Help accessing data

[amitsud]

Dear Ramon and colleagues,

Great work and thank you for making this data available. I am trying to access the data via level 4 (R) using the following command:
devtools::install_github("massonix/HCATonsilData", build_vignettes = TRUE)

However I get the following error message:
**Quitting from lines 117-119 (HCATonsilData.Rmd)
Error: processing vignette 'HCATonsilData.Rmd' failed with diagnostics:
HDF5. File accessibility. Unable to open file.
--- failed re-building 'HCATonsilData.Rmd'

SUMMARY: processing the following file failed:
'HCATonsilData.Rmd'

Error: Vignette re-building failed.
Execution halted**

Apologies if I am doing something wrong - can you please help?

Many thanks

BW

Amit

[massonix]

Hi @amitsud! Could you please copy&paste the output of your sessionInfo(), please?

[amitsud]

Thanks for the quick reply

Sorry - I am getting a new error (not sure why it has changed):

**devtools::install_github("massonix/HCATonsilData",` build_vignettes = TRUE)**
Downloading GitHub repo massonix/HCATonsilData@HEAD
v  checking for file '/tmp/Rtmp4ZmIBn/remotes194cad282fff6f/massonix-HCATonsilData-59187d4/DESCRIPTION' ...
-  preparing 'HCATonsilData':
v  checking DESCRIPTION meta-information ...
-  installing the package to build vignettes
         -----------------------------------
-  installing *source* package 'HCATonsilData' ...
   ** using staged installation
   ** R
   Error in parse(outFile) :
     /tmp/RtmpqqLHoP/Rbuild1bbed83785c9f0/HCATonsilData/R/HCATonsilData.R:52:33: unexpected input
   51:                        "pca", "harmony", "umap")
   52:   filePaths <- sapply(suffixes, \
                                       ^
   ERROR: unable to collate and parse R files for package 'HCATonsilData'
-  removing '/tmp/RtmpqqLHoP/Rinst1bbed828c2322f/HCATonsilData'
         -----------------------------------
   ERROR: package installation failed
Error: Failed to install 'HCATonsilData' from GitHub:
  ! System command 'R' failed

**sessionInfo()**
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8 (Core)

Matrix products: default
BLAS:   /usr/lib64/libblas.so.3.8.0
LAPACK: /opt/software/compilers/R/4.0.2/lib64/R/lib/libRlapack.so

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] ps_1.7.1          prettyunits_1.1.1 withr_2.5.0       rprojroot_2.0.3
 [5] crayon_1.5.1      R6_2.5.1          lifecycle_1.0.1   magrittr_2.0.3
 [9] rlang_1.0.3       cachem_1.0.6      cli_3.3.0         curl_4.3.2
[13] remotes_2.4.2     fs_1.5.2          callr_3.7.0       ellipsis_0.3.2
[17] devtools_2.4.3    tools_4.0.2       glue_1.6.2        purrr_0.3.4
[21] pkgload_1.3.0     fastmap_1.1.0     compiler_4.0.2    processx_3.6.1
[25] pkgbuild_1.3.1    sessioninfo_1.2.2 tcltk_4.0.2       memoise_2.0.1
[29] `usethis_2.1.6

Thanks so much and sorry for bothering you.

BW

Amit

[massonix]

Hi Amit,

I think I know what is the issue. The data was uploaded to ExperimentHub and released with Bioconductor 3.15. As you can see here, to install BioC 3.15 you need R >=4.2.0. Thus, the steps you need to follow are:

1. Install R 4.2.0 and BioConductor 3.15.
2. Install HCATonsilData.

Please let me know if you run into any issues when building the vignette. If it takes too long, you can intall it with build_vignettes = FALSE

Hope this helps!