Browse code

Allow Bioc devel builds to fail on Travis

sherman5 authored on 26/11/2019 03:14:10
Showing1 changed files
... ...
@@ -12,6 +12,8 @@ jobs:
12 12
   allow_failures:
13 13
     - name: Linting
14 14
     - name: Code Formatting
15
+    - name: Bioconductor Devel Testing - Linux
16
+    - name: Bioconductor Devel Testing - OSX
15 17
   include:
16 18
     - name: "Bioconductor Release Testing - Linux"
17 19
       os: linux
Browse code

Remove ccache usage on Travis for Mac

Tom Sherman authored on 17/07/2019 21:53:25
Showing1 changed files
... ...
@@ -40,8 +40,6 @@ jobs:
40 40
       r: bioc-release
41 41
       repos:
42 42
         CRAN: http://cran.rstudio.com/ 
43
-      before_install:
44
-        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) clang$(VER) -std=gnu99\nCXX=$(CCACHE) clang++$(VER)\nC11=$(CCACHE) clang++$(VER)\nC14=$(CCACHE) clang++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
45 43
 
46 44
     - name: "Bioconductor Devel Testing - OSX"
47 45
       os: osx
... ...
@@ -50,8 +48,6 @@ jobs:
50 48
       r: bioc-devel
51 49
       repos:
52 50
         CRAN: http://cran.rstudio.com/ 
53
-      before_install:
54
-        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) clang$(VER) -std=gnu99\nCXX=$(CCACHE) clang++$(VER)\nC11=$(CCACHE) clang++$(VER)\nC14=$(CCACHE) clang++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
55 51
 
56 52
     - name: "Test Running in Debug Mode"
57 53
       if: tag IS NOT present
Browse code

Use clang for Travis builds on Mac

Tom Sherman authored on 17/07/2019 21:38:03
Showing1 changed files
... ...
@@ -41,7 +41,7 @@ jobs:
41 41
       repos:
42 42
         CRAN: http://cran.rstudio.com/ 
43 43
       before_install:
44
-        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
44
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) clang$(VER) -std=gnu99\nCXX=$(CCACHE) clang++$(VER)\nC11=$(CCACHE) clang++$(VER)\nC14=$(CCACHE) clang++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
45 45
 
46 46
     - name: "Bioconductor Devel Testing - OSX"
47 47
       os: osx
... ...
@@ -51,7 +51,7 @@ jobs:
51 51
       repos:
52 52
         CRAN: http://cran.rstudio.com/ 
53 53
       before_install:
54
-        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
54
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) clang$(VER) -std=gnu99\nCXX=$(CCACHE) clang++$(VER)\nC11=$(CCACHE) clang++$(VER)\nC14=$(CCACHE) clang++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
55 55
 
56 56
     - name: "Test Running in Debug Mode"
57 57
       if: tag IS NOT present
Browse code

test on osx as well as linux

Tom Sherman authored on 02/07/2019 17:58:43
Showing1 changed files
... ...
@@ -7,18 +7,14 @@ addons:
7 7
 
8 8
 cache: ccache
9 9
 
10
-os:
11
-  - linux
12
-  - osx
13
-
14 10
 jobs:
15 11
   fast_finish: true
16 12
   allow_failures:
17 13
     - name: Linting
18 14
     - name: Code Formatting
19 15
   include:
20
-    - name: "Bioconductor Release Testing"
21
-      
16
+    - name: "Bioconductor Release Testing - Linux"
17
+      os: linux
22 18
       if: tag IS NOT present
23 19
       language: r
24 20
       r: bioc-release
... ...
@@ -26,7 +22,9 @@ jobs:
26 22
         CRAN: http://cran.rstudio.com/ 
27 23
       before_install:
28 24
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
29
-    - name: "Bioconductor Devel Testing"
25
+
26
+    - name: "Bioconductor Devel Testing - Linux"
27
+      os: linux
30 28
       if: tag IS NOT present
31 29
       language: r
32 30
       r: bioc-devel
... ...
@@ -34,6 +32,27 @@ jobs:
34 32
         CRAN: http://cran.rstudio.com/ 
35 33
       before_install:
36 34
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
35
+
36
+    - name: "Bioconductor Release Testing - OSX"
37
+      os: osx
38
+      if: tag IS NOT present
39
+      language: r
40
+      r: bioc-release
41
+      repos:
42
+        CRAN: http://cran.rstudio.com/ 
43
+      before_install:
44
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
45
+
46
+    - name: "Bioconductor Devel Testing - OSX"
47
+      os: osx
48
+      if: tag IS NOT present
49
+      language: r
50
+      r: bioc-devel
51
+      repos:
52
+        CRAN: http://cran.rstudio.com/ 
53
+      before_install:
54
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
55
+
37 56
     - name: "Test Running in Debug Mode"
38 57
       if: tag IS NOT present
39 58
       language: r
... ...
@@ -46,9 +65,11 @@ jobs:
46 65
         - R CMD build --no-build-vignettes .
47 66
         - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
48 67
       script: R -f inst/scripts/debugRuns.R
68
+
49 69
     - name: "Linting"
50 70
       if: tag IS NOT present
51 71
       script: echo "linting not implemented"
72
+
52 73
     - name: "Code Formatting"
53 74
       if: tag IS NOT present
54 75
       script: echo "formatting not implemented"
Browse code

test on osx as well as linux

Tom Sherman authored on 02/07/2019 17:56:21
Showing1 changed files
... ...
@@ -7,6 +7,10 @@ addons:
7 7
 
8 8
 cache: ccache
9 9
 
10
+os:
11
+  - linux
12
+  - osx
13
+
10 14
 jobs:
11 15
   fast_finish: true
12 16
   allow_failures:
... ...
@@ -14,6 +18,7 @@ jobs:
14 18
     - name: Code Formatting
15 19
   include:
16 20
     - name: "Bioconductor Release Testing"
21
+      
17 22
       if: tag IS NOT present
18 23
       language: r
19 24
       r: bioc-release
Browse code

don't run Travis on tags

Tom Sherman authored on 02/07/2019 17:53:32
Showing1 changed files
... ...
@@ -14,6 +14,7 @@ jobs:
14 14
     - name: Code Formatting
15 15
   include:
16 16
     - name: "Bioconductor Release Testing"
17
+      if: tag IS NOT present
17 18
       language: r
18 19
       r: bioc-release
19 20
       repos:
... ...
@@ -21,6 +22,7 @@ jobs:
21 22
       before_install:
22 23
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
23 24
     - name: "Bioconductor Devel Testing"
25
+      if: tag IS NOT present
24 26
       language: r
25 27
       r: bioc-devel
26 28
       repos:
... ...
@@ -28,6 +30,7 @@ jobs:
28 30
       before_install:
29 31
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
30 32
     - name: "Test Running in Debug Mode"
33
+      if: tag IS NOT present
31 34
       language: r
32 35
       r: release
33 36
       before_install:
... ...
@@ -39,8 +42,10 @@ jobs:
39 42
         - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
40 43
       script: R -f inst/scripts/debugRuns.R
41 44
     - name: "Linting"
45
+      if: tag IS NOT present
42 46
       script: echo "linting not implemented"
43 47
     - name: "Code Formatting"
48
+      if: tag IS NOT present
44 49
       script: echo "formatting not implemented"
45 50
 
46 51
 #- stage: Valgrind Analysis
Browse code

proper argument for BiocManager::install in travis

sherman5 authored on 26/06/2019 18:31:48
Showing1 changed files
... ...
@@ -34,7 +34,7 @@ jobs:
34 34
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
35 35
       install:
36 36
         - R -e 'install.packages(c("BiocManager", "desc"), repos="http://cran.rstudio.com/")'
37
-        - R -e 'BiocManager::install(desc::desc_get_deps()$package, repos="http://cran.rstudio.com/")'
37
+        - R -e 'BiocManager::install(desc::desc_get_deps()$package, site_repository=c("http://cran.rstudio.com/"))'
38 38
         - R CMD build --no-build-vignettes .
39 39
         - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
40 40
       script: R -f inst/scripts/debugRuns.R
Browse code

fix all repos

sherman5 authored on 26/06/2019 18:22:48
Showing1 changed files
... ...
@@ -16,11 +16,15 @@ jobs:
16 16
     - name: "Bioconductor Release Testing"
17 17
       language: r
18 18
       r: bioc-release
19
+      repos:
20
+        CRAN: http://cran.rstudio.com/ 
19 21
       before_install:
20 22
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
21 23
     - name: "Bioconductor Devel Testing"
22 24
       language: r
23 25
       r: bioc-devel
26
+      repos:
27
+        CRAN: http://cran.rstudio.com/ 
24 28
       before_install:
25 29
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
26 30
     - name: "Test Running in Debug Mode"
... ...
@@ -29,8 +33,8 @@ jobs:
29 33
       before_install:
30 34
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
31 35
       install:
32
-        - R -e 'install.packages(c("BiocManager", "desc"), repos='http://cran.rstudio.com/')'
33
-        - R -e 'BiocManager::install(desc::desc_get_deps()$package, repos='http://cran.rstudio.com/')'
36
+        - R -e 'install.packages(c("BiocManager", "desc"), repos="http://cran.rstudio.com/")'
37
+        - R -e 'BiocManager::install(desc::desc_get_deps()$package, repos="http://cran.rstudio.com/")'
34 38
         - R CMD build --no-build-vignettes .
35 39
         - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
36 40
       script: R -f inst/scripts/debugRuns.R
Browse code

change package repo

sherman5 authored on 26/06/2019 17:56:53
Showing1 changed files
... ...
@@ -29,8 +29,8 @@ jobs:
29 29
       before_install:
30 30
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
31 31
       install:
32
-        - R -e 'install.packages(c("BiocManager", "desc"))'
33
-        - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
32
+        - R -e 'install.packages(c("BiocManager", "desc"), repos='http://cran.rstudio.com/')'
33
+        - R -e 'BiocManager::install(desc::desc_get_deps()$package, repos='http://cran.rstudio.com/')'
34 34
         - R CMD build --no-build-vignettes .
35 35
         - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
36 36
       script: R -f inst/scripts/debugRuns.R
Browse code

specift language in each job

Tom Sherman authored on 26/06/2019 16:31:30
Showing1 changed files
... ...
@@ -1,13 +1,11 @@
1
-language: r
2
-cache: ccache
3
-#sudo: required
1
+notifications:
2
+  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
4 3
 
5 4
 addons:
6 5
   apt:
7 6
     packages: ccache
8 7
 
9
-notifications:
10
-  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
8
+cache: ccache
11 9
 
12 10
 jobs:
13 11
   fast_finish: true
... ...
@@ -16,14 +14,18 @@ jobs:
16 14
     - name: Code Formatting
17 15
   include:
18 16
     - name: "Bioconductor Release Testing"
17
+      language: r
19 18
       r: bioc-release
20 19
       before_install:
21 20
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
22 21
     - name: "Bioconductor Devel Testing"
22
+      language: r
23 23
       r: bioc-devel
24 24
       before_install:
25 25
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
26 26
     - name: "Test Running in Debug Mode"
27
+      language: r
28
+      r: release
27 29
       before_install:
28 30
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
29 31
       install:
Browse code

travis

Tom Sherman authored on 26/06/2019 16:02:01
Showing1 changed files
... ...
@@ -15,45 +15,37 @@ jobs:
15 15
     - name: Linting
16 16
     - name: Code Formatting
17 17
   include:
18
-    - stage: "Testing"
19
-
20
-      - name: "Bioconductor Release Testing"
21
-        r: bioc-release
22
-        before_install:
23
-          - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
24
-
25
-      - name: "Bioconductor Devel Testing"
26
-        r: bioc-devel
27
-        before_install:
28
-          - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
29
-    
30
-      - name: "Test Running in Debug Mode"
31
-        before_install:
32
-          - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
33
-        install:
34
-          - R -e 'install.packages(c("BiocManager", "desc"))'
35
-          - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
36
-          - R CMD build --no-build-vignettes .
37
-          - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
38
-        script: R -f inst/scripts/debugRuns.R
39
-
40
-      - name: "Linting"
41
-        script: echo "linting not implemented"
42
-
43
-      - name: "Code Formatting"
44
-        script: echo "formatting not implemented"
45
-
46
-
47
-
48
-    #- stage: Valgrind Analysis
49
-    #  before_install:
50
-    #    - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
51
-    #    - sudo apt-get update -qq
52
-    #    - sudo apt-get install -qq valgrind
53
-    #  install:
54
-    #    - R -e 'install.packages(c("BiocManager", "desc"))'
55
-    #    - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
56
-    #    - R CMD build --no-build-vignettes .
57
-    #    - R CMD INSTALL --configure-args=" --disable-openmp " *tar.gz
58
-    #  script: R -d "valgrind --tool=memcheck --leak-check=yes" -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
18
+    - name: "Bioconductor Release Testing"
19
+      r: bioc-release
20
+      before_install:
21
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
22
+    - name: "Bioconductor Devel Testing"
23
+      r: bioc-devel
24
+      before_install:
25
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
26
+    - name: "Test Running in Debug Mode"
27
+      before_install:
28
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
29
+      install:
30
+        - R -e 'install.packages(c("BiocManager", "desc"))'
31
+        - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
32
+        - R CMD build --no-build-vignettes .
33
+        - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
34
+      script: R -f inst/scripts/debugRuns.R
35
+    - name: "Linting"
36
+      script: echo "linting not implemented"
37
+    - name: "Code Formatting"
38
+      script: echo "formatting not implemented"
39
+
40
+#- stage: Valgrind Analysis
41
+#  before_install:
42
+#    - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
43
+#    - sudo apt-get update -qq
44
+#    - sudo apt-get install -qq valgrind
45
+#  install:
46
+#    - R -e 'install.packages(c("BiocManager", "desc"))'
47
+#    - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
48
+#    - R CMD build --no-build-vignettes .
49
+#    - R CMD INSTALL --configure-args=" --disable-openmp " *tar.gz
50
+#  script: R -d "valgrind --tool=memcheck --leak-check=yes" -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
59 51
 
Browse code

use travis build stages correctly

Tom Sherman authored on 26/06/2019 15:59:14
Showing1 changed files
... ...
@@ -12,28 +12,38 @@ notifications:
12 12
 jobs:
13 13
   fast_finish: true
14 14
   allow_failures:
15
-    - stage: Linting
16
-    - stage: Code Formatting
15
+    - name: Linting
16
+    - name: Code Formatting
17 17
   include:
18
-    - stage: Bioconductor Release Testing
19
-      r: bioc-release
20
-      before_install:
21
-        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
22
-
23
-    - stage: Bioconductor Devel Testing
24
-      r: bioc-devel
25
-      before_install:
26
-        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
27
-
28
-    - stage: Test Running in Debug Mode
29
-      before_install:
30
-        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
31
-      install:
32
-        - R -e 'install.packages(c("BiocManager", "desc"))'
33
-        - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
34
-        - R CMD build --no-build-vignettes .
35
-        - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
36
-      script: R -f inst/scripts/debugRuns.R
18
+    - stage: "Testing"
19
+
20
+      - name: "Bioconductor Release Testing"
21
+        r: bioc-release
22
+        before_install:
23
+          - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
24
+
25
+      - name: "Bioconductor Devel Testing"
26
+        r: bioc-devel
27
+        before_install:
28
+          - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
29
+    
30
+      - name: "Test Running in Debug Mode"
31
+        before_install:
32
+          - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
33
+        install:
34
+          - R -e 'install.packages(c("BiocManager", "desc"))'
35
+          - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
36
+          - R CMD build --no-build-vignettes .
37
+          - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
38
+        script: R -f inst/scripts/debugRuns.R
39
+
40
+      - name: "Linting"
41
+        script: echo "linting not implemented"
42
+
43
+      - name: "Code Formatting"
44
+        script: echo "formatting not implemented"
45
+
46
+
37 47
 
38 48
     #- stage: Valgrind Analysis
39 49
     #  before_install:
... ...
@@ -47,9 +57,3 @@ jobs:
47 57
     #    - R CMD INSTALL --configure-args=" --disable-openmp " *tar.gz
48 58
     #  script: R -d "valgrind --tool=memcheck --leak-check=yes" -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
49 59
 
50
-    - stage: Linting
51
-      script: echo "linting not implemented"
52
-
53
-    - stage: Code Formatting
54
-      script: echo "formatting not implemented"
55
-
Browse code

use jobs instead of matrix for travis

Tom Sherman authored on 26/06/2019 15:54:53
Showing1 changed files
... ...
@@ -1,12 +1,15 @@
1 1
 language: r
2 2
 cache: ccache
3
-sudo: required
3
+#sudo: required
4 4
 
5 5
 addons:
6 6
   apt:
7 7
     packages: ccache
8 8
 
9
-matrix:
9
+notifications:
10
+  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
11
+
12
+jobs:
10 13
   fast_finish: true
11 14
   allow_failures:
12 15
     - stage: Linting
... ...
@@ -16,10 +19,12 @@ matrix:
16 19
       r: bioc-release
17 20
       before_install:
18 21
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
22
+
19 23
     - stage: Bioconductor Devel Testing
20 24
       r: bioc-devel
21 25
       before_install:
22 26
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
27
+
23 28
     - stage: Test Running in Debug Mode
24 29
       before_install:
25 30
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
... ...
@@ -29,21 +34,22 @@ matrix:
29 34
         - R CMD build --no-build-vignettes .
30 35
         - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
31 36
       script: R -f inst/scripts/debugRuns.R
32
-    - stage: Valgrind Analysis
33
-      before_install:
34
-        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
35
-        - sudo apt-get update -qq
36
-        - sudo apt-get install -qq valgrind
37
-      install:
38
-        - R -e 'install.packages(c("BiocManager", "desc"))'
39
-        - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
40
-        - R CMD build --no-build-vignettes .
41
-        - R CMD INSTALL --configure-args=" --disable-openmp " *tar.gz
42
-      script: R -d "valgrind --tool=memcheck --leak-check=yes" -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
37
+
38
+    #- stage: Valgrind Analysis
39
+    #  before_install:
40
+    #    - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
41
+    #    - sudo apt-get update -qq
42
+    #    - sudo apt-get install -qq valgrind
43
+    #  install:
44
+    #    - R -e 'install.packages(c("BiocManager", "desc"))'
45
+    #    - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
46
+    #    - R CMD build --no-build-vignettes .
47
+    #    - R CMD INSTALL --configure-args=" --disable-openmp " *tar.gz
48
+    #  script: R -d "valgrind --tool=memcheck --leak-check=yes" -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
49
+
43 50
     - stage: Linting
44 51
       script: echo "linting not implemented"
52
+
45 53
     - stage: Code Formatting
46 54
       script: echo "formatting not implemented"
47 55
 
48
-notifications:
49
-  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
Browse code

full travis build

Tom Sherman authored on 26/06/2019 04:29:33
Showing1 changed files
... ...
@@ -12,17 +12,23 @@ matrix:
12 12
     - stage: Linting
13 13
     - stage: Code Formatting
14 14
   include:
15
-    #- stage: Bioconductor Release Testing
16
-    #  r: bioc-release
17
-    #- stage: Bioconductor Devel Testing
18
-    #  r: bioc-devel
19
-    #- stage: Test Running in Debug Mode
20
-    #  install:
21
-    #    - R -e 'install.packages(c("BiocManager", "remotes"))'
22
-    #    - R -e 'BiocManager::install("FertigLab/CoGAPS")'
23
-    #    - R CMD build --no-build-vignettes .
24
-    #    - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
25
-    #  script: R -f inst/scripts/debugRuns.R
15
+    - stage: Bioconductor Release Testing
16
+      r: bioc-release
17
+      before_install:
18
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
19
+    - stage: Bioconductor Devel Testing
20
+      r: bioc-devel
21
+      before_install:
22
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
23
+    - stage: Test Running in Debug Mode
24
+      before_install:
25
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
26
+      install:
27
+        - R -e 'install.packages(c("BiocManager", "desc"))'
28
+        - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
29
+        - R CMD build --no-build-vignettes .
30
+        - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
31
+      script: R -f inst/scripts/debugRuns.R
26 32
     - stage: Valgrind Analysis
27 33
       before_install:
28 34
         - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
Browse code

add ccache to travis

Tom Sherman authored on 26/06/2019 04:26:20
Showing1 changed files
... ...
@@ -1,7 +1,11 @@
1 1
 language: r
2
-cache: packages
2
+cache: ccache
3 3
 sudo: required
4 4
 
5
+addons:
6
+  apt:
7
+    packages: ccache
8
+
5 9
 matrix:
6 10
   fast_finish: true
7 11
   allow_failures:
... ...
@@ -21,11 +25,12 @@ matrix:
21 25
     #  script: R -f inst/scripts/debugRuns.R
22 26
     - stage: Valgrind Analysis
23 27
       before_install:
28
+        - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
24 29
         - sudo apt-get update -qq
25 30
         - sudo apt-get install -qq valgrind
26 31
       install:
27
-        - R -e 'install.packages(c("BiocManager", "remotes", "desc"))'
28
-        - R -e 'library(desc); BiocManager::install(desc_get_deps()$package)'
32
+        - R -e 'install.packages(c("BiocManager", "desc"))'
33
+        - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
29 34
         - R CMD build --no-build-vignettes .
30 35
         - R CMD INSTALL --configure-args=" --disable-openmp " *tar.gz
31 36
       script: R -d "valgrind --tool=memcheck --leak-check=yes" -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
Browse code

travis syntax error

Tom Sherman authored on 26/06/2019 04:04:15
Showing1 changed files
... ...
@@ -25,7 +25,7 @@ matrix:
25 25
         - sudo apt-get install -qq valgrind
26 26
       install:
27 27
         - R -e 'install.packages(c("BiocManager", "remotes", "desc"))'
28
-        - R -e 'BiocManager::install(desc_get_deps()$package)
28
+        - R -e 'library(desc); BiocManager::install(desc_get_deps()$package)'
29 29
         - R CMD build --no-build-vignettes .
30 30
         - R CMD INSTALL --configure-args=" --disable-openmp " *tar.gz
31 31
       script: R -d "valgrind --tool=memcheck --leak-check=yes" -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
Browse code

directly install dependencies in travis

Tom Sherman authored on 26/06/2019 04:00:26
Showing1 changed files
... ...
@@ -24,8 +24,8 @@ matrix:
24 24
         - sudo apt-get update -qq
25 25
         - sudo apt-get install -qq valgrind
26 26
       install:
27
-        - R -e 'install.packages(c("BiocManager", "remotes"))'
28
-        - R -e 'BiocManager::install("FertigLab/CoGAPS")'
27
+        - R -e 'install.packages(c("BiocManager", "remotes", "desc"))'
28
+        - R -e 'BiocManager::install(desc_get_deps()$package)
29 29
         - R CMD build --no-build-vignettes .
30 30
         - R CMD INSTALL --configure-args=" --disable-openmp " *tar.gz
31 31
       script: R -d "valgrind --tool=memcheck --leak-check=yes" -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
Browse code

disable openmp when checking with valgrind

Tom Sherman authored on 26/06/2019 03:52:21
Showing1 changed files
... ...
@@ -27,8 +27,8 @@ matrix:
27 27
         - R -e 'install.packages(c("BiocManager", "remotes"))'
28 28
         - R -e 'BiocManager::install("FertigLab/CoGAPS")'
29 29
         - R CMD build --no-build-vignettes .
30
-        - R CMD INSTALL *tar.gz
31
-      script: R -d valgrind -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
30
+        - R CMD INSTALL --configure-args=" --disable-openmp " *tar.gz
31
+      script: R -d "valgrind --tool=memcheck --leak-check=yes" -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
32 32
     - stage: Linting
33 33
       script: echo "linting not implemented"
34 34
     - stage: Code Formatting
Browse code

install valgrind in travis

sherman5 authored on 25/06/2019 23:30:54
Showing1 changed files
... ...
@@ -1,5 +1,6 @@
1 1
 language: r
2 2
 cache: packages
3
+sudo: required
3 4
 
4 5
 matrix:
5 6
   fast_finish: true
... ...
@@ -19,6 +20,9 @@ matrix:
19 20
     #    - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
20 21
     #  script: R -f inst/scripts/debugRuns.R
21 22
     - stage: Valgrind Analysis
23
+      before_install:
24
+        - sudo apt-get update -qq
25
+        - sudo apt-get install -qq valgrind
22 26
       install:
23 27
         - R -e 'install.packages(c("BiocManager", "remotes"))'
24 28
         - R -e 'BiocManager::install("FertigLab/CoGAPS")'
Browse code

test out valgrind analysis

sherman5 authored on 25/06/2019 23:20:36
Showing1 changed files
... ...
@@ -11,19 +11,20 @@ matrix:
11 11
     #  r: bioc-release
12 12
     #- stage: Bioconductor Devel Testing
13 13
     #  r: bioc-devel
14
-    - stage: Test Running in Debug Mode
15
-      #before_install: mkdir -p $HOME/Rpackages
16
-      #install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
17
-      #install: R -e 'pkgLib=paste(Sys.getenv("HOME"), "/Rpackages", sep=""); install.packages("devtools", lib=pkgLib); devtools::install_deps(dep=TRUE, lib=pkgLib)'
14
+    #- stage: Test Running in Debug Mode
15
+    #  install:
16
+    #    - R -e 'install.packages(c("BiocManager", "remotes"))'
17
+    #    - R -e 'BiocManager::install("FertigLab/CoGAPS")'
18
+    #    - R CMD build --no-build-vignettes .
19
+    #    - R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
20
+    #  script: R -f inst/scripts/debugRuns.R
21
+    - stage: Valgrind Analysis
18 22
       install:
19 23
         - R -e 'install.packages(c("BiocManager", "remotes"))'
20 24
         - R -e 'BiocManager::install("FertigLab/CoGAPS")'
21 25
         - R CMD build --no-build-vignettes .
22
-        - R CMD INSTALL --configure-args="" *tar.gz
23
-      script: R -f inst/scripts/debugRuns.R
24
-    #- stage: Valgrind Analysis
25
-    #  install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T)'
26
-    #  script: R -d valgrind -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
26
+        - R CMD INSTALL *tar.gz
27
+      script: R -d valgrind -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
27 28
     - stage: Linting
28 29
       script: echo "linting not implemented"
29 30
     - stage: Code Formatting
... ...
@@ -31,15 +32,3 @@ matrix:
31 32
 
32 33
 notifications:
33 34
   slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
34
-
35
-#cache:
36
-#  - packages: true
37
-#  - ccache
38
-
39
-#addons:
40
-#  apt:
41
-#    packages:
42
-#     - ccache
43
-
44
-#before_install:
45
-#  - mkdir -p $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
Browse code

don't build vignettes for debug testing

sherman5 authored on 25/06/2019 23:10:01
Showing1 changed files
... ...
@@ -18,8 +18,8 @@ matrix:
18 18
       install:
19 19
         - R -e 'install.packages(c("BiocManager", "remotes"))'
20 20
         - R -e 'BiocManager::install("FertigLab/CoGAPS")'
21
-        - R CMD build .
22
-        - R CMD INSTALL *tar.gz
21
+        - R CMD build --no-build-vignettes .
22
+        - R CMD INSTALL --configure-args="" *tar.gz
23 23
       script: R -f inst/scripts/debugRuns.R
24 24
     #- stage: Valgrind Analysis
25 25
     #  install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T)'
Browse code

travis testing :

sherman5 authored on 25/06/2019 22:58:34
Showing1 changed files
... ...
@@ -12,13 +12,18 @@ matrix:
12 12
     #- stage: Bioconductor Devel Testing
13 13
     #  r: bioc-devel
14 14
     - stage: Test Running in Debug Mode
15
-      before_install: mkdir -p $HOME/Rpackages
15
+      #before_install: mkdir -p $HOME/Rpackages
16 16
       #install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
17
-      install: R -e 'pkgLib=paste(Sys.getenv("HOME"), "/Rpackages", sep=""); install.packages("devtools", lib=pkgLib); devtools::install_deps(dep=TRUE, lib=pkgLib)'
17
+      #install: R -e 'pkgLib=paste(Sys.getenv("HOME"), "/Rpackages", sep=""); install.packages("devtools", lib=pkgLib); devtools::install_deps(dep=TRUE, lib=pkgLib)'
18
+      install:
19
+        - R -e 'install.packages(c("BiocManager", "remotes"))'
20
+        - R -e 'BiocManager::install("FertigLab/CoGAPS")'
21
+        - R CMD build .
22
+        - R CMD INSTALL *tar.gz
18 23
       script: R -f inst/scripts/debugRuns.R
19
-    - stage: Valgrind Analysis
20
-      install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T)'
21
-      script: R -d valgrind -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
24
+    #- stage: Valgrind Analysis
25
+    #  install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T)'
26
+    #  script: R -d valgrind -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
22 27
     - stage: Linting
23 28
       script: echo "linting not implemented"
24 29
     - stage: Code Formatting
Browse code

travis testing

sherman5 authored on 25/06/2019 22:34:01
Showing1 changed files
... ...
@@ -12,9 +12,9 @@ matrix:
12 12
     #- stage: Bioconductor Devel Testing
13 13
     #  r: bioc-devel
14 14
     - stage: Test Running in Debug Mode
15
-      before_install: R -e 'install.packages("devtools")'
15
+      before_install: mkdir -p $HOME/Rpackages
16 16
       #install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
17
-      install: R -e 'print(list.files()); devtools::install_deps(dep = T)'
17
+      install: R -e 'pkgLib=paste(Sys.getenv("HOME"), "/Rpackages", sep=""); install.packages("devtools", lib=pkgLib); devtools::install_deps(dep=TRUE, lib=pkgLib)'
18 18
       script: R -f inst/scripts/debugRuns.R
19 19
     - stage: Valgrind Analysis
20 20
       install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T)'
Browse code

fix compiler warnings

sherman5 authored on 25/06/2019 22:21:06
Showing1 changed files
... ...
@@ -14,7 +14,7 @@ matrix:
14 14
     - stage: Test Running in Debug Mode
15 15
       before_install: R -e 'install.packages("devtools")'
16 16
       #install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
17
-      install: R -e 'devtools::install_deps(dep = T)'
17
+      install: R -e 'print(list.files()); devtools::install_deps(dep = T)'
18 18
       script: R -f inst/scripts/debugRuns.R
19 19
     - stage: Valgrind Analysis
20 20
       install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T)'
Browse code

travis testing

Tom Sherman authored on 25/06/2019 16:02:14
Showing1 changed files
... ...
@@ -13,7 +13,8 @@ matrix:
13 13
     #  r: bioc-devel
14 14
     - stage: Test Running in Debug Mode
15 15
       before_install: R -e 'install.packages("devtools")'
16
-      install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
16
+      #install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
17
+      install: R -e 'devtools::install_deps(dep = T)'
17 18
       script: R -f inst/scripts/debugRuns.R
18 19
     - stage: Valgrind Analysis
19 20
       install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T)'
Browse code

travis testing

Tom Sherman authored on 25/06/2019 15:52:30
Showing1 changed files
... ...
@@ -12,7 +12,8 @@ matrix:
12 12
     #- stage: Bioconductor Devel Testing
13 13
     #  r: bioc-devel
14 14
     - stage: Test Running in Debug Mode
15
-      install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
15
+      before_install: R -e 'install.packages("devtools")'
16
+      install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
16 17
       script: R -f inst/scripts/debugRuns.R
17 18
     - stage: Valgrind Analysis
18 19
       install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T)'
Browse code

travis testing

Tom Sherman authored on 25/06/2019 15:40:08
Showing1 changed files
... ...
@@ -7,12 +7,12 @@ matrix:
7 7
     - stage: Linting
8 8
     - stage: Code Formatting
9 9
   include:
10
-    - stage: Bioconductor Release Testing
11
-      r: bioc-release
12
-    - stage: Bioconductor Devel Testing
13
-      r: bioc-devel
10
+    #- stage: Bioconductor Release Testing
11
+    #  r: bioc-release
12
+    #- stage: Bioconductor Devel Testing
13
+    #  r: bioc-devel
14 14
     - stage: Test Running in Debug Mode
15
-      install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
15
+      install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
16 16
       script: R -f inst/scripts/debugRuns.R
17 17
     - stage: Valgrind Analysis
18 18
       install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T)'
Browse code

install devtools package in travis

Tom Sherman authored on 24/06/2019 22:55:49
Showing1 changed files
... ...
@@ -15,7 +15,7 @@ matrix:
15 15
       install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
16 16
       script: R -f inst/scripts/debugRuns.R
17 17
     - stage: Valgrind Analysis
18
-      install: R -e 'devtools::install_deps(dep = T)'
18
+      install: R -e 'install.packages("devtools"); devtools::install_deps(dep = T)'
19 19
       script: R -d valgrind -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
20 20
     - stage: Linting
21 21
       script: echo "linting not implemented"
Browse code

fixed documentation and vignette errors

Tom Sherman authored on 24/06/2019 20:10:07
Showing1 changed files
... ...
@@ -15,6 +15,7 @@ matrix:
15 15
       install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
16 16
       script: R -f inst/scripts/debugRuns.R
17 17
     - stage: Valgrind Analysis
18
+      install: R -e 'devtools::install_deps(dep = T)'
18 19
       script: R -d valgrind -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
19 20
     - stage: Linting
20 21
       script: echo "linting not implemented"
Browse code

clean up linter warnings

Tom Sherman authored on 24/06/2019 19:44:02
Showing1 changed files
... ...
@@ -2,6 +2,10 @@ language: r
2 2
 cache: packages
3 3
 
4 4
 matrix:
5
+  fast_finish: true
6
+  allow_failures:
7
+    - stage: Linting
8
+    - stage: Code Formatting
5 9
   include:
6 10
     - stage: Bioconductor Release Testing
7 11
       r: bioc-release
... ...
@@ -10,6 +14,12 @@ matrix:
10 14
     - stage: Test Running in Debug Mode
11 15
       install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
12 16
       script: R -f inst/scripts/debugRuns.R
17
+    - stage: Valgrind Analysis
18
+      script: R -d valgrind -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'
19
+    - stage: Linting
20
+      script: echo "linting not implemented"
21
+    - stage: Code Formatting
22
+      script: echo "formatting not implemented"
13 23
 
14 24
 notifications:
15 25
   slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
Browse code

run debug tests in travis

Tom Sherman authored on 24/06/2019 14:55:36
Showing1 changed files
... ...
@@ -1,7 +1,5 @@
1
-# necessary yml
2 1
 language: r
3
-#cache: packages
4
-#sudo: required
2
+cache: packages
5 3
 
6 4
 matrix:
7 5
   include:
... ...
@@ -10,9 +8,12 @@ matrix:
10 8
     - stage: Bioconductor Devel Testing
11 9
       r: bioc-devel
12 10
     - stage: Test Running in Debug Mode
13
-      r: release
11
+      install: R -e 'devtools::install_deps(dep = T, configure.args = c(debugMode = " --enable-debug " ))'
14 12
       script: R -f inst/scripts/debugRuns.R
15 13
 
14
+notifications:
15
+  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
16
+
16 17
 #cache:
17 18
 #  - packages: true
18 19
 #  - ccache
... ...
@@ -24,14 +25,3 @@ matrix:
24 25
 
25 26
 #before_install:
26 27
 #  - mkdir -p $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
27
-
28
-
29
-
30
-# use bioconductor
31
-#bioc_required: true
32
-#bioc_use_devel: false
33
-
34
-
35
-# notification setup
36
-notifications:
37
-  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
Browse code

travis testing

Tom Sherman authored on 24/06/2019 14:30:50
Showing1 changed files
... ...
@@ -5,8 +5,13 @@ language: r
5 5
 
6 6
 matrix:
7 7
   include:
8
-    - r: bioc-release
9
-    - r: bioc-devel
8
+    - stage: Bioconductor Release Testing
9
+      r: bioc-release
10
+    - stage: Bioconductor Devel Testing
11
+      r: bioc-devel
12
+    - stage: Test Running in Debug Mode
13
+      r: release
14
+      script: R -f inst/scripts/debugRuns.R
10 15
 
11 16
 #cache:
12 17
 #  - packages: true
... ...
@@ -28,5 +33,5 @@ matrix:
28 33
 
29 34
 
30 35
 # notification setup
31
-#notifications:
32
-#  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
36
+notifications:
37
+  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
Browse code

travis testing

Tom Sherman authored on 24/06/2019 14:23:07
Showing1 changed files
... ...
@@ -1,24 +1,32 @@
1 1
 # necessary yml
2 2
 language: r
3
-cache: packages
4
-sudo: required
3
+#cache: packages
4
+#sudo: required
5 5
 
6
-# use bioconductor
7
-bioc_required: true
8
-bioc_use_devel: false
6
+matrix:
7
+  include:
8
+    - r: bioc-release
9
+    - r: bioc-devel
10
+
11
+#cache:
12
+#  - packages: true
13
+#  - ccache
14
+
15
+#addons:
16
+#  apt:
17
+#    packages:
18
+#     - ccache
9 19
 
10
-cache:
11
-  - packages: true
12
-  - ccache
20
+#before_install:
21
+#  - mkdir -p $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
13 22
 
14
-addons:
15
-  apt:
16
-    packages:
17
-     - ccache
18 23
 
19
-before_install:
20
-  - mkdir -p $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
24
+
25
+# use bioconductor
26
+#bioc_required: true
27
+#bioc_use_devel: false
28
+
21 29
 
22 30
 # notification setup
23
-notifications:
24
-  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
31
+#notifications:
32
+#  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
Browse code

ccache and package cache on travis to improve build times

Tom Sherman authored on 18/06/2019 15:11:54
Showing1 changed files
... ...
@@ -7,6 +7,18 @@ sudo: required
7 7
 bioc_required: true
8 8
 bioc_use_devel: false
9 9
 
10
+cache:
11
+  - packages: true
12
+  - ccache
13
+
14
+addons:
15
+  apt:
16
+    packages:
17
+     - ccache
18
+
19
+before_install:
20
+  - mkdir -p $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
21
+
10 22
 # notification setup
11 23
 notifications:
12 24
   slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
Browse code

Bioc devel not working with travis CI right now

Tom Sherman authored on 08/12/2018 00:32:35
Showing1 changed files
... ...
@@ -5,7 +5,7 @@ sudo: required
5 5
 
6 6
 # use bioconductor
7 7
 bioc_required: true
8
-bioc_use_devel: true
8
+bioc_use_devel: false
9 9
 
10 10
 # notification setup
11 11
 notifications:
Browse code

removed travis commands to make ocnfigure executable withing build system

Tom Sherman authored on 29/10/2018 20:03:54
Showing1 changed files
... ...
@@ -7,15 +7,6 @@ sudo: required
7 7
 bioc_required: true
8 8
 bioc_use_devel: true
9 9
 
10
-# create executable temp directory
11
-env:
12
-  global:
13
-    - TMPDIR=$HOME
14
-
15
-# make sure configure is executable
16
-before_install:
17
-  - chmod +x configure
18
-
19 10
 # notification setup
20 11
 notifications:
21 12
   slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
Browse code

updated git config so that permissions get committed

Tom Sherman authored on 29/10/2018 20:03:19
Showing1 changed files
1 1
old mode 100644
2 2
new mode 100755
Browse code

moved computation inside if statement

Tom Sherman authored on 03/08/2018 19:58:43
Showing1 changed files
... ...
@@ -12,6 +12,7 @@ env:
12 12
   global:
13 13
     - TMPDIR=$HOME
14 14
 
15
+# make sure configure is executable
15 16
 before_install:
16 17
   - chmod +x configure
17 18
 
Browse code

explicitly make configure executable

Tom Sherman authored on 02/08/2018 20:14:28
Showing1 changed files
... ...
@@ -12,6 +12,9 @@ env:
12 12
   global:
13 13
     - TMPDIR=$HOME
14 14
 
15
+before_install:
16
+  - chmod +x configure
17
+
15 18
 # notification setup
16 19
 notifications:
17 20
   slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
Browse code

remove extras

Tom Sherman authored on 02/08/2018 20:07:16
Showing1 changed files
... ...
@@ -12,19 +12,6 @@ env:
12 12
   global:
13 13
     - TMPDIR=$HOME
14 14
 
15
-# before installing, lint c++ code
16
-#before_install:
17
-  #- deb http://us.archive.ubuntu.com/ubuntu precise main universe
18
-  #- sudo apt-get update -qq
19
-  #- sudo apt-get install cpplint -y
20
-  #- cpplint src
21
-
22
-# test code coverage
23
-r_github_packages:
24
-  - jimhester/covr
25
-after_success:
26
-  - Rscript -e 'covr::codecov()'
27
-
28 15
 # notification setup
29 16
 notifications:
30 17
   slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
Browse code

try user home dir for travis

Tom Sherman authored on 02/08/2018 19:58:15
Showing1 changed files
... ...
@@ -10,7 +10,7 @@ bioc_use_devel: true
10 10
 # create executable temp directory
11 11
 env:
12 12
   global:
13
-    - TMPDIR=/home
13
+    - TMPDIR=$HOME
14 14
 
15 15
 # before installing, lint c++ code
16 16
 #before_install:
Browse code

try home directory for travis

Tom Sherman authored on 02/08/2018 19:30:52
Showing1 changed files
... ...
@@ -10,7 +10,7 @@ bioc_use_devel: true
10 10
 # create executable temp directory
11 11
 env:
12 12
   global:
13
-    - TMPDIR=/tmp
13
+    - TMPDIR=/home
14 14
 
15 15
 # before installing, lint c++ code
16 16
 #before_install:
Browse code

cleaned up configure

Tom Sherman authored on 02/08/2018 19:09:46
Showing1 changed files
... ...
@@ -7,6 +7,11 @@ sudo: required
7 7
 bioc_required: true
8 8
 bioc_use_devel: true
9 9
 
10
+# create executable temp directory
11
+env:
12
+  global:
13
+    - TMPDIR=/tmp
14
+
10 15
 # before installing, lint c++ code
11 16
 #before_install:
12 17
   #- deb http://us.archive.ubuntu.com/ubuntu precise main universe
Browse code

travis config

Tom Sherman authored on 12/06/2018 20:02:51
Showing1 changed files
... ...
@@ -1,5 +1,6 @@
1 1
 # necessary yml
2 2
 language: r
3
+cache: packages
3 4
 sudo: required
4 5
 
5 6
 # use bioconductor
Browse code

Comment out cpplint stuff in travis for now

Jacob Carey authored on 04/01/2016 16:32:59
Showing1 changed files
... ...
@@ -7,11 +7,11 @@ bioc_required: true
7 7
 bioc_use_devel: true
8 8
 
9 9
 # before installing, lint c++ code
10
-before_install:
11
-  - deb http://us.archive.ubuntu.com/ubuntu precise main universe
12
-  - sudo apt-get update -qq
13
-  - sudo apt-get install cpplint -y
14
-  - cpplint src
10
+#before_install:
11
+  #- deb http://us.archive.ubuntu.com/ubuntu precise main universe
12
+  #- sudo apt-get update -qq
13
+  #- sudo apt-get install cpplint -y
14
+  #- cpplint src
15 15
 
16 16
 # test code coverage
17 17
 r_github_packages:
Browse code

Add repository for installing cpplint

Jacob Carey authored on 04/01/2016 14:43:31
Showing1 changed files
... ...
@@ -8,6 +8,8 @@ bioc_use_devel: true
8 8
 
9 9
 # before installing, lint c++ code
10 10
 before_install:
11
+  - deb http://us.archive.ubuntu.com/ubuntu precise main universe
12
+  - sudo apt-get update -qq
11 13
   - sudo apt-get install cpplint -y
12 14
   - cpplint src
13 15
 
Browse code

Lint src with cpplint before installing on travis

Jacob Carey authored on 04/01/2016 14:17:15
Showing1 changed files
... ...
@@ -6,6 +6,11 @@ sudo: required
6 6
 bioc_required: true
7 7
 bioc_use_devel: true
8 8
 
9
+# before installing, lint c++ code
10
+before_install:
11
+  - sudo apt-get install cpplint -y
12
+  - cpplint src
13
+
9 14
 # test code coverage
10 15
 r_github_packages:
11 16
   - jimhester/covr
Browse code

Add Codecov for tracking test coverage

Jacob Carey authored on 28/12/2015 18:18:56
Showing1 changed files
... ...
@@ -6,6 +6,12 @@ sudo: required
6 6
 bioc_required: true
7 7
 bioc_use_devel: true
8 8
 
9
+# test code coverage
10
+r_github_packages:
11
+  - jimhester/covr
12
+after_success:
13
+  - Rscript -e 'covr::codecov()'
14
+
9 15
 # notification setup
10 16
 notifications:
11 17
   slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
Browse code

Include Bioconductor in travis

Jacob Carey authored on 18/12/2015 21:21:33
Showing1 changed files
... ...
@@ -2,6 +2,10 @@
2 2
 language: r
3 3
 sudo: required
4 4
 
5
+# use bioconductor
6
+bioc_required: true
7
+bioc_use_devel: true
8
+
5 9
 # notification setup
6 10
 notifications:
7 11
   slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
Browse code

Add Travis CI integration

Jacob Carey authored on 18/12/2015 21:13:40
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,7 @@
1
+# necessary yml
2
+language: r
3
+sudo: required
4
+
5
+# notification setup
6
+notifications:
7
+  slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts