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r-hub / rhub-linux-builders

Docker configuration for the R-hub Linux builders
GNU General Public License v2.0
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Cannot run rhck locally: problem in installing Bioconductor packages #42

Closed strboul closed 5 years ago

strboul commented 5 years ago

I get the following error when I try to run the rhub/ubuntu-rchk image locally via Docker. I believe that the package download mechanism has recently been changed on the Bioconductor side.

> rhub::local_check_linux(path = ".", image = "rhub/ubuntu-rchk")
...
Sysreqs platform: linux-x86_64-ubuntu-gcc
No system requirements

>>>>>==================== Installing system requirements
75db945a0d7e53068db902ad589d0a75da8fa27b979426f114cb3ca64ace8f12

>>>>>==================== Starting Docker container
8605f70c390dea39a849ca5279354b095745ee73529b96e150baf364764b937f
/
> source('https://bioconductor.org/biocLite.R')
Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install
Execution halted
Error in run(bash, c(file.path(wd, "rhub-linux.sh"), args), echo = TRUE,  :
  System command error
Calls: <Anonymous> -> with_dir -> force -> run
Execution halted
maelle commented 5 years ago

What version of the remotes package is installed on your machine?

strboul commented 5 years ago 
> packageVersion("remotes")
[1] ‘2.0.2’

And the session infomation below:

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] whoami_1.3.0      prettyunits_1.0.2 ps_1.3.0.9000     withr_2.1.2
 [5] digest_0.6.18     crayon_1.3.4      rprojroot_1.3-2   assertthat_0.2.1
 [9] rappdirs_0.3.1    R6_2.4.0          jsonlite_1.6      backports_1.1.4
[13] magrittr_1.5      pillar_1.3.1      httr_1.4.0        rlang_0.3.2
[17] cli_1.1.0         uuid_0.1-2        rematch_1.0.1     callr_3.1.1
[21] parsedate_1.2.0   desc_1.2.0        rcmdcheck_1.3.2   rhub_1.1.1
[25] compiler_3.5.2    processx_3.2.1    xopen_1.0.0       pkgbuild_1.0.2
romainfrancois commented 5 years ago

Same problem with remotes 2.0.4

romainfrancois commented 5 years ago

Looks like this is where this happens: https://github.com/r-hub/rhub/blob/5dd0679a88d50e602a3bda1c24d404817631bcf0/inst/bin/rhub-linux-docker.sh#L40

gaborcsardi commented 5 years ago

Fixed in https://github.com/r-hub/rhub/commit/4471f797d2a257320c74030a18b58c996a3cc633