1. mzR
  2. .travis.yml
Browse code

don't specify exact distribution

Steffen Neumann authored on 09/09/2020 08:35:41
Showing 1 changed files
.travis.yml
History View file @ 4121d10357
... ... 
@@ -3,7 +3,7 @@ r: bioc-devel
3 3 
 cache: packages
4 4 
 sudo: false       # use container based build system
5 5 
 warnings_are_errors: true
6 
-dist: trusty
6 
+#dist: trusty
7 7
8 8 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
9 9 
 # this was causing mzR installation to fail
Browse code

revert last travis changes

Laurent authored on 16/05/2018 18:59:46
Showing 1 changed files
.travis.yml
History View file @ 37f2a82b95
... ... 
@@ -1,8 +1,9 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 3 
 cache: packages
4 
-sudo: true       # use container based build system
4 
+sudo: false       # use container based build system
5 5 
 warnings_are_errors: true
6 
+dist: trusty
6 7
7 8 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
8 9 
 # this was causing mzR installation to fail
... ... 
@@ -14,7 +15,6 @@ before_install:
14 15 
 addons:
15 16 
   apt:
16 17 
     packages:
17 
-      - libmagick++-dev
18 18 
       - libnetcdf-dev
19 19 
       - netcdf-bin # libnetcdf-dev doesn't contain nc-config in ubuntu 12.04 (in 16.04 it is part of libnetcdf-dev)
20 20 
       - libhdf5-dev
Browse code

try with sudo

Laurent authored on 16/05/2018 10:29:21
Showing 1 changed files
.travis.yml
History View file @ 7b69f7ead6
... ... 
@@ -1,7 +1,7 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 3 
 cache: packages
4 
-sudo: false       # use container based build system
4 
+sudo: true       # use container based build system
5 5 
 warnings_are_errors: true
6 6
7 7 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
Browse code

explicit libmagick++-dev dep installation

Laurent authored on 16/05/2018 10:28:22
Showing 1 changed files
.travis.yml
History View file @ c845055f66
... ... 
@@ -14,6 +14,7 @@ before_install:
14 14 
 addons:
15 15 
   apt:
16 16 
     packages:
17 
+      - libmagick++-dev
17 18 
       - libnetcdf-dev
18 19 
       - netcdf-bin # libnetcdf-dev doesn't contain nc-config in ubuntu 12.04 (in 16.04 it is part of libnetcdf-dev)
19 20 
       - libhdf5-dev
Browse code

don't set trusty

Laurent authored on 16/05/2018 10:25:14
Showing 1 changed files
.travis.yml
History View file @ a77989f042
... ... 
@@ -3,7 +3,6 @@ r: bioc-devel
3 3 
 cache: packages
4 4 
 sudo: false       # use container based build system
5 5 
 warnings_are_errors: true
6 
-dist: trusty
7 6
8 7 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
9 8 
 # this was causing mzR installation to fail
Browse code

also wait when building

Laurent authored on 09/05/2018 13:25:33
Showing 1 changed files
.travis.yml
History View file @ 4f8384667a
... ... 
@@ -21,5 +21,5 @@ addons:
21 21
22 22 
 script:
23 23 
   - |
24 
-    R CMD build .
25 
-    travis_wait 45 R CMD check --no-build-vignettes --no-vignettes mzR*tar.gz
24 
+    travis_wait 30 R CMD build .
25 
+    travis_wait 30 R CMD check --no-build-vignettes --no-vignettes mzR*tar.gz
Browse code

why don't you use travis_wait?

Laurent authored on 09/05/2018 09:08:49
Showing 1 changed files
.travis.yml
History View file @ 47494772b7
... ... 
@@ -22,4 +22,4 @@ addons:
22 22 
 script:
23 23 
   - |
24 24 
     R CMD build .
25 
-    travis_wait 40 R CMD check --no-build-vignettes --no-vignettes mzR*tar.gz
25 
+    travis_wait 45 R CMD check --no-build-vignettes --no-vignettes mzR*tar.gz
Browse code

update .travis file

Laurent authored on 09/05/2018 08:39:45
Showing 1 changed files
.travis.yml
History View file @ f82fd8c547
... ... 
@@ -1,32 +1,25 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 
-sudo: required
4 
-
5 
-r_packages:
6 
-  - devtools
7 
-  - knitr
8 
-  - XML
9 
-  - plyr
10 
-  - doParallel
11 
-  - foreach
12 
-  - iterators
13 
-
14 
-addons:
15 
-  apt:
16 
-    packages:
17 
-    - libnetcdf-dev
18 
-    - netcdf-bin
3 
+cache: packages
4 
+sudo: false       # use container based build system
5 
+warnings_are_errors: true
6 
+dist: trusty
19 7
20 8 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
21 
-# Thanks to jimhester pointing this out!
9 
+# this was causing mzR installation to fail
10 
+# see https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17189
11 
+# workaround stolen from https://github.com/hadley/devtools/blob/1ce84b04568ff7846c3da754f28e7e22a23c8737/.travis.yml#L23-L26
22 12 
 before_install:
23 13 
   - if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi
24 
-  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
25 
-  - chmod 755 ./travis-tool.sh
26 
-  - ./travis-tool.sh bootstrap
27 14
28 
-## Work around timeout, following
29 
-## https://github.com/craigcitro/r-travis/wiki
15 
+addons:
16 
+  apt:
17 
+    packages:
18 
+      - libnetcdf-dev
19 
+      - netcdf-bin # libnetcdf-dev doesn't contain nc-config in ubuntu 12.04 (in 16.04 it is part of libnetcdf-dev)
20 
+      - libhdf5-dev
30 21
31 
-script:
32 
-  - travis_wait ./travis-tool.sh run_tests
22 
+script:
23 
+  - |
24 
+    R CMD build .
25 
+    travis_wait 40 R CMD check --no-build-vignettes --no-vignettes mzR*tar.gz
Browse code

revert sudo in travis, required by travis-tools

Steffen Neumann authored on 04/01/2018 09:27:34
Showing 1 changed files
.travis.yml
History View file @ fc40aeef63
... ... 
@@ -1,6 +1,6 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 
-#sudo: required
3 
+sudo: required
4 4
5 5 
 r_packages:
6 6 
   - devtools
Browse code

add travis-tool download

Steffen Neumann authored on 04/01/2018 09:23:29
Showing 1 changed files
.travis.yml
History View file @ 9b96f6e0fc
... ... 
@@ -21,6 +21,9 @@ addons:
21 21 
 # Thanks to jimhester pointing this out!
22 22 
 before_install:
23 23 
   - if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi
24 
+  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
25 
+  - chmod 755 ./travis-tool.sh
26 
+  - ./travis-tool.sh bootstrap
24 27
25 28 
 ## Work around timeout, following
26 29 
 ## https://github.com/craigcitro/r-travis/wiki
Browse code

add workaround for travis timeout

Steffen Neumann authored on 04/01/2018 09:02:33
Showing 1 changed files
.travis.yml
History View file @ 190a504469
... ... 
@@ -21,3 +21,9 @@ addons:
21 21 
 # Thanks to jimhester pointing this out!
22 22 
 before_install:
23 23 
   - if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi
24 
+
25 
+## Work around timeout, following
26 
+## https://github.com/craigcitro/r-travis/wiki
27 
+
28 
+script:
29 
+  - travis_wait ./travis-tool.sh run_tests
Browse code

switch to apt addon for dependency installation

Steffen Neumann authored on 04/01/2018 08:58:14
Showing 1 changed files
.travis.yml
History View file @ 1ee00b489b
... ... 
@@ -11,9 +11,11 @@ r_packages:
11 11 
   - foreach
12 12 
   - iterators
13 13
14 
-apt_packages:
15 
-  - libnetcdf-dev
16 
-  - netcdf-bin
14 
+addons:
15 
+  apt:
16 
+    packages:
17 
+    - libnetcdf-dev
18 
+    - netcdf-bin
17 19
18 20 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
19 21 
 # Thanks to jimhester pointing this out!
Browse code

remove sudo requirement in travis

Steffen Neumann authored on 04/01/2018 08:50:02
Showing 1 changed files
.travis.yml
History View file @ bf3a3dba41
... ... 
@@ -1,6 +1,6 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 
-sudo: required
3 
+#sudo: required
4 4
5 5 
 r_packages:
6 6 
   - devtools
Browse code

replace system dependency libhdf5-dev with BioC package Rhdf5lib

Steffen Neumann authored on 03/01/2018 22:22:13
Showing 1 changed files
.travis.yml
History View file @ 305e813d01
... ... 
@@ -13,7 +13,6 @@ r_packages:
13 13
14 14 
 apt_packages:
15 15 
   - libnetcdf-dev
16 
-  - libhdf5-dev
17 16 
   - netcdf-bin
18 17
19 18 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
Browse code

require devtools

Laurent authored on 21/12/2017 13:59:31
Showing 1 changed files
.travis.yml
History View file @ 62b6b29d04
... ... 
@@ -3,6 +3,7 @@ r: bioc-devel
3 3 
 sudo: required
4 4
5 5 
 r_packages:
6 
+  - devtools
6 7 
   - knitr
7 8 
   - XML
8 9 
   - plyr
Browse code

Remove manual script section and timeout

Sebastian Gibb authored on 23/11/2017 21:57:43
Showing 1 changed files
.travis.yml
History View file @ 285eedac0a
... ... 
@@ -19,10 +19,3 @@ apt_packages:
19 19 
 # Thanks to jimhester pointing this out!
20 20 
 before_install:
21 21 
   - if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi
22 
-
23 
-script:
24 
-  - |
25 
-    travis_wait 20 R CMD build .
26 
-    R CMD check --no-build-vignettes --no-vignettes mzR*tar.gz
27 
-
28 
-
Browse code

Add libhdf5-dev as dependency

Sebastian Gibb authored on 23/11/2017 21:22:39
Showing 1 changed files
.travis.yml
History View file @ 4c1f1d6305
... ... 
@@ -12,6 +12,7 @@ r_packages:
12 12
13 13 
 apt_packages:
14 14 
   - libnetcdf-dev
15 
+  - libhdf5-dev
15 16 
   - netcdf-bin
16 17
17 18 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
Browse code

update travis for longer waiting time

Laurent authored on 19/09/2017 16:07:49
Showing 1 changed files
.travis.yml
History View file @ 85c0b0f443
... ... 
@@ -1,6 +1,7 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 3 
 sudo: required
4 
+
4 5 
 r_packages:
5 6 
   - knitr
6 7 
   - XML
... ... 
@@ -8,6 +9,7 @@ r_packages:
8 9 
   - doParallel
9 10 
   - foreach
10 11 
   - iterators
12 
+
11 13 
 apt_packages:
12 14 
   - libnetcdf-dev
13 15 
   - netcdf-bin
... ... 
@@ -17,4 +19,9 @@ apt_packages:
17 19 
 before_install:
18 20 
   - if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi
19 21
22 
+script:
23 
+  - |
24 
+    travis_wait 20 R CMD build .
25 
+    R CMD check --no-build-vignettes --no-vignettes mzR*tar.gz
26 
+
20 27
Browse code

no need to latex apt packages

Laurent authored on 22/08/2017 14:34:21
Showing 1 changed files
.travis.yml
History View file @ af4ff8e2d5
... ... 
@@ -1,7 +1,6 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 3 
 sudo: required
4 
-dist: precise
5 4 
 r_packages:
6 5 
   - knitr
7 6 
   - XML
... ... 
@@ -10,9 +9,6 @@ r_packages:
10 9 
   - foreach
11 10 
   - iterators
12 11 
 apt_packages:
13 
-  - texlive-latex-extra
14 
-  - texlive-fonts-extra
15 
-  - texlive-latex-recommended
16 12 
   - libnetcdf-dev
17 13 
   - netcdf-bin
18 14
Browse code

use precise

Laurent authored on 22/08/2017 14:19:33
Showing 1 changed files
.travis.yml
History View file @ af4993fb8f
... ... 
@@ -1,6 +1,7 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 3 
 sudo: required
4 
+dist: precise
4 5 
 r_packages:
5 6 
   - knitr
6 7 
   - XML
Browse code

add other texlive deps

Laurent authored on 06/06/2017 15:45:29
Showing 1 changed files
.travis.yml
History View file @ 6a99bfaea6
... ... 
@@ -11,6 +11,7 @@ r_packages:
11 11 
 apt_packages:
12 12 
   - texlive-latex-extra
13 13 
   - texlive-fonts-extra
14 
+  - texlive-latex-recommended
14 15 
   - libnetcdf-dev
15 16 
   - netcdf-bin
16 17
Browse code

add texlive deps

Laurent authored on 06/06/2017 15:11:56
Showing 1 changed files
.travis.yml
History View file @ 45ffbf9fc6
... ... 
@@ -8,7 +8,9 @@ r_packages:
8 8 
   - doParallel
9 9 
   - foreach
10 10 
   - iterators
11 
-apt_packages:
11 
+apt_packages:
12 
+  - texlive-latex-extra
13 
+  - texlive-fonts-extra
12 14 
   - libnetcdf-dev
13 15 
   - netcdf-bin
14 16
... ... 
@@ -16,3 +18,5 @@ apt_packages:
16 18 
 # Thanks to jimhester pointing this out!
17 19 
 before_install:
18 20 
   - if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi
21 
+
22 
+
Browse code

update travis config

Laurent authored on 06/06/2017 14:30:19
Showing 1 changed files
.travis.yml
History View file @ 4945a86eca
... ... 
@@ -1,6 +1,6 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 
-sudo: true
3 
+sudo: required
4 4 
 r_packages:
5 5 
   - knitr
6 6 
   - XML
Browse code

need bioc-devel to build

Laurent authored on 25/03/2017 19:04:48
Showing 1 changed files
.travis.yml
History View file @ c061936503
... ... 
@@ -1,5 +1,5 @@
1 1 
 language: r
2 
-r: bioc-release
2 
+r: bioc-devel
3 3 
 sudo: true
4 4 
 r_packages:
5 5 
   - knitr
Browse code

fix merge commits

From: Steffen Neumann <sneumann@ipb-halle.de>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@126467 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 05/02/2017 13:12:31
Showing 0 changed files
Browse code

try other CXX hack

Laurent authored on 25/01/2017 16:03:10
Showing 1 changed files
.travis.yml
History View file @ 4a852b029e
... ... 
@@ -15,4 +15,4 @@ apt_packages:
15 15 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 16 
 # Thanks to jimhester pointing this out!
17 17 
 before_install:
18 
-  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ CXX1X=g++ ' > ~/.R/Makevars; fi
19 18 
\ No newline at end of file
19 
+  - if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi
20 20 
\ No newline at end of file
Browse code

remove spurious \n in travis file

Laurent authored on 25/01/2017 15:51:05
Showing 1 changed files
.travis.yml
History View file @ af38f44251
... ... 
@@ -15,4 +15,4 @@ apt_packages:
15 15 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 16 
 # Thanks to jimhester pointing this out!
17 17 
 before_install:
18 
-  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ \nCXX1X=g++ ' > ~/.R/Makevars; fi
19 18 
\ No newline at end of file
19 
+  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ CXX1X=g++ ' > ~/.R/Makevars; fi
20 20 
\ No newline at end of file
Browse code

need bioc devel

Laurent authored on 24/01/2017 13:35:55
Showing 1 changed files
.travis.yml
History View file @ 1396df8a7f
... ... 
@@ -1,5 +1,5 @@
1 1 
 language: r
2 
-r: bioc-release
2 
+r: bioc-devel
3 3 
 sudo: true
4 4 
 r_packages:
5 5 
   - knitr
Browse code

fix merge conflict

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125207 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 11:00:07
Showing 1 changed files
.travis.yml
History View file @ 1b4b2b9059
... ... 
@@ -15,4 +15,4 @@ apt_packages:
15 15 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 16 
 # Thanks to jimhester pointing this out!
17 17 
 before_install:
18 
-  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ \nCXX1X=g++ ' > ~/.R/Makevars; fi
18 
+  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ \nCXX1X=g++ ' > ~/.R/Makevars; fi
19 19 
\ No newline at end of file
Browse code

Avoid fixing cxx standard

From: sneumann <sneumann@ipb-halle.de>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125205 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 10:59:37
Showing 1 changed files
.travis.yml
History View file @ b63506a56d
... ... 
@@ -15,4 +15,4 @@ apt_packages:
15 15 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 16 
 # Thanks to jimhester pointing this out!
17 17 
 before_install:
18 
-  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x \nCXX1X=g++ -std=c++0x -g -O2 -fPIC ' > ~/.R/Makevars; fi
18 
+  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ \nCXX1X=g++ ' > ~/.R/Makevars; fi
Browse code

Try bioc-release to avoid CXX1X issue

From: sneumann <sneumann@ipb-halle.de>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125199 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 10:57:47
Showing 1 changed files
.travis.yml
History View file @ 47b62b6e2c
... ... 
@@ -1,5 +1,5 @@
1 1 
 language: r
2 
-r: bioc-devel
2 
+r: bioc-release
3 3 
 sudo: true
4 4 
 r_packages:
5 5 
   - knitr
Browse code

Fix TRAVIS_R_VERSION_STRING check

From: sneumann <sneumann@ipb-halle.de>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125198 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 10:57:35
Showing 1 changed files
.travis.yml
History View file @ bab5c0ce39
... ... 
@@ -15,4 +15,4 @@ apt_packages:
15 15 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 16 
 # Thanks to jimhester pointing this out!
17 17 
 before_install:
18 
-  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x \nCXX1X=g++ -std=c++0x -g -O2 -fPIC ' > ~/.R/Makevars; fi
18 
+  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x \nCXX1X=g++ -std=c++0x -g -O2 -fPIC ' > ~/.R/Makevars; fi
Browse code

set both CXX1X and SHARED_CXX1XLD variables

From: sneumann <sneumann@ipb-halle.de>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125197 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 10:57:22
Showing 1 changed files
.travis.yml
History View file @ 574ebbb07c
... ... 
@@ -15,4 +15,4 @@ apt_packages:
15 15 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 16 
 # Thanks to jimhester pointing this out!
17 17 
 before_install:
18 
-  - if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x ' > ~/.R/Makevars; fi
18 
+  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x \nCXX1X=g++ -std=c++0x -g -O2 -fPIC ' > ~/.R/Makevars; fi
Browse code

Try SHLIB_CXX1XLD for travis.

From: sneumann <sneumann@ipb-halle.de>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125196 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 10:57:09
Showing 1 changed files
.travis.yml
History View file @ 3748b49257
... ... 
@@ -15,4 +15,4 @@ apt_packages:
15 15 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 16 
 # Thanks to jimhester pointing this out!
17 17 
 before_install:
18 
-  - if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi
18 
+  - if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x ' > ~/.R/Makevars; fi
Browse code

Explicitly set CXX1X as workaround for R-devel issue

From: sneumann <sneumann@ipb-halle.de>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125195 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 10:56:56
Showing 1 changed files
.travis.yml
History View file @ 774e210010
... ... 
@@ -12,3 +12,7 @@ apt_packages:
12 12 
   - libnetcdf-dev
13 13 
   - netcdf-bin
14 14
15 
+# Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 
+# Thanks to jimhester pointing this out!
17 
+before_install:
18 
+  - if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi
Browse code

add r pkg deps

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125194 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 10:56:44
Showing 1 changed files
.travis.yml
History View file @ a24c36b662
... ... 
@@ -1,6 +1,13 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 3 
 sudo: true
4 
+r_packages:
5 
+  - knitr
6 
+  - XML
7 
+  - plyr
8 
+  - doParallel
9 
+  - foreach
10 
+  - iterators
4 11 
 apt_packages:
5 12 
   - libnetcdf-dev
6 13 
   - netcdf-bin
Browse code

add dependency package with nc-config

From: Steffen Neumann <sneumann@ipb-halle.de>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125190 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 10:54:16
Showing 1 changed files
.travis.yml
History View file @ c5874ba63f
... ... 
@@ -1,4 +1,7 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 3 
 sudo: true
4 
-apt_packages: libnetcdf-dev
4 
+apt_packages:
5 
+  - libnetcdf-dev
6 
+  - netcdf-bin
7 
+
Browse code

Merge branch 'master' into new_pwiz

Laurent Gatto authored on 15/12/2016 09:37:26 • GitHub committed on 15/12/2016 09:37:26
Showing 0 changed files
Browse code

Avoid fixing cxx standard

sneumann authored on 14/12/2016 14:16:48 • GitHub committed on 14/12/2016 14:16:48
Showing 1 changed files
.travis.yml
History View file @ 21ca2aa4e4
... ... 
@@ -15,4 +15,4 @@ apt_packages:
15 15 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 16 
 # Thanks to jimhester pointing this out!
17 17 
 before_install:
18 
-  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x \nCXX1X=g++ -std=c++0x -g -O2 -fPIC ' > ~/.R/Makevars; fi
18 
+  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ \nCXX1X=g++ ' > ~/.R/Makevars; fi
Browse code

Try bioc-release to avoid CXX1X issue

sneumann authored on 13/12/2016 07:37:59 • GitHub committed on 13/12/2016 07:37:59
Showing 1 changed files
.travis.yml
History View file @ b300995e10
... ... 
@@ -1,5 +1,5 @@
1 1 
 language: r
2 
-r: bioc-devel
2 
+r: bioc-release
3 3 
 sudo: true
4 4 
 r_packages:
5 5 
   - knitr
Browse code

Fix TRAVIS_R_VERSION_STRING check

sneumann authored on 13/12/2016 07:22:53 • GitHub committed on 13/12/2016 07:22:53
Showing 1 changed files
.travis.yml
History View file @ da2d5c053e
... ... 
@@ -15,4 +15,4 @@ apt_packages:
15 15 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 16 
 # Thanks to jimhester pointing this out!
17 17 
 before_install:
18 
-  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x \nCXX1X=g++ -std=c++0x -g -O2 -fPIC ' > ~/.R/Makevars; fi
18 
+  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x \nCXX1X=g++ -std=c++0x -g -O2 -fPIC ' > ~/.R/Makevars; fi
Browse code

set both CXX1X and SHARED_CXX1XLD variables

sneumann authored on 12/12/2016 18:57:01 • GitHub committed on 12/12/2016 18:57:01
Showing 1 changed files
.travis.yml
History View file @ 5e45248946
... ... 
@@ -15,4 +15,4 @@ apt_packages:
15 15 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 16 
 # Thanks to jimhester pointing this out!
17 17 
 before_install:
18 
-  - if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x ' > ~/.R/Makevars; fi
18 
+  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x \nCXX1X=g++ -std=c++0x -g -O2 -fPIC ' > ~/.R/Makevars; fi
Browse code

Try SHLIB_CXX1XLD for travis.

sneumann authored on 12/12/2016 16:27:37 • GitHub committed on 12/12/2016 16:27:37
Showing 1 changed files
.travis.yml
History View file @ 8c8bea4523
... ... 
@@ -15,4 +15,4 @@ apt_packages:
15 15 
 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 16 
 # Thanks to jimhester pointing this out!
17 17 
 before_install:
18 
-  - if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi
18 
+  - if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ -std=c++0x ' > ~/.R/Makevars; fi
Browse code

Explicitly set CXX1X as workaround for R-devel issue

sneumann authored on 12/12/2016 16:18:40 • GitHub committed on 12/12/2016 16:18:40
Showing 1 changed files
.travis.yml
History View file @ c21967dce6
... ... 
@@ -12,3 +12,7 @@ apt_packages:
12 12 
   - libnetcdf-dev
13 13 
   - netcdf-bin
14 14
15 
+# Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
16 
+# Thanks to jimhester pointing this out!
17 
+before_install:
18 
+  - if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi
Browse code

add r pkg deps

Laurent authored on 12/12/2016 10:42:34
Showing 1 changed files
.travis.yml
History View file @ 678d9718ab
... ... 
@@ -1,6 +1,13 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 3 
 sudo: true
4 
+r_packages:
5 
+  - knitr
6 
+  - XML
7 
+  - plyr
8 
+  - doParallel
9 
+  - foreach
10 
+  - iterators
4 11 
 apt_packages:
5 12 
   - libnetcdf-dev
6 13 
   - netcdf-bin
Browse code

also add knitr

Laurent authored on 12/12/2016 10:30:59
Showing 1 changed files
.travis.yml
History View file @ 84051e9608
... ... 
@@ -2,6 +2,7 @@ language: r
2 2 
 r: bioc-devel
3 3 
 sudo: true
4 4 
 r_packages:
5 
+  - knitr
5 6 
   - XML
6 7 
   - plyr
7 8 
   - doParallel
Browse code

add mzID deps

Laurent authored on 12/12/2016 10:25:13
Showing 1 changed files
.travis.yml
History View file @ aeb10eff19
... ... 
@@ -1,4 +1,10 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 3 
 sudo: true
4 
+r_packages:
5 
+  - XML
6 
+  - plyr
7 
+  - doParallel
8 
+  - foreach
9 
+  - iterators
4 10 
 apt_packages: libnetcdf-dev
Browse code

add dependency package with nc-config

Steffen Neumann authored on 29/11/2016 08:41:26
Showing 1 changed files
.travis.yml
History View file @ f5a8b3330a
... ... 
@@ -1,4 +1,7 @@
1 1 
 language: r
2 2 
 r: bioc-devel
3 3 
 sudo: true
4 
-apt_packages: libnetcdf-dev
4 
+apt_packages:
5 
+  - libnetcdf-dev
6 
+  - netcdf-bin
7 
+
Browse code

merge conflicts

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@121284 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 23/09/2016 08:43:32
Showing 1 changed files
.travis.yml
History View file @ 8516f59b6f
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,4 @@
1 
+language: r
2 
+r: bioc-devel
3 
+sudo: true
4 
+apt_packages: libnetcdf-dev