Browse code

Added GitHub workflows and removed Travis yml

Joshua D. Campbell authored on 12/09/2021 16:05:59
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deleted file mode 100644
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@@ -1,26 +0,0 @@
1
-language: r
2
-cache: packages
3
-sudo: false
4
-warnings_are_errors: false
5
-bioc_required: true
6
-r_build_args: "--no-build-vignettes"
7
-r_check_args: "--no-vignettes --no-build-vignettes --as-cran"
8
-notifications:
9
-  slack:
10
-    secure: 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
11
-
12
-r_github_packages:
13
-  - r-lib/covr
14
-  - jimhester/lintr
15
-  - spatstat/spatstat@v1.64-1
16
-after_success:
17
-  - R CMD INSTALL $PKG_TARBALL
18
-  - Rscript -e 'covr::coveralls()'
19
-  - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL, cyclocomp_linter(complexity_limit = 100)), exclusions = list("R/RcppExports.R"))'
20
-
21
-addons:
22
-  apt:
23
-    sources:
24
-    - sourceline: 'ppa:opencpu/imagemagick'
25
-    packages:
26
-    - libmagick++-dev
Browse code

package update

Joshua D. Campbell authored on 15/03/2021 21:18:11
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@@ -12,7 +12,7 @@ notifications:
12 12
 r_github_packages:
13 13
   - r-lib/covr
14 14
   - jimhester/lintr
15
-  - spatstat/spatstat@66c4540
15
+  - spatstat/spatstat@v1.64-1
16 16
 after_success:
17 17
   - R CMD INSTALL $PKG_TARBALL
18 18
   - Rscript -e 'covr::coveralls()'
Browse code

package update

Joshua D. Campbell authored on 15/03/2021 20:53:06
Showing 1 changed files
... ...
@@ -12,6 +12,7 @@ notifications:
12 12
 r_github_packages:
13 13
   - r-lib/covr
14 14
   - jimhester/lintr
15
+  - spatstat/spatstat@66c4540
15 16
 after_success:
16 17
   - R CMD INSTALL $PKG_TARBALL
17 18
   - Rscript -e 'covr::coveralls()'
Browse code

add addons to .travis.yml to fix magick error on TRAVIS CI

zhewa authored on 30/09/2020 02:14:11
Showing 1 changed files
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@@ -16,3 +16,10 @@ after_success:
16 16
   - R CMD INSTALL $PKG_TARBALL
17 17
   - Rscript -e 'covr::coveralls()'
18 18
   - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL, cyclocomp_linter(complexity_limit = 100)), exclusions = list("R/RcppExports.R"))'
19
+
20
+addons:
21
+  apt:
22
+    sources:
23
+    - sourceline: 'ppa:opencpu/imagemagick'
24
+    packages:
25
+    - libmagick++-dev
Browse code

remove before_install: update.pacakges

zhewa authored on 29/09/2020 20:46:15
Showing 1 changed files
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@@ -3,8 +3,6 @@ cache: packages
3 3
 sudo: false
4 4
 warnings_are_errors: false
5 5
 bioc_required: true
6
-before_install:
7
-  - Rscript -e 'update.packages(ask = FALSE)'
8 6
 r_build_args: "--no-build-vignettes"
9 7
 r_check_args: "--no-vignettes --no-build-vignettes --as-cran"
10 8
 notifications:
Browse code

remove dist: trusty

zhewa authored on 29/09/2020 20:32:55
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@@ -1,6 +1,5 @@
1 1
 language: r
2 2
 cache: packages
3
-dist: trusty
4 3
 sudo: false
5 4
 warnings_are_errors: false
6 5
 bioc_required: true
Browse code

merged vignette fixes

Joshua D. Campbell authored on 13/03/2020 00:44:31
Showing 0 changed files
Browse code

unscript

Joshua D. Campbell authored on 02/03/2020 15:20:52
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@@ -4,7 +4,6 @@ dist: trusty
4 4
 sudo: false
5 5
 warnings_are_errors: false
6 6
 bioc_required: true
7
-script: true
8 7
 before_install:
9 8
   - Rscript -e 'update.packages(ask = FALSE)'
10 9
 r_build_args: "--no-build-vignettes"
Browse code

script

Joshua D. Campbell authored on 02/03/2020 15:11:17
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@@ -4,6 +4,7 @@ dist: trusty
4 4
 sudo: false
5 5
 warnings_are_errors: false
6 6
 bioc_required: true
7
+script: true
7 8
 before_install:
8 9
   - Rscript -e 'update.packages(ask = FALSE)'
9 10
 r_build_args: "--no-build-vignettes"
Browse code

Updated docs. Fixed package referncing in celdaMarkerPlot. Updated DESCRIPTION.

Joshua D. Campbell authored on 02/03/2020 04:51:11
Showing 1 changed files
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@@ -15,6 +15,7 @@ notifications:
15 15
 r_github_packages:
16 16
   - r-lib/covr
17 17
   - jimhester/lintr
18
+  - LTLA/BiocNeighbors
18 19
 after_success:
19 20
   - R CMD INSTALL $PKG_TARBALL
20 21
   - Rscript -e 'covr::coveralls()'
Browse code

travis

Joshua D. Campbell authored on 11/02/2020 20:45:38
Showing 1 changed files
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@@ -4,12 +4,6 @@ dist: trusty
4 4
 sudo: false
5 5
 warnings_are_errors: false
6 6
 bioc_required: true
7
-jobs:
8
-  include:
9
-    - stage: prepare cache
10
-      script: true
11
-    - stage: run
12
-      script: false
13 7
 before_install:
14 8
   - Rscript -e 'update.packages(ask = FALSE)'
15 9
 r_build_args: "--no-build-vignettes"
Browse code

travis

Joshua D. Campbell authored on 11/02/2020 20:06:50
Showing 1 changed files
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@@ -8,7 +8,8 @@ jobs:
8 8
   include:
9 9
     - stage: prepare cache
10 10
       script: true
11
-    - stage: test
11
+    - stage: run
12
+      script: false
12 13
 before_install:
13 14
   - Rscript -e 'update.packages(ask = FALSE)'
14 15
 r_build_args: "--no-build-vignettes"
Browse code

travis

Joshua D. Campbell authored on 11/02/2020 19:08:10
Showing 1 changed files
... ...
@@ -6,10 +6,9 @@ warnings_are_errors: false
6 6
 bioc_required: true
7 7
 jobs:
8 8
   include:
9
-    - stage: precache
9
+    - stage: prepare cache
10 10
       script: true
11 11
     - stage: test
12
-      test: true
13 12
 before_install:
14 13
   - Rscript -e 'update.packages(ask = FALSE)'
15 14
 r_build_args: "--no-build-vignettes"
Browse code

travis

Joshua D. Campbell authored on 11/02/2020 18:57:38
Showing 1 changed files
... ...
@@ -8,7 +8,8 @@ jobs:
8 8
   include:
9 9
     - stage: precache
10 10
       script: true
11
-    - test
11
+    - stage: test
12
+      test: true
12 13
 before_install:
13 14
   - Rscript -e 'update.packages(ask = FALSE)'
14 15
 r_build_args: "--no-build-vignettes"
Browse code

added test stage

Joshua D. Campbell authored on 11/02/2020 18:37:52
Showing 1 changed files
... ...
@@ -8,6 +8,7 @@ jobs:
8 8
   include:
9 9
     - stage: precache
10 10
       script: true
11
+    - test
11 12
 before_install:
12 13
   - Rscript -e 'update.packages(ask = FALSE)'
13 14
 r_build_args: "--no-build-vignettes"
Browse code

Added step to warm up the cache

Joshua D. Campbell authored on 11/02/2020 16:55:20
Showing 1 changed files
... ...
@@ -4,6 +4,10 @@ dist: trusty
4 4
 sudo: false
5 5
 warnings_are_errors: false
6 6
 bioc_required: true
7
+jobs:
8
+  include:
9
+    - stage: precache
10
+      script: true
7 11
 before_install:
8 12
   - Rscript -e 'update.packages(ask = FALSE)'
9 13
 r_build_args: "--no-build-vignettes"
Browse code

Manually point to Seurat github install

Joshua D. Campbell authored on 11/02/2020 03:10:01
Showing 1 changed files
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@@ -15,6 +15,7 @@ notifications:
15 15
 r_github_packages:
16 16
   - r-lib/covr
17 17
   - jimhester/lintr
18
+  - satijalab/seurat
18 19
 after_success:
19 20
   - R CMD INSTALL $PKG_TARBALL
20 21
   - Rscript -e 'covr::coveralls()'
Browse code

Changed lint settings and removed R devel

Joshua D. Campbell authored on 22/01/2020 03:18:20
Showing 1 changed files
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@@ -1,7 +1,5 @@
1 1
 language: r
2 2
 cache: packages
3
-r:
4
-  - devel
5 3
 dist: trusty
6 4
 sudo: false
7 5
 warnings_are_errors: false
... ...
@@ -20,4 +18,4 @@ r_github_packages:
20 18
 after_success:
21 19
   - R CMD INSTALL $PKG_TARBALL
22 20
   - Rscript -e 'covr::coveralls()'
23
-  - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL, cyclocomp_linter(complexity_limit = 40)), exclusions = list("R/RcppExports.R"))'
21
+  - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL, cyclocomp_linter(complexity_limit = 100)), exclusions = list("R/RcppExports.R"))'
Browse code

test removing install of limprf

Joshua D. Campbell authored on 22/01/2020 02:48:15
Showing 1 changed files
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@@ -10,10 +10,6 @@ before_install:
10 10
   - Rscript -e 'update.packages(ask = FALSE)'
11 11
 r_build_args: "--no-build-vignettes"
12 12
 r_check_args: "--no-vignettes --no-build-vignettes --as-cran"
13
-addons:
14
-  apt:
15
-    packages:
16
-    - libmpfr-dev
17 13
 notifications:
18 14
   slack:
19 15
     secure: 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
Browse code

reverted travis.yml

Joshua D. Campbell authored on 22/01/2020 01:01:03
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@@ -1,9 +1,5 @@
1 1
 language: r
2
-cache:
3
-  directories:
4
-    - $TRAVIS_BUILD_DIR/packrat/src
5
-    - $TRAVIS_BUILD_DIR/packrat/lib
6
-  packages: true
2
+cache: packages
7 3
 r:
8 4
   - devel
9 5
 dist: trusty
Browse code

Updated travis.yml to cache packages

Joshua D. Campbell authored on 22/01/2020 00:41:08
Showing 1 changed files
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@@ -1,7 +1,4 @@
1 1
 language: r
2
-install:
3
-  - R -e "0" --args --bootstrap-packrat
4
-  - R -e "packrat::restore(restart = FALSE)"
5 2
 cache:
6 3
   directories:
7 4
     - $TRAVIS_BUILD_DIR/packrat/src
Browse code

Updated travis.yml to cache packages

Joshua D. Campbell authored on 22/01/2020 00:34:18
Showing 1 changed files
... ...
@@ -1,7 +1,14 @@
1 1
 language: r
2
+install:
3
+  - R -e "0" --args --bootstrap-packrat
4
+  - R -e "packrat::restore(restart = FALSE)"
5
+cache:
6
+  directories:
7
+    - $TRAVIS_BUILD_DIR/packrat/src
8
+    - $TRAVIS_BUILD_DIR/packrat/lib
9
+  packages: true
2 10
 r:
3 11
   - devel
4
-cache: packages
5 12
 dist: trusty
6 13
 sudo: false
7 14
 warnings_are_errors: false
... ...
@@ -24,4 +31,4 @@ r_github_packages:
24 31
 after_success:
25 32
   - R CMD INSTALL $PKG_TARBALL
26 33
   - Rscript -e 'covr::coveralls()'
27
-  - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL, cyclocomp_linter(complexity_limit = 40)), exclusions = list("R/RcppExports.R"))'
28 34
\ No newline at end of file
35
+  - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL, cyclocomp_linter(complexity_limit = 40)), exclusions = list("R/RcppExports.R"))'
Browse code

cyclocomp_linter(complexity_limit = 40)

87875172 authored on 18/09/2019 14:33:08
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@@ -24,4 +24,4 @@ r_github_packages:
24 24
 after_success:
25 25
   - R CMD INSTALL $PKG_TARBALL
26 26
   - Rscript -e 'covr::coveralls()'
27
-  - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL), exclusions = list("R/RcppExports.R"))'
28 27
\ No newline at end of file
28
+  - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL, cyclocomp_linter(complexity_limit = 40)), exclusions = list("R/RcppExports.R"))'
29 29
\ No newline at end of file
Browse code

fix lints

zhewa authored on 12/04/2019 15:46:11
Showing 1 changed files
... ...
@@ -24,4 +24,4 @@ r_github_packages:
24 24
 after_success:
25 25
   - R CMD INSTALL $PKG_TARBALL
26 26
   - Rscript -e 'covr::coveralls()'
27
-  - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL))'
28 27
\ No newline at end of file
28
+  - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL), exclusions = list("R/RcppExports.R"))'
29 29
\ No newline at end of file
Browse code

add lintr integration

zhewa authored on 10/04/2019 02:09:20
Showing 1 changed files
... ...
@@ -20,5 +20,8 @@ notifications:
20 20
 
21 21
 r_github_packages:
22 22
   - r-lib/covr
23
+  - jimhester/lintr
23 24
 after_success:
25
+  - R CMD INSTALL $PKG_TARBALL
24 26
   - Rscript -e 'covr::coveralls()'
27
+  - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL))'
25 28
\ No newline at end of file
Browse code

change .travis.yml R version to devel

87875172 authored on 27/03/2019 15:34:09
Showing 1 changed files
... ...
@@ -1,4 +1,6 @@
1 1
 language: r
2
+r:
3
+  - devel
2 4
 cache: packages
3 5
 dist: trusty
4 6
 sudo: false
Browse code

Updating Travis configuration

Former-commit-id: 56ccd0901a120679364ba2e1669f9024b555d866

Sean Corbett authored on 19/10/2018 17:26:36
Showing 1 changed files
... ...
@@ -2,12 +2,12 @@ language: r
2 2
 cache: packages
3 3
 dist: trusty
4 4
 sudo: false
5
-warnings_are_errors: true
5
+warnings_are_errors: false
6 6
 bioc_required: true
7 7
 before_install:
8 8
   - Rscript -e 'update.packages(ask = FALSE)'
9 9
 r_build_args: "--no-build-vignettes"
10
-r_check_args: "--no-build-vignettes --as-cran"
10
+r_check_args: "--no-vignettes --no-build-vignettes --as-cran"
11 11
 addons:
12 12
   apt:
13 13
     packages:
Browse code

Putting coveralls back into Travis

Former-commit-id: c85d3c076c4bf9046a0cffc0fdc1dc7c97a8a6e5

Sean Corbett authored on 29/08/2018 06:16:47
Showing 1 changed files
... ...
@@ -16,7 +16,7 @@ notifications:
16 16
   slack:
17 17
     secure: 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
18 18
 
19
-#r_github_packages:
20
-#  - r-lib/covr
21
-#after_success:
22
-#  - Rscript -e 'covr::coveralls()'
19
+r_github_packages:
20
+  - r-lib/covr
21
+after_success:
22
+  - Rscript -e 'covr::coveralls()'
Browse code

Removing coveralls in build; it takes way too long.

Former-commit-id: 8816731967dddacbdffffd3f9139a7a4d29d1ad4

Sean Corbett authored on 29/08/2018 05:42:29
Showing 1 changed files
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@@ -16,7 +16,7 @@ notifications:
16 16
   slack:
17 17
     secure: 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
18 18
 
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-r_github_packages:
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-  - r-lib/covr
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-after_success:
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-  - Rscript -e 'covr::coveralls()'
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+#r_github_packages:
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+#  - r-lib/covr
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+#after_success:
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+#  - Rscript -e 'covr::coveralls()'
Browse code

Fixing broken example, skipping broken unit test. Adding Coveralls.

Former-commit-id: 13cd4a49bbefdf3354bd423b90b854b9c8aa1157

Sean Corbett authored on 29/08/2018 05:16:23
Showing 1 changed files
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@@ -15,3 +15,8 @@ addons:
15 15
 notifications:
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   slack:
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     secure: 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+
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+r_github_packages:
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+  - r-lib/covr
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+after_success:
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+  - Rscript -e 'covr::coveralls()'
Browse code

Fix argument checking in wrapper (#269)

* Fix parameter checking code in celda wrapper.
* Removing deprecated parameter. Refactoring test.
* Updating documentation.
* Add SummarizedExperiment to Depends.
* Added _ prefix to C function names. Add data.table to namespace


Former-commit-id: f2efa67d604e95f3250f7ec6c4023f944cdcd859

Sean authored on 03/07/2018 20:25:20 • GitHub committed on 03/07/2018 20:25:20
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@@ -5,7 +5,7 @@ sudo: false
5 5
 warnings_are_errors: true
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 bioc_required: true
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 before_install:
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-- Rscript -e 'update.packages(ask = FALSE)'
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+  - Rscript -e 'update.packages(ask = FALSE)'
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 r_build_args: "--no-build-vignettes"
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 r_check_args: "--no-build-vignettes --as-cran"
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 addons:
Browse code

Added travis slack integration, added .travis.yml to Rbuildignore

Former-commit-id: 61fae36348b6f56a7b8741b4d16dbd4e24b8d9e1

David Jenkins authored on 02/06/2017 18:35:03
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@@ -11,4 +11,7 @@ r_check_args: "--no-build-vignettes --as-cran"
11 11
 addons:
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   apt:
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     packages:
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-    - libmpfr-dev
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\ No newline at end of file
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+    - libmpfr-dev
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+notifications:
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+  slack:
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+    secure: 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
Browse code

build and check args

Former-commit-id: 1c1696a85d1c6d909a95ad100ba4f0c46d0ef29c

David Jenkins authored on 31/05/2017 22:52:02
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@@ -6,6 +6,8 @@ warnings_are_errors: true
6 6
 bioc_required: true
7 7
 before_install:
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 - Rscript -e 'update.packages(ask = FALSE)'
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+r_build_args: "--no-build-vignettes"
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+r_check_args: "--no-build-vignettes --as-cran"
9 11
 addons:
10 12
   apt:
11 13
     packages:
Browse code

Added requirement for libmpfr-dev

Former-commit-id: e25aca009b77d37a4649c9f57f4030bfebf5e0b1

David Jenkins authored on 31/05/2017 19:26:13
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@@ -6,3 +6,7 @@ warnings_are_errors: true
6 6
 bioc_required: true
7 7
 before_install:
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 - Rscript -e 'update.packages(ask = FALSE)'
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+addons:
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+  apt:
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+    packages:
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+    - libmpfr-dev
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\ No newline at end of file
Browse code

Travis integration

Former-commit-id: 346147fe79e79ee71961e9cf790ad46f87e3d848

David Jenkins authored on 31/05/2017 18:59:53
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new file mode 100644
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@@ -0,0 +1,8 @@
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+language: r
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+cache: packages
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+dist: trusty
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+sudo: false
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+warnings_are_errors: true
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+bioc_required: true
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+before_install:
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+- Rscript -e 'update.packages(ask = FALSE)'