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multimeric avatar multimeric commented on June 8, 2024

I suspect your home directory is/was full, I don't believe this is an issue with the package itself. I can't replicate the issue:

> get_metadata() |> 
+     dplyr::filter(file_id_db=="e427efe71e8e94de5b3e48eb98236323") |> get_single_cell_experiment()
ℹ Downloading 1 file, totalling 0.48 GB
ℹ Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/metadata/metadata.0.2.3.parquet to /home/users/allstaff/milton.m/.cache/R/CuratedAtlasQueryR/metadata.0.2.3.parquet
  |=============================================================================================================================| 100%
ℹ Realising metadata.
ℹ Synchronising files
ℹ Downloading 2 files, totalling 0.06 GB
ℹ Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellxgene-0.2.1-hdf5/original/e427efe71e8e94de5b3e48eb98236323/assays.h5 to /home/users/allstaff/milton.m/.cache/R/CuratedAtlasQueryR/0.2.1/original/e427efe71e8e94de5b3e48eb98236323/assays.h5
ℹ Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellxgene-0.2.1-hdf5/original/e427efe71e8e94de5b3e48eb98236323/se.rds to /home/users/allstaff/milton.m/.cache/R/CuratedAtlasQueryR/0.2.1/original/e427efe71e8e94de5b3e48eb98236323/se.rds
ℹ Reading files.
ℹ Compiling Single Cell Experiment.
class: SingleCellExperiment 
dim: 36229 3979 
metadata(0):
assays(1): counts
rownames(36229): A1BG A1BG-AS1 ... ZZEF1 ZZZ3
rowData names(0):
colnames(3979): RU699_227364270922139_1 RU675_N_169174309170077_1 ... RU685_N_205449200090022_1
  RU661_T_236288388295404_1
colData names(56): sample_ cell_type ... updated_at_y original_cell_id
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):

from curatedatlasqueryr.

stemangiola avatar stemangiola commented on June 8, 2024

Would it be worth intercepting the error message and, adding a message (besides the original one) saying

CuratedAtlasQueryR says: it is possible that this error is due to the disk being full.

This might avoid issue like this opened in the future,

from curatedatlasqueryr.

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