vjcitn
commented
1 year ago I can't reproduce your error. Please verify that you are using Bioconductor 3.17, that BiocManager::valid is TRUE and then send your error with sessionInfo.
> x = getOnto("cellOnto", "2023")
snapshotDate(): 2023-04-06
loading from cache
> x
Ontology with 17206 terms
format-version: 1.2
data-version: releases/2023-02-15
ontology: cl
Properties:
id: character
name: character
parents: list
children: list
ancestors: list
obsolete: logical
format-version: list
data-version: list
subsetdef: list
synonymtypedef: list
remark: list
ontology: list
property_value: list
def: character
disjoint_from: list
part_of: list
is_a: list
equivalent_to: list
comment: character
subset: list
intersection_of: list
bearer_of: list
synonym: list
xref: list
union_of: list
has_component: list
creation_date: character
namespace: list
has_parent_hydride: list
is_conjugate_base_of: list
RO:0000087: list
is_conjugate_acid_of: list
alt_id: list
is_tautomer_of: list
has_part: list
has_functional_parent: list
is_enantiomer_of: list
is_substituent_group_from: list
only_in_taxon: list
replaced_by: list
consider: list
develops_from: list
capable_of_part_of: list
capable_of: list
participates_in: list
present_in_taxon: list
in_taxon: list
lacks_plasma_membrane_part: list
RO:0002104: list
produces: list
adjacent_to: list
never_in_taxon: list
located_in: list
RO:0015016: list
lacks_part: list
RO:0015015: list
RO:0002100: list
dc-contributor: list
output_of: list
RO:0002203: list
RO:0002120: list
has_not_completed: list
RO:0002102: list
RO:0002103: list
RO:0002292: list
RO:0002388: list
RO:0001000: list
RO:0013001: list
RO:0002130: list
RO:0002101: list
existence_starts_and_ends_during: list
existence_ends_during: list
existence_starts_during: list
seeAlso: list
created_by: character
RO:0013007: list
innervates: list
synapsed_by: list
results_in_distribution_of: list
regulates: list
has_input: list
has_primary_input: list
results_in_assembly_of: list
starts_with: list
bounding_layer_of: list
results_in_organization_of: list
has_primary_output: list
results_in_fission_of: list
results_in_fusion_of: list
results_in_morphogenesis_of: list
results_in_development_of: list
results_in_formation_of: list
results_in_growth_of: list
results_in_acquisition_of_features_of: list
results_in_maturation_of: list
has_participant: list
directly_positively_regulates: list
has_primary_input_or_output: list
results_in_movement_of: list
occurs_in: list
acts_on_population_of: list
negatively_regulates: list
positively_regulates: list
process_has_causal_agent: list
has_output: list
has_end_location: list
has_start_location: list
directly_negatively_regulates: list
regulated_by: list
directly_regulates: list
ends_with: list
results_in_transport_across: list
has_target_start_location: list
has_target_end_location: list
results_in_disassembly_of: list
results_in_transport_to_from_or_in: list
results_in_developmental_progression_of: list
results_in_transport_along: list
regulates_levels_of: list
overlaps: list
RO:0015011: list
RO:0015007: list
RO:0015008: list
RO:0015010: list
continuous_with: list
contributes_to_morphology_of: list
connects: list
in_lateral_side_of: list
has_skeleton: list
immediate_transformation_of: list
composed_primarily_of: list
immediately_deep_to: list
attaches_to: list
has_quality: list
has_potential_to_develop_into: list
surrounds: list
location_of: list
extends_fibers_into: list
channel_for: list
channels_from: list
channels_into: list
conduit_for: list
existence_ends_during_or_before: list
existence_starts_during_or_after: list
has_boundary: list
preceded_by: list
precedes: list
simultaneous_with: list
immediately_preceded_by: list
ends: list
surrounded_by: list
developmentally_replaces: list
developmentally_induced_by: list
starts: list
transformation_of: list
anterior_to: list
has_developmental_contribution_from: list
proximalmost_part_of: list
luminal_space_of: list
subdivision_of: list
has_member: list
functionally_related_to: list
dorsal_to: list
connected_to: list
contains: list
produced_by: list
branching_part_of: list
attaches_to_part_of: list
drains: list
in_left_side_of: list
supplies: list
existence_ends_with: list
existence_starts_with: list
has_muscle_insertion: list
has_muscle_origin: list
in_anterior_side_of: list
anteriorly_connected_to: list
posteriorly_connected_to: list
proximally_connected_to: list
distally_connected_to: list
preaxialmost_part_of: list
contains_process: list
distalmost_part_of: list
innervated_by: list
has_muscle_antagonist: list
in_right_side_of: list
protects: list
lumen_of: list
tributary_of: list
sexually_homologous_to: list
develops_in: list
filtered_through: list
skeleton_of: list
postaxialmost_part_of: list
directly_develops_from: list
indirectly_supplies: list
in_posterior_side_of: list
deep_to: list
site_of: list
superficial_to: list
immediately_superficial_to: list
ventral_to: list
trunk_part_of: list
distal_to: list
proximal_to: list
in_deep_part_of: list
in_superficial_part_of: list
posterior_to: list
has_potential_to_developmentally_contribute_to: list
intersects_midsagittal_plane_of: list
layer_part_of: list
in_proximal_side_of: list
in_dorsal_side_of: list
develops_from_part_of: list
is_functional: list
inverse_of: list
domain: list
range: list
holds_over_chain: list
is_transitive: list
transitive_over: list
expand_expression_to: list
is_symmetric: list
is_inverse_functional: list
is_metadata_tag: list
is_asymmetric: list
expand_assertion_to: list
is_class_level: list
equivalent_to: list
Roots:
PR:000000001 - protein
BFO:0000003 - occurrent
functionally_related_to - functionally related to
GO:0050878 - regulation of body fluid levels
RO:0002323 - mereotopologically related to
has_participant - has participant
RO:0002222 - temporally related to
CHEBI:36342 - subatomic particle
RO:0002410 - causally related to
GO:0010817 - regulation of hormone levels
... 92 more
> sessionInfo()
``
R Under development (unstable) (2023-03-18 r84003)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /home/stvjc/R-43dev-dist/lib/R/lib/libRblas.so
LAPACK: /home/stvjc/R-43dev-dist/lib/R/lib/libRlapack.so; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/San_Marino
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ontoProc_1.22.0 ontologyIndex_2.11 rmarkdown_2.21
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.30.1 KEGGREST_1.40.0
[3] xfun_0.39 htmlwidgets_1.6.2
[5] ontologyPlot_1.6 lattice_0.21-8
[7] Biobase_2.60.0 vctrs_0.6.2
[9] tools_4.3.0 bitops_1.0-7
[11] generics_0.1.3 stats4_4.3.0
[13] curl_5.0.0 tibble_3.2.1
[15] fansi_1.0.4 AnnotationDbi_1.62.1
[17] RSQLite_2.3.1 blob_1.2.4
[19] pkgconfig_2.0.3 Matrix_1.5-4.1
[21] dbplyr_2.3.2 S4Vectors_0.38.1
[23] graph_1.78.0 GenomeInfoDbData_1.2.10
[25] lifecycle_1.0.3 compiler_4.3.0
[27] Biostrings_2.68.1 httpuv_1.6.11
[29] GenomeInfoDb_1.36.0 htmltools_0.5.5
[31] RCurl_1.98-1.12 yaml_2.3.7
[33] interactiveDisplayBase_1.38.0 later_1.3.1
[35] pillar_1.9.0 crayon_1.5.2
[37] ellipsis_0.3.2 DT_0.28
[39] DelayedArray_0.26.3 cachem_1.0.8
[41] mime_0.12 AnnotationHub_3.8.0
[43] tidyselect_1.2.0 digest_0.6.31
[45] purrr_1.0.1 dplyr_1.1.2
[47] BiocVersion_3.17.1 paintmap_1.0
[49] fastmap_1.1.1 grid_4.3.0
[51] cli_3.6.1 magrittr_2.0.3
[53] S4Arrays_1.0.4 utf8_1.2.3
[55] withr_2.5.0 filelock_1.0.2
[57] promises_1.2.0.1 rappdirs_0.3.3
[59] bit64_4.0.5 XVector_0.40.0
[61] httr_1.4.6 matrixStats_0.63.0
[63] igraph_1.4.3 bit_4.0.5
[65] png_0.1-8 memoise_2.0.1
[67] shiny_1.7.4 evaluate_0.21
[69] knitr_1.43 GenomicRanges_1.52.0
[71] IRanges_2.34.0 BiocFileCache_2.8.0
[73] rlang_1.1.1 Rcpp_1.0.10
[75] startup_0.20.0 xtable_1.8-4
[77] glue_1.6.2 DBI_1.1.3
[79] Rgraphviz_2.44.0 BiocManager_1.30.20
[81] BiocGenerics_0.46.0 R6_2.5.1
[83] MatrixGenerics_1.12.0 zlibbioc_1.46.0
dear vjcitn, hello, I have upgraded the package. Then I found the following error message.
I cannot download the 2023 version data in the tutorial. The 2022 version is ok, I can download and save the cache. But the second import failed again.
How can I resolve this error？