theislab / zellkonverter

Conversion between scRNA-seq objects
https://theislab.github.io/zellkonverter/
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Installation fails on R 4.0.4 #82

Closed royfrancis closed 1 year ago

royfrancis commented 1 year ago

Using remotes:

> remotes::install_github("theislab/zellkonverter",upgrade="never",dependencies="TRUE")

Downloading GitHub repo theislab/zellkonverter@HEAD
✔  checking for file ‘/scratch/31367182/RtmpgS8CTv/remotes24854df9622b/theislab-zellkonverter-fa22a44/DESCRIPTION’ (393ms)
─  preparing ‘zellkonverter’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘zellkonverter_1.9.0.tar.gz’
   Warning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/domus/h1/royfranc/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
Welcome!
* installing *source* package ‘zellkonverter’ ...
** using non-staged installation via StagedInstall field
Welcome!
** R
** inst
** byte-compile and prepare package for lazy loading
Welcome!
Error: object ‘I’ is not exported by 'namespace:S4Vectors'
Execution halted
ERROR: lazy loading failed for package ‘zellkonverter’
* removing ‘/domus/h1/royfranc/R/x86_64-pc-linux-gnu-library/4.0/zellkonverter’
Warning message:
In i.p(...) :
  installation of package ‘/scratch/31367182/RtmpgS8CTv/file24855ccaab79/zellkonverter_1.9.0.tar.gz’ had non-zero exit status

Using BiocManager:

> BiocManager::install("zellkonverter")

Bioconductor version 3.12 (BiocManager 1.30.19), R 4.0.4 (2021-02-15)
Error in sprintf(fmt, ...) : 
  'fmt' length exceeds maximal format length 8192
In addition: Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'zellkonverter' 
lazappi commented 1 year ago

Hi @royfrancis

Thanks for giving {zellkonverter} a go! The first error I think is because you are trying to install the most recent version of {zellkonverter} with an old version of R where you have older, incompatible versions of other Bioconductor packages. This is not supposed to work and I should probably have updated the R dependency in the last release to make that impossible.

The second one should work in theory, letting you install the correct versions for the Bioconductor 3.12 release. As you can see the error message isn't very helpful so I'm not sure how much I can help. Maybe there is a way to increase the size of the message? Are you able to install other Bioconductor packages this way?

royfrancis commented 1 year ago

I managed to install it on R 4.1.1