xia-lab/miRNetR

Cannot install

Closed this issue · 7 comments

cebercoto commented

Cannot install mirnetR following the commands with the following output:

devtools::install_github("xia-lab/miRNetR", build = TRUE, build_opts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE, force = TRUE)
Downloading GitHub repo xia-lab/miRNetR@HEAD
Skipping 5 packages not available: genefilter, HTqPCR, edgeR, limma, preprocessCore
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────✔ checking for file ‘/tmp/RtmpTiqGqn/remotesd9a9232970dfb/xia-lab-miRNetR-1f28123/DESCRIPTION’ ...
─ preparing ‘miRNetR’:
✔ checking DESCRIPTION meta-information ...
─ installing the package to build vignettes
-----------------------------------
─ installing source package ‘miRNetR’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘miRNetR’ in namespaceExport(ns, exports):
undefined exports: GetRandomMirTargetGenes, GetRandomXenoMirTargetGenes, LoadClusterLib, LoadDiseaseLib, LoadFuncLib, LoadGOLib, LoadHMDDLib, LoadKEGGLib, LoadREACTOMELib, LoadTFLib, LoadTissueLib, LoadmiRFamLib
Error: loading failed
Execution halted
ERROR: loading failed
─ removing ‘/tmp/RtmpEZ0XG9/Rinstd9d7a242c5f76/miRNetR’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'miRNetR' from GitHub:
! System command 'R' failed

All the previous steps don't produce any errors

Thanks

fiyhui commented

Hello! The issue should be fixed now.
Please try again and don't hesitate to contact us if you still see the error.

  • ❤️1
cebercoto commented

Hi! many thanks I was able to install it now. but now it is saying:

library(miRNetR)
Init.Data("mir", "mirlist")
Error in Init.Data("mir", "mirlist") :
could not find function "Init.Data"

can you look into this?
FYI, I was already a user for quite some time, not that I am new to mirnetR :)

Thanks

cebercoto commented

Hi again, I'm guessing there are things going on since the error has changed now after reinstallation of the R package (just FYI in case it helps):

Init.Data("mir", "mirlist")
Error in Init.Data("mir", "mirlist") : object '.on.public.web' not found

Cheers

fiyhui commented

Good day! Thank you for the feedback, it's much appreciated. Indeed, we are aiming to push an update in the R code to solve this issue by the end of the week. In the meantime, feel free to install a previous commit - the last commit version from 2022 will be more stable.

cebercoto commented

Thanks! yes, indeed I did an upgrade of R version recently and reinstalled all packages, hence all my problems. The last version of 2022 is working fine now. Any idea of when the new version will be "stable"? will it be announced somewhere?

Many thanks!

fiyhui commented

Hi! The recent updates are mostly for improving web interface and user experience, there is no major changes to R functionality. If we do a major update, it will for sure be announced on the miRNet webpage.

cebercoto commented

Perfect! many thanks. and thanks for all the hard work!