Cannot open loom file

[yonatans2]

The package fails to open the file dev_all.agg.loom (from Mouse Brain Atlas), giving the following error:

clust_mat = connect(filename='dev_all.agg.loom')
Error in validateLoom(object = self) :
There can only be 5 groups in the loom file: 'row_attrs', 'col_attrs', 'layers', 'row_graphs', 'col_graphs'

Would appreciate any help.

Thanks,
Yonatan

[squatrim]

I have been having the same error with the same file.

My session info can be found below.

Thanks
Best,
Massimo

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] loomR_0.2.1.9000 hdf5r_1.3.2 R6_2.5.0

loaded via a namespace (and not attached):
[1] compiler_4.0.2 prettyunits_1.1.1 remotes_2.2.0 tools_4.0.2 testthat_2.3.2 digest_0.6.25
[7] pkgbuild_1.1.0 pkgload_1.1.0 bit_4.0.4 lattice_0.20-41 memoise_1.1.0 rlang_0.4.7
[13] Matrix_1.2-18 cli_2.0.2 rstudioapi_0.11 parallel_4.0.2 curl_4.3 xfun_0.16
[19] stringr_1.4.0 withr_2.2.0 desc_1.2.0 fs_1.4.2 devtools_2.3.1 rprojroot_1.3-2
[25] bit64_4.0.5 grid_4.0.2 glue_1.4.1 processx_3.4.3 pbapply_1.4-3 fansi_0.4.1
[31] sessioninfo_1.1.1 callr_3.4.3 magrittr_1.5 backports_1.1.8 ps_1.3.3 ellipsis_0.3.1
[37] usethis_1.6.1 assertthat_0.2.1 tinytex_0.25 stringi_1.5.3 crayon_1.3.4

[FloWuenne]

I was running into the same issue today and I believe this is answered in the following issue: #55

TLDR: the solution is to add the skip.validate = TRUE argument to your connect command!

lfile <- connect(filename = your_loom_file,
                 mode = "r+",
                 skip.validate = TRUE)
                 ```

[squatrim]

Thanks Flo!
skip.validate = TRUE indeed solved the issue. I cannot still get the gene names out of the matrix, but I guess that is related to the actual file I am working with.