Extraction of annotation files error with getAnnotation(bgee)

[Ni-Ar]

Hi again,

I tried to specify a folder where to dump all Bgee data as following and I get unzipping problems I believe. My goal, would be to
specify the path to a cluster that is mounted on my laptop so that I don't need to have all the species data on my computer but can be stored and cached somewhere else.

library(BgeeDB)

Specify a simple folder in my home directory.

Bgee_path <- "~/Bgee"

Create a new Bgee object like this:

bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq", 
                 pathToData = Bgee_path, release = "15.0")
Querying Bgee to get release information...

Building URL to query species in Bgee release 15_0...

Submitting URL to Bgee webservice... (https://bgee.org/bgee15_0/api/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.20.1)

Query to Bgee webservice successful!

API key built: 839b6b011488b [omissis] 9c4a13

Get mouse annotation

annotation_bgee_mouse <- getAnnotation(bgee)

tar: could not chdir to '~/Bgee/Mus_musculus_Bgee_15_0'


Saved annotation files in ~/Bgee/Mus_musculus_Bgee_15_0 folder.
Error in getAnnotation(bgee) : 
  ERROR: extraction of annotation files from downloaded zip file went wrong.
In addition: Warning messages:
1: In untar(file.path(myBgeeObject$pathToData, annotationFile), exdir = myBgeeObject$pathToData) :
  ‘/usr/bin/tar -xf '/Users/niar/Bgee/Mus_musculus_Bgee_15_0/Mus_musculus_RNA-Seq_experiments_libraries.tar.gz' -C '~/Bgee/Mus_musculus_Bgee_15_0'’ returned error code 1
2: In file.rename(from = myData, to = file.path(myBgeeObject$pathToData,  :
  cannot rename file '/Users/niar/Bgee/Mus_musculus_Bgee_15_0/Mus_musculus_RNA-Seq_experiments_libraries/Mus_musculus_RNA-Seq_experiments.tsv' to '/Users/niar/Bgee/Mus_musculus_Bgee_15_0/Mus_musculus_RNA-Seq_experiments.tsv', reason 'No such file or directory'
3: In file.rename(from = myData, to = file.path(myBgeeObject$pathToData,  :
  cannot rename file '/Users/niar/Bgee/Mus_musculus_Bgee_15_0/Mus_musculus_RNA-Seq_experiments_libraries/Mus_musculus_RNA-Seq_libraries.tsv' to '/Users/niar/Bgee/Mus_musculus_Bgee_15_0/Mus_musculus_RNA-Seq_libraries.tsv', reason 'No such file or directory'

And if I check in the subfolder:

ls -1 ~/Bgee/
Mus_musculus
Mus_musculus_Bgee_15_0
release.tsv

and the subfolders are all empty, while the release.tsv file seems okay.

My system tar version

/usr/bin/tar  --version
bsdtar 3.3.2 - libarchive 3.3.2 zlib/1.2.11 liblzma/5.0.5 bz2lib/1.0.6

R details:

packageVersion("BgeeDB")
[1] ‘2.20.1’

─ Session info ─────────────────────────────────────────────
 setting  value
 version  R version 4.1.2 (2021-11-01)
 os       macOS Catalina 10.15.7
 system   x86_64, darwin17.0
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Madrid
 date     2022-07-07
 rstudio  2022.02.3+492 Prairie Trillium (desktop)
 pandoc   2.10.1 @ /usr/local/bin/pandoc

Thanks!