qiime2R installed by doesnt read qza

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1

Hello,

I've gone through the download process, and made sure that I have all the necessary packages installed. However, at the very first step, I am getting this error:

qza_table <- read_qza("~/Iceland-2014-data/Iceland-2014-table-data2.qza")
Error in read_qza("~/Iceland-2014-data/Iceland-2014-table-data2.qza") :
could not find function "read_qza"

... even though the install seemed to work fine, as seen here:

devtools::install_github("jbisanz/qiime2R")
Downloading GitHub repo jbisanz/qiime2R@master
✓ checking for file ‘/private/var/folders/7p/pdccn9652m19v_p5qskwvcq80000gq/T/RtmpwqIKvf/remotes2fef15fcc521/jbisanz-qiime2R-ffb19df/DESCRIPTION’ (471ms)
─ preparing ‘qiime2R’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘qiime2R_0.99.23.tar.gz’

  • installing source package ‘qiime2R’ ...
    ** using staged installation
    ** R
    ** inst
    ** 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
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (qiime2R)

I am also unable to get ?read_qza to return anything, however, ??read_qza does open the documentation in the help window.

Any suggestions would be appreciated. Thanks.

1 Like
2

Hi @16sIceland!
I don’t have much mileage in R, but I suspect that you’re unable to use the function because you haven’t loaded the library yet. Can you double-check that you’ve loaded the library using the library command?

I think ? only works if the library’s been loaded, but ?? will bring up search results for any installed libraries regardless of loading.

Best,
Chris :snake:

2 Likes
3

OK, I fixed it! I forgot to load the library with library(qiime2R).

4 Likes