000 +0100
@@ -35,11 +35,13 @@
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
+ - unixodbc # [not win]
run:
- r-base
- {{native}}gcc-libs # [win]
- libgcc # [not win]
+ - unixodbc # [not win]
test:
commands:
diff -urN r-packages-new/r-rserve/build.sh r-packages-new.fixed/r-rserve/build.sh
--- r-packages-new/r-rserve/build.sh 2017-06-14 17:11:12.000000000 +0100
+++ r-packages-new.fixed/r-rserve/build.sh 2017-06-14 15:21:01.000000000 +0100
@@ -4,7 +4,17 @@
mv DESCRIPTION DESCRIPTION.old
grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
-$R CMD INSTALL --build .
+# This package makes a standalone binary and needs to find libraries essential to R.
+# It is likely that src/Makevars.in should use $(MAIN_LINK) from lib/R/etc/Makeconf
+# for this instead of having to pass it in via the PKG_LIBS environment variable.
+if [[ $(uname) == Darwin ]]; then
+ PKG_LIBS="-L${PREFIX}/lib" $R CMD INSTALL --build .
+else
+ # .. on Linux the situation is even worse:
+ LD_LIBRARY_PATH=${PREFIX}/lib/R/lib:${PREFIX}/lib \
+ PKG_LIBS="-L${PREFIX}/lib -L${PREFIX}/lib/R/lib -lR -lRblas" \
+ $R CMD INSTALL --build .
+fi
# Add more build steps here, if they are necessary.
diff -urN r-packages-new/r-rserve/meta.yaml r-packages-new.fixed/r-rserve/meta.yaml
--- r-packages-new/r-rserve/meta.yaml 2017-06-14 17:11:12.000000000 +0100
+++ r-packages-new.fixed/r-rserve/meta.yaml 2017-06-14 16:53:31.000000000 +0100
@@ -35,11 +35,13 @@
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
+ - libiconv # [osx]
run:
- r-base
- {{native}}gcc-libs # [win]
- libgcc # [not win]
+ - libiconv # [osx]
test:
commands:
diff -urN r-packages-new/r-rzmq/meta.yaml r-packages-new.fixed/r-rzmq/meta.yaml
--- r-packages-new/r-rzmq/meta.yaml 2017-06-14 17:11:23.000000000 +0100
+++ r-packages-new.fixed/r-rzmq/meta.yaml 2017-06-14 16:55:10.000000000 +0100
@@ -33,6 +33,9 @@
build:
- r-base
- posix # [win]
+ - {{posix}}pkg-config
+ - {{native}}zeromq # [win]
+ - zeromq 4.1.* # [not win]
- {{native}}toolchain # [win]
- gcc # [not win]
@@ -40,6 +43,8 @@
- r-base
- {{native}}gcc-libs # [win]
- libgcc # [not win]
+ - {{native}}zeromq # [win]
+ - zeromq 4.1.* # [not win]
test:
commands:
diff -urN r-packages-new/r-testit/meta.yaml r-packages-new.fixed/r-testit/meta.yaml
--- r-packages-new/r-testit/meta.yaml 2017-06-14 17:12:07.000000000 +0100
+++ r-packages-new.fixed/r-testit/meta.yaml 2017-06-14 15:21:01.000000000 +0100
@@ -53,7 +53,7 @@
license: GPL
summary: Provides two convenience functions assert() and test_pkg() to facilitate testing R
packages.
- license_family: GPL
+ license_family: GPL3
# The original CRAN metadata for this package was:
diff -urN r-packages-new/r-timedate/meta.yaml r-packages-new.fixed/r-timedate/meta.yaml
--- r-packages-new/r-timedate/meta.yaml 2017-06-14 17:12:22.000000000 +0100
+++ r-packages-new.fixed/r-timedate/meta.yaml 2017-06-14 15:21:01.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-ttr/meta.yaml r-packages-new.fixed/r-ttr/meta.yaml
--- r-packages-new/r-ttr/meta.yaml 2017-06-14 17:12:28.000000000 +0100
+++ r-packages-new.fixed/r-ttr/meta.yaml 2017-06-14 15:05:10.000000000 +0100
@@ -32,7 +32,7 @@
requirements:
build:
- r-base
- - r-xts
+ - r-xts >=0.9_3
- r-zoo
- posix # [win]
- {{native}}toolchain # [win]
@@ -40,7 +40,7 @@
run:
- r-base
- - r-xts
+ - r-xts >=0.9_3
- r-zoo
- {{native}}gcc-libs # [win]
- libgcc # [not win]
diff -urN r-packages-new/r-weatherdata/meta.yaml r-packages-new.fixed/r-weatherdata/meta.yaml
--- r-packages-new/r-weatherdata/meta.yaml 2017-06-14 17:12:43.000000000 +0100
+++ r-packages-new.fixed/r-weatherdata/meta.yaml 2017-06-14 15:21:01.000000000 +0100
@@ -58,7 +58,7 @@
summary: Functions that help in fetching weather data from websites. Given a location and a
date range, these functions help fetch weather data (temperature, pressure etc.)
for any weather related analysis.
- license_family: GPL
+ license_family: GPL3
# The original CRAN metadata for this package was:
diff -urN r-packages-new/r-whisker/meta.yaml r-packages-new.fixed/r-whisker/meta.yaml
--- r-packages-new/r-whisker/meta.yaml 2017-06-14 17:12:45.000000000 +0100
+++ r-packages-new.fixed/r-whisker/meta.yaml 2017-06-14 15:21:01.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-xlsx/meta.yaml r-packages-new.fixed/r-xlsx/meta.yaml
--- r-packages-new/r-xlsx/meta.yaml 2017-06-14 17:12:48.000000000 +0100
+++ r-packages-new.fixed/r-xlsx/meta.yaml 2017-06-14 15:21:01.000000000 +0100
@@ -28,6 +28,7 @@
- lib/R/lib/
- lib/
+ skip: true # [linux]
requirements:
build:
diff -urN r-packages-new/r-xlsxjars/meta.yaml r-packages-new.fixed/r-xlsxjars/meta.yaml
--- r-packages-new/r-xlsxjars/meta.yaml 2017-06-14 17:12:52.000000000 +0100
+++ r-packages-new.fixed/r-xlsxjars/meta.yaml 2017-06-14 15:21:01.000000000 +0100
@@ -28,10 +28,12 @@
- lib/R/lib/
- lib/
+ skip: true # [linux]
requirements:
build:
- r-base
+ - {{posix}}curl # [win]
- r-rjava
run:
diff -urN r-packages-new/r-xml/bld.bat r-packages-new.fixed/r-xml/bld.bat
--- r-packages-new/r-xml/bld.bat 2017-06-14 17:12:53.000000000 +0100
+++ r-packages-new.fixed/r-xml/bld.bat 2017-06-14 15:21:01.000000000 +0100
@@ -1,3 +1,8 @@
+@rem :: Prevent interpretation of \? as escaped character.
+@rem :: (where I'm not sure which character ? represents)
+set PREFIXS=%PREFIX:\=/%
+set LIB_XML=%PREFIXS%/Library/mingw-w64
+
"%R%" CMD INSTALL --build .
if errorlevel 1 exit 1
diff -urN r-packages-new/r-xml/meta.yaml r-packages-new.fixed/r-xml/meta.yaml
--- r-packages-new/r-xml/meta.yaml 2017-06-14 17:12:53.000000000 +0100
+++ r-packages-new.fixed/r-xml/meta.yaml 2017-06-14 16:57:17.000000000 +0100
@@ -35,11 +35,13 @@
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
+ - {{native}}libxml2
run:
- r-base
- {{native}}gcc-libs # [win]
- libgcc # [not win]
+ - {{native}}libxml2
test:
commands:
diff -urN r-packages-new/r-xml2/meta.yaml r-packages-new.fixed/r-xml2/meta.yaml
--- r-packages-new/r-xml2/meta.yaml 2017-06-14 17:12:55.000000000 +0100
+++ r-packages-new.fixed/r-xml2/meta.yaml 2017-06-14 16:59:28.000000000 +0100
@@ -37,6 +37,7 @@
- posix # [win]
- {{native}}toolchain # [win]
- gcc # [not win]
+ - {{native}}libxml2
run:
- r-base
@@ -44,6 +45,7 @@
- r-rcpp >=0.11.4.6
- {{native}}gcc-libs # [win]
- libgcc # [not win]
+ - {{native}}libxml2
test:
commands:
diff -urN r-packages-new/r-xml2/meta.yaml.rej r-packages-new.fixed/r-xml2/meta.yaml.rej
--- r-packages-new/r-xml2/meta.yaml.rej 1970-01-01 01:00:00.000000000 +0100
+++ r-packages-new.fixed/r-xml2/meta.yaml.rej 2017-06-14 15:21:01.000000000 +0100
@@ -0,0 +1,35 @@
+***************
+*** 33,47 ****
+ build:
+ - r-base
+ - r-bh
+- - r-rcpp
+ - posix # [win]
+ - {{native}}toolchain # [win]
+ - gcc # [not win]
+
+ run:
+ - r-base
+ - r-bh
+- - r-rcpp
+
+ test:
+ commands:
+--- 33,49 ----
+ build:
+ - r-base
+ - r-bh
++ - r-rcpp >=0.11.4.6
+ - posix # [win]
+ - {{native}}toolchain # [win]
+ - gcc # [not win]
++ - {{native}}libxml2
+
+ run:
+ - r-base
+ - r-bh
++ - r-rcpp >=0.11.4.6
++ - {{native}}libxml2
+
+ test:
+ commands:
diff -urN r-packages-new/r-xts/meta.yaml r-packages-new.fixed/r-xts/meta.yaml
--- r-packages-new/r-xts/meta.yaml 2017-06-14 17:12:59.000000000 +0100
+++ r-packages-new.fixed/r-xts/meta.yaml 2017-06-14 15:21:01.000000000 +0100
@@ -21,7 +21,7 @@
build:
# If this is a new build for the same version, increment the build number.
- number: 0
+ number: 2
# This is required to make R link correctly on Linux.
rpaths:
diff -urN r-packages-new/r-yaml/build.sh r-packages-new.fixed/r-yaml/build.sh
--- r-packages-new/r-yaml/build.sh 2017-06-14 17:13:00.000000000 +0100
+++ r-packages-new.fixed/r-yaml/build.sh 2017-06-14 15:21:01.000000000 +0100
@@ -4,6 +4,13 @@
mv DESCRIPTION DESCRIPTION.old
grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+# On OS X, the only way to build packages currently is by having
+# DYLD_FALLBACK_LIBRARY_PATH set. We do not use DYLD_LIBRARY_PATH because that
+# screws up some of the system libraries that have older versions of libjpeg
+# than the one in Anaconda. DYLD_FALLBACK_LIBRARY_PATH will only come
+# into play if it cannot find the library via normal means. The default comes
+# from 'man dyld'.
+export DYLD_FALLBACK_LIBRARY_PATH=$PREFIX/lib
$R CMD INSTALL --build .
# Add more build steps here, if they are necessary.