fedora-clang-devel (https://builder.r-hub.io/status/dupree_0.2.0.tar.gz-2a2ad3c22aa6408499d5a2fcb42c82d2); this seems to result from not being able to install xml2=1.2.2 (due to the absence of libxml2). My package built ok on a couple of other platforms and on appveyor/travis - so I'm wondering if there's anything I need to do to ensure xml2 can be installed on rhub's fedora platform
standalone.cls (https://builder.r-hub.io/status/texPreview_1.4.2.tar.gz-8f384c90899541f296ad7034829a77d4). What is the appropriate way to reslove this issue? I do not seem to be getting this same error on CRAN checks (the failure there is more downstream after the tex is rendered) https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/texPreview-00check.html.
Hi there,
this is my first time using R-hub. As the maintainer of the mousetrap package, I received an email today from CRAN about an error message that occurs when the package is checked with r-devel-linux-x86_64-debian-clang. To replicate the error, I ran the following code (in the local copy of my GitHub repository):
check_results <- rhub::check_for_cran()
However, the code always gets stuck at:
- Preparing build, see status at
I also tried using the web interface but it failed (https://builder.r-hub.io/status/mousetrap_3.1.3.tar.gz-beb8e6f6d385740880017a3c766d2067)
Do you have any idea what went wrong and if I made a mistake?
Thanks! Best, Pascal
rhub::list_my_checks() to see if your check(s) are in progress or not.
rhub::get_check(<id>)$livelog() to get the live log.
units and the installation was not successfulhttps://builder.r-hub.io/status/graphcoloring_0.1.0.tar.gz-713467a70c044624965268be39a6af15#L3937
Configuration failed because libudunits2.so was not found. Try installing:
* deb: libudunits2-dev (Debian, Ubuntu, ...)
1 reply
fedora-clang-devel, but other platforms seem to be fine (more details for instance here https://gitlab.com/jozefhajnala/jhaddins/-/jobs/396859774)
Hello!! I have been developing a package for migration analysis, which I consider is in a late state. However, I am an amateur doing packages, and I have had a frequent error which has been my pain in the neck since long time ago. I searched on internet meetups groups and other kind of help and got this website. Believe me, I have been working on it but no hints!
My package is already on Github, it works, I have made some CMD checks in order to get 0 errors 0 warnings and 0 messages. However, I get always the same error when I run it, which I consider is not a package matter, is more about a misunderstanding of a function.
package address is: https://github.com/elflacosebas/migraR
Check the example very well before you go to the stackoverflow tag: https://stackoverflow.com/questions/59249678/eval-trouble-into-r-package
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
...had been told earlier by Gabor Czardi that with debian-clang this is an rhub bug, bot it now also happens with "rhub/debian-gcc-devel-nold". Anything that can be done about this, or is rhub unusable for packages that require some stuff that requires some Bioconductor stuff? (I'm not even directly using it, one of the Depends packages brings it is.)
#> checking for gsl-config... no
#> configure: error: gsl-config not found, is GSL installed?
#> ERROR: configuration failed for package ‘eaf’
#> * removing ‘/Users/userBFG8H6lm/R/eaf’
#> Warning message:
#> In i.p(...) :
#> installation of package ‘/Users/userBFG8H6lm/Rtemp/Rtmp7chVso/file1cc825ac16d8/eaf_1.9.tar.gz’ had non-zero exit status
"ENOSPC: no space left on device, write
" and from R: Error in query("SUBMIT PACKAGE", data = list(email = unbox(email), token = unbox(email_get_token(email)), :
rhub error. Any chance to check "rhub's status" somewhere?
I am trying to check the package dmdScheme locally by using local_cha=eck_linux("."), but I get the following error:
> chk <- local_check_linux(".")
─ Building package
Container name: fcc97700-0b57-4985-9e6b-3e750c3349ef-2
It will _not_ be removed after the check.
R-hub Linux builder script v0.10.0 (c) R Consortium, 2018-2019
Package: /var/folders/50/wcr5bjwn75q595n6x82gxj280000gq/T//RtmpvsL4dV/file4533679525f/dmdScheme_1.2.tar.gz
Docker image: rhub/debian-gcc-devel
Env vars:
R CMD check arguments:
Sysreqs platform: linux-x86_64-debian-gcc
Error in contrib.url(repos, type) :
trying to use CRAN without setting a mirror
Calls: cat ... sysreqs -> get_cran_deps -> <Anonymous> -> contrib.url
Execution halted
No system requirements
>>>>>==================== Installing system requirements
e041a03cdc0f7799ebdb1f95136f2b34fcec4c9d9af1902663edda9003e991d4
>>>>>==================== Starting Docker container
a91c0420fa4959904b511c198946202a0731e7ca4427ff74b18be117272c583a
> 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 'bash' failed, exit status: 1, stdout & stderr were printed
Type .Last.error.trace to see where the error occured
> .Last.error.trace
Stack trace:
1. rhub:::local_check_linux(".")
2. withr:::with_dir(wd, run(bash, c(file.path(wd, "rhub-linux.sh"), ...
3. base:::force(code)
4. processx:::run(bash, c(file.path(wd, "rhub-linux.sh"), args), ...
5. throw(new_process_error(res, call = sys.call(), echo = echo, ...
x System command 'bash' failed, exit status: 1, stdout & stderr were printed
>Any ideas what is going on? I am not aware, that I have bioconductor dependencies?
Hello folks, first of all I want to thank the maintainers of r-hub, it's been super helpful for me and a great setup.
Is there a preferred process for sending in PRs for updates or additions to sysreqsdb? I've been sending PRs (e.g. r-hub/sysreqsdb#81) to cut down on the number of issues/PRs/etc. people have to triage, but I wanted to make sure that was in-line with what the maintainers were hoping for.
local_check_linux(), I did discover that it would be possible with a bit of modification (https://github.com/r-hub/sysreqs/compare/master...jonkeane:url-config) to let one set the URL the sysreqs looks to and uses in that process. If this is a feature that is helpful to others, I'm happy to put together a PR for that as well.
I'm getting periodic error messages like below when using check_on_linux() with https://builder.r-hub.io/status/SwimmeR_0.4.1.tar.gz-1d36d5c04d514d6aae2291102e3b3d11 Despite the error message directing me to check logs I haven't received any logs. These messages are accompanied by longer than expected (~4 hours and counting) processing times. Anyone seen something similar, have any thoughts?
3 replies
https://builder.r-hub.io/status/vivid_0.1.0.tar.gz-cf5dc8a8606447ea9e62a83aa8ae436f
The proj4 dependency failed to install:
4924#> configure: error: libproj and/or proj.h/proj_api.h not found in standard search locations.
4925#> *** Install PROJ library and if necessary set PKG_CPPFLAGS/PKG_LIBS accordingly.
4926#> ERROR: configuration failed for package ‘proj4’
4927#> * removing ‘/home/docker/R/proj4’Even though libproj-dev is installed. You can try to install proj4 in the rhub/ubuntu-gcc-release container, to see why this fails.
