qiime2R unable to access index for repository when downloading

Other Bioinformatics Tools
1

I am trying to utilize qiime2R in RStudio (version 2024.04.1+748).

I first did the following:
install.packages("qiime2R)

But I get this error error:
Warning in install.packages :
package ‘qiime2R’ is not available for this version of R

I then did the following:
install.packages('remotes')
library(remotes)
remotes::install_github('jbisanz/qiime2R')

I then received the following errors and was unable to download qiime2R. I also tried this with older versions of RStudio with the same result.

Screenshot 2024-06-07 at 1.24.07 PM
Screenshot 2024-06-07 at 1.24.07 PM1390×456 88.3 KB

Screenshot 2024-06-07 at 1.24.23 PM
Screenshot 2024-06-07 at 1.24.23 PM1390×204 20.6 KB

Any help getting this resolved would be greatly appreciated.

2

Hi @kwoodruff,
This post might be able to answer your question!

Hope this helps!
:turtle:

1 Like
3

Hello. When researching my error I did come accross this post and I followed the steps for downloading via github. However from the error above it is saying "unable to access index for repository". Are there any suggestions for resolving this?

Thanks!
Kelly

4

Hi @kwoodruff,
Check out this r - Warning in install.packages: unable to access index for repository - Stack Overflow

I think what you are seeing might stem from some Firewall restrictions? If you are at a university, you may have to loop in your IT staff for help with this issue!

5

Hello. I will look into this with IT however I have successfully used qiime2R in the past. I spoke with an individual at another institution who has tried using it within the last few months and was encountering this same issue.

6

Hi, I'm having a similar issue and am unable to install qiime2R. While OP got "Unable to access" errors, I'm getting 404 errors:

Example:

Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES.rds': HTTP status was '404 Not Found'

7

Hello @PWS,

What operating system are you using? I ask because I see "windows" in the url in the error message. What instructions did you follow? I'm able to install qiime2R following the instructions on the software's GitHub on an M-series Mac as of today.

8

Hi @colinvwood,

Thanks for the response! I'm on Windows 11 and was sent .qza files to by a mac qiime2 user. I'm trying to install with the following code from the github:

if (!requireNamespace("devtools", quietly = TRUE)){install.packages("devtools")}
devtools::install_github("jbisanz/qiime2R")

I am no longer getting the 404 error but am still unable to access the packages. The current errors read like the one below:

Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'

9

Hello @PWS,

Did you look through the link posted by Chloe above (from June 11)?

10

Hi @colinvwood,

Yes, I did and have unchecked the 'secure download method' option. It did not help. I have also uninstalled and re-installed R and R studio and attempted to scour the forums before posting.

One thing I haven't tried is using a different computer, which I can trial this evening.

11

I want to report that I have solved the issue. Changing computers did not alter the results, I was still getting 'unable to access index for repository' errors.

I made a list of all of the dependencies that were inaccessible and sought out installers for each. With all dependencies installed the qiime2r installation was able to complete.

Thanks @colinvwood for taking the time to assist.

1 Like