I am trying to use travis for my R package.
The check are fine for R 3.4, results are here
For R 3.3, Travis is KO because Travis install the package rhdf5 but it's not the correct version. Results are here
I have in my description file, the following lines
Imports:
data.table,
methods,
stats
Suggests:
rhdf5 (>= 2.20.0),
parallel,
testthat,
knitr,
rmarkdown,
covr
For R 3.4, travis does this
Installing R packages: rhdf5, zlibbioc
108.31s$ Rscript -e 'install.packages(c("rhdf5", "zlibbioc"));if (!all(c("rhdf5", "zlibbioc") %in% installed.packages())) { q(status = 1, save = "no")}'
Installing packages into ‘/home/travis/R/Library’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib /rhdf5_2.22.0.tar.gz'
Content type 'application/x-gzip' length 5475293 bytes (5.2 MB)
For R 3.3, travis does this
Installing R packages: rhdf5, zlibbioc
7.09s$ Rscript -e 'install.packages(c("rhdf5", "zlibbioc"));if (!all(c("rhdf5", "zlibbioc") %in% installed.packages())) { q(status = 1, save = "no")}'
Installing packages into ‘/Users/travis/R/Library’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks /contrib/3.3/rhdf5_2.18.0.tgz'
Content type 'application/x-gzip' length 1557714 bytes (1.5 MB)
So for R 3.3, Travis install rhdf5 2.18 but in my description file I specified 2.20.
Result of the check for R 3.3
* checking package dependencies ... ERROR
Package required and available but unsuitable version: ‘rhdf5’
How to tell to Travis to install rhdf5 but only if the version 2.20 is available ?
I didn't find this information in the travis Doc here
Must I set _R_CHECK_FORCE_SUGGESTS to FALSE ?
Currently this is my yaml file
language: R
sudo: true
cache: packages
bioc_required: true
bioc_use_devel: true
os:
- linux
- osx
r:
- oldrel
- release
- devel
r_github_packages:
- hadley/devtools#1263
- rte-antares-rpackage/antares-rpackageRead@develop
#before - Bioconductor-mirror/zlibbioc
# - Bioconductor-mirror/rhdf5
#after
bioc_packages:
- rhdf5
- zlibbioc
r_packages:
- covr
- devtools
- data.table
- lubridate
- plyr
- stringr
- shiny
- knitr
- testthat
- rmarkdown
after_success:
- Rscript -e 'library(covr); codecov()'
