[ci run] bulk linux updates

bioconda · Jul 12, 2023 · 51f1186 · 51f1186
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commit 51f1186
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diff --git a/recipes/bioconductor-bgmix/build.sh b/recipes/bioconductor-bgmix/build.sh
@@ -8,4 +8,4 @@ CXX=$CXX
 CXX98=$CXX
 CXX11=$CXX
 CXX14=$CXX" > ~/.R/Makevars
-$R CMD INSTALL --build .
+CXXFLAGS="${CXXFLAGS} -std=c++14" $R CMD INSTALL --build .
diff --git a/recipes/bioconductor-chemmineob/meta.yaml b/recipes/bioconductor-chemmineob/meta.yaml
@@ -12,6 +12,8 @@ source:
     - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: 5d721ca0fa36f8b42fecca0ab4f98910
+  patches:
+    - patch
 build:
   number: 0
   rpaths:
@@ -28,12 +30,16 @@ requirements:
     - 'r-rcpp >=0.11.0'
     - libblas
     - liblapack
+    - openbabel >=3
+    - eigen
   run:
     - 'bioconductor-biocgenerics >=0.46.0,<0.47.0'
     - 'bioconductor-zlibbioc >=1.46.0,<1.47.0'
     - r-base
     - r-bh
     - 'r-rcpp >=0.11.0'
+    - openbabel >=3
+    - eigen
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}

diff --git a/recipes/bioconductor-gemma.r/meta.yaml b/recipes/bioconductor-gemma.r/meta.yaml
@@ -39,6 +39,7 @@ requirements:
     - r-stringr
     - r-tibble
     - r-tidyr
+    - r-digest
   run:
     - 'bioconductor-biobase >=2.60.0,<2.61.0'
     - 'bioconductor-s4vectors >=0.38.0,<0.39.0'
@@ -58,6 +59,7 @@ requirements:
     - r-stringr
     - r-tibble
     - r-tidyr
+    - r-digest
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

diff --git a/recipes/bioconductor-gpumagic/meta.yaml b/recipes/bioconductor-gpumagic/meta.yaml
@@ -13,6 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: e9b10f314b0124f19525cc73763e9b15
 build:
+  skip: True  # [osx]
   number: 0
   rpaths:
     - lib/R/lib/
@@ -31,6 +32,7 @@ requirements:
     - r-stringr
     - libblas
     - liblapack
+    - ocl-icd
   run:
     - 'bioconductor-biocgenerics >=0.46.0,<0.47.0'
     - r-base
@@ -40,6 +42,7 @@ requirements:
     - r-pryr
     - r-rcpp
     - r-stringr
+    - ocl-icd
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}

diff --git a/recipes/bioconductor-rawrr/meta.yaml b/recipes/bioconductor-rawrr/meta.yaml
@@ -23,8 +23,10 @@ build:
 requirements:
   host:
     - r-base
+    - mono >=4.5.1
   run:
     - r-base
+    - mono >=4.5.1
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

diff --git a/recipes/bioconductor-sictools/build.sh b/recipes/bioconductor-sictools/build.sh
@@ -2,10 +2,10 @@
 mv DESCRIPTION DESCRIPTION.old
 grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
 mkdir -p ~/.R
-echo -e "CC=$CC
+echo -e "CC=$CC -I$PREFIX/include -L$PREFIX/lib
 FC=$FC
-CXX=$CXX
+CXX=$CXX -I$PREFIX/include -L$PREFIX/lib
 CXX98=$CXX
 CXX11=$CXX
 CXX14=$CXX" > ~/.R/Makevars
-$R CMD INSTALL --build .
+MAKE="make LIBCURSES=-lncurses" $R CMD INSTALL --build .
diff --git a/recipes/bioconductor-sictools/meta.yaml b/recipes/bioconductor-sictools/meta.yaml
@@ -31,6 +31,8 @@ requirements:
     - 'r-stringr >=0.6.2'
     - libblas
     - liblapack
+    - zlib
+    - ncurses
   run:
     - 'bioconductor-biostrings >=2.68.0,<2.69.0'
     - 'bioconductor-genomicranges >=1.52.0,<1.53.0'
@@ -41,6 +43,8 @@ requirements:
     - 'r-matrixstats >=0.10.0'
     - 'r-plyr >=1.8.3'
     - 'r-stringr >=0.6.2'
+    - zlib
+    - ncurses
   build:
     - {{ compiler('c') }}
     - make

diff --git a/recipes/r-DGEclustering/meta.yaml b/recipes/r-DGEclustering/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{sha256}}
 
 build:
-  number: 4
+  number: 5
   skip: true  # [win32]
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-abdiv/meta.yaml b/recipes/r-abdiv/meta.yaml
@@ -9,7 +9,7 @@ source:
   sha256: 49484975fda33200175fd58b5387ea6dff120b66566b740018be699417497414
 
 build:
-  number: 1
+  number: 2
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-acidbase/meta.yaml b/recipes/r-acidbase/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 2e11efcb9e4deb2c9b9ae94b17d032a600ad374ee289e5c0a6e4b3f09b03a09b
 
 build:
-  number: 0
+  number: 1
   noarch: generic
 
 requirements:

diff --git a/recipes/r-acidcli/meta.yaml b/recipes/r-acidcli/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: b27b6f9c6f7990a1a41bd0b650f870bcd18e0f4541ccc7a398676306cf1fbf55
 
 build:
-  number: 1
+  number: 2
   noarch: generic
 
 requirements:

diff --git a/recipes/r-acidexperiment/meta.yaml b/recipes/r-acidexperiment/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 0dd42744cb2953550fb15fda5b4a59d87d00b12aa117f7c9f0cd6965436ed38c
 
 build:
-  number: 1
+  number: 2
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-acidgenerics/meta.yaml b/recipes/r-acidgenerics/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 095d751088d965cc5f602fc44e68426ee358e6d8fbb1f1172b5fb2be2a500118
 
 build:
-  number: 1
+  number: 2
   noarch: generic
 
 requirements:

diff --git a/recipes/r-acidgenomes/meta.yaml b/recipes/r-acidgenomes/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 60cfa3476363bfc8ec876667091f498f1d2f6ed8aa1361cc82347dbcb8b5ce67
 
 build:
-  number: 1
+  number: 2
   noarch: generic
 
 requirements:

diff --git a/recipes/r-acidgsea/meta.yaml b/recipes/r-acidgsea/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 73678edbac84cf77eef75d8e917d3c2bad89f67a3fe7d64fbe7ee5e6481e3a4c
 
 build:
-  number: 1
+  number: 2
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-acidmarkdown/meta.yaml b/recipes/r-acidmarkdown/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: cd875e70167137312ada7dad289eaae58817d943604a15c862fa95bd0ca87514
 
 build:
-  number: 1
+  number: 2
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-acidplots/meta.yaml b/recipes/r-acidplots/meta.yaml
@@ -11,7 +11,7 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: 2
 
 requirements:
   host:

diff --git a/recipes/r-acidplyr/meta.yaml b/recipes/r-acidplyr/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 3dadd35b680bcd090b2660d6516d13bc1827355b00ef11d2430b8f8e79c06565
 
 build:
-  number: 1
+  number: 2
   noarch: generic
 
 requirements:

diff --git a/recipes/r-acidsinglecell/meta.yaml b/recipes/r-acidsinglecell/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 8fd2d56349c8377dbae16ce5e844ca259cd4d6793bcc13830b15af619350ecc9
 
 build:
-  number: 1
+  number: 2
   noarch: generic
 
 requirements:

diff --git a/recipes/r-alakazam/meta.yaml b/recipes/r-alakazam/meta.yaml
@@ -13,7 +13,7 @@ source:
   sha256: 161c87a946857da2b876f679abc4ae8d265835c92c0d56e0ecacf0aea04084d4
 
 build:
-  number: 2
+  number: 3
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/r-ampvis/meta.yaml b/recipes/r-ampvis/meta.yaml
@@ -10,7 +10,7 @@ source:
   md5: e898bf83d56eb7bfc17535b563932690
 
 build:
-  number: 5
+  number: 6
 
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-ampvis2/meta.yaml b/recipes/r-ampvis2/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: b75f2e92e3d8999e47b8004824b7d1e0a9bb7b0c5fb116296e11a0d87ec0ac4a
 
 build:
-  number: 1
+  number: 2
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-anndata/meta.yaml b/recipes/r-anndata/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 35561748978b82739eb75b64e0532919b122eccebf8cc765c964e549884a56cd
 
 build:
-  number: 1
+  number: 2
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-annotables/meta.yaml b/recipes/r-annotables/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: 779d888f641544d85f2e072cd3b6f144b34bbc69989ba37c4310b888a74af805
 
 build:
-  number: 0
+  number: 1
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-aroma.affymetrix/meta.yaml b/recipes/r-aroma.affymetrix/meta.yaml
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 2
+  number: 3
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/r-aroma.core/meta.yaml b/recipes/r-aroma.core/meta.yaml
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/r-autospill/meta.yaml b/recipes/r-autospill/meta.yaml
@@ -9,7 +9,7 @@ source:
   sha256: 902d87a7b5dec2fe20b024b39f13c80e24e29d1b69e899dff69546b98fd26599 
 
 build:
-  number: 1
+  number: 2
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-basejump/meta.yaml b/recipes/r-basejump/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 98a0c18f37fdcff995fd98020828a3ef91a5ca1314d5968b27793ddd2975203d
 
 build:
-  number: 0
+  number: 1
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-bayesprism/meta.yaml b/recipes/r-bayesprism/meta.yaml
@@ -9,7 +9,7 @@ source:
   sha256: 5fbb453d57706d39a88b186497d7a777fcc2e18bd36bff58ee3e7189a0c14599
 
 build:
-  number: 2
+  number: 3
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/r-bcbiobase/meta.yaml b/recipes/r-bcbiobase/meta.yaml
@@ -11,7 +11,7 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: 2
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/r-bcbiornaseq/meta.yaml b/recipes/r-bcbiornaseq/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: ecd2d205a3337d0ad7cf77bcf5a119cef279a45a4818c924b90ab642a7e461c2
 
 build:
-  number: 1
+  number: 2
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-bcbiosinglecell/meta.yaml b/recipes/r-bcbiosinglecell/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: b33c69257835391967fe23e30c8ef62bb5aab81cbe72598a5201b940ba656752
 
 build:
-  number: 1
+  number: 2
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-bedtoolsr/meta.yaml b/recipes/r-bedtoolsr/meta.yaml
@@ -10,7 +10,7 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: 2
 
 requirements:
   host:

diff --git a/recipes/r-beyondcell/meta.yaml b/recipes/r-beyondcell/meta.yaml
@@ -14,7 +14,7 @@ source:
 
 build:
   merge_build_host: True  # [win]
-  number: 1
+  number: 2
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/r-biodb/meta.yaml b/recipes/r-biodb/meta.yaml
@@ -9,7 +9,7 @@ source:
   sha256: abc4c533a2824e98bb6b4e94b5288bf89c6cf2ba5e62804d0e8dc75147eecb88
 
 build:
-  number: 7
+  number: 8
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/r-biomartr/meta.yaml b/recipes/r-biomartr/meta.yaml
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/r-bisquerna/meta.yaml b/recipes/r-bisquerna/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: 76886871c497a71427929654ca0e257ae949f23af53a6cf43e31bf642e2d775c
 
 build:
-  number: 1
+  number: 2
   noarch: generic
   rpaths:
     - lib/R/lib/

diff --git a/recipes/r-boutroslabplottinggeneral/meta.yaml b/recipes/r-boutroslabplottinggeneral/meta.yaml
@@ -3,7 +3,7 @@ package:
   version: "5.3.4"
 
 build:
-  number: 4
+  number: 5
 
 source:
   url: https://depot.galaxyproject.org/software/boutroslabplottinggeneral/boutroslabplottinggeneral_5.3.4_src_all.tar.gz