`get_ctd`:`Error in gzfile(file) : invalid 'description' argument`
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bschilder commented
1. Bug description
Error when downloading multiple CTDs.
Console output
Warning in if (!file.exists(tmp)) { :
the condition has length > 1 and only the first element will be used
ℹ Downloading "ctd_AIBS.rda"...
|=======================================================================================| 100%
ℹ Downloading "ctd_allKI.rda"...
|=======================================================================================| 100%
ℹ Downloading "ctd_BlueLake2018_FrontalCortexOnly.rda"...
|=======================================================================================| 100%
ℹ Downloading "ctd_BlueLake2018_VisualCortexOnly.rda"...
|=======================================================================================| 100%
ℹ Downloading "ctd_DivSeq.rda"...
|=======================================================================================| 100%
ℹ Downloading "ctd_DRONC_human.rda"...
|=======================================================================================| 100%
ℹ Downloading "ctd_DRONC_mouse.rda"...
|=======================================================================================| 100%
ℹ Downloading "ctd_Saunders.rda"...
|=======================================================================================| 100%
ℹ Downloading "ctd_Tasic.rda"...
|=======================================================================================| 100%
Error in gzfile(file) : invalid 'description' argument
Expected behaviour
Returns a list of CTDs.
2. Reproducible example
Code
ctd_magma <- MAGMA.Celltyping::get_ctd()
3. Session info
R Under development (unstable) (2022-02-25 r81808)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] ica_1.0-3 class_7.3-20 ps_1.7.1
[4] Rsamtools_2.13.3 foreach_1.5.2 lmtest_0.9-40
[7] rprojroot_2.0.3 crayon_1.5.1 spatstat.core_2.4-4
[10] MASS_7.3-58 rhdf5filters_1.9.0 nlme_3.1-158
[13] backports_1.4.1 basilisk_1.9.2 rlang_1.0.4
[16] XVector_0.37.0 ROCR_1.0-11 readxl_1.4.0
[19] irlba_2.3.5 nloptr_2.0.3 callr_3.7.1
[22] limma_3.53.4 filelock_1.0.2 BiocParallel_1.31.10
[25] rjson_0.2.21 bit64_4.0.5 scKirby_0.1.0
[28] glue_1.6.2 sctransform_0.3.3 parallel_4.2.0
[31] processx_3.7.0 spatstat.sparse_2.1-1 AnnotationDbi_1.59.1
[34] BiocGenerics_0.43.0 HGNChelper_0.8.1 spatstat.geom_2.4-0
[37] tidyselect_1.1.2 SummarizedExperiment_1.27.1 usethis_2.1.6
[40] SeuratObject_4.1.0 fitdistrplus_1.1-8 XML_3.99-0.10
[43] tidyr_1.2.0 zoo_1.8-10 ggpubr_0.4.0
[46] GenomicAlignments_1.33.0 ontologyIndex_2.7 xtable_1.8-4
[49] magrittr_2.0.3 evaluate_0.15 ggplot2_3.3.6
[52] cli_3.3.0 zlibbioc_1.43.0 rstudioapi_0.13
[55] miniUI_0.1.1.1 sp_1.5-0 rpart_4.1.16
[58] fastmatch_1.1-3 treeio_1.21.0 maps_3.4.0
[61] shiny_1.7.2 xfun_0.31 clue_0.3-61
[64] pkgbuild_1.3.1 cluster_2.1.3 caTools_1.18.2
[67] echoconda_0.99.6 TSP_1.2-1 GeneOverlap_1.33.0
[70] KEGGREST_1.37.3 clusterGeneration_1.3.7 tibble_3.1.8
[73] interactiveDisplayBase_1.35.0 expm_0.999-6 ggrepel_0.9.1
[76] ape_5.6-2 listenv_0.8.0 dendextend_1.16.0
[79] Biostrings_2.65.1 png_0.1-7 future_1.27.0
[82] bitops_1.0-7 plyr_1.8.7 cellranger_1.1.0
[85] e1071_1.7-11 coda_0.19-4 pillar_1.8.0
[88] gplots_3.1.3 GlobalOptions_0.1.2 cachem_1.0.6
[91] GenomicFeatures_1.49.5 fs_1.5.2 googleAuthR_2.0.0
[94] scatterplot3d_0.3-41 GetoptLong_1.0.5 vctrs_0.4.1
[97] ellipsis_0.3.2 generics_0.1.3 gh_1.3.0
[100] devtools_2.4.4 tools_4.2.0 munsell_0.5.0
[103] proxy_0.4-27 DelayedArray_0.23.0 fastmap_1.1.0
[106] compiler_4.2.0 pkgload_1.3.0 abind_1.4-5
[109] httpuv_1.6.5 rtracklayer_1.57.0 ExperimentHub_2.5.0
[112] sessioninfo_1.2.2 ewceData_1.5.0 DescTools_0.99.45
[115] plotly_4.10.0 rgeos_0.5-9 GenomeInfoDbData_1.2.8
[118] gridExtra_2.3 lattice_0.20-45 dir.expiry_1.5.0
[121] deldir_1.0-6 gitcreds_0.1.1 sceasy_0.0.6
[124] utf8_1.2.2 later_1.3.0 dplyr_1.0.9
[127] BiocFileCache_2.5.0 jsonlite_1.8.0 scales_1.2.0
[130] gld_2.6.5 tidytree_0.3.9 pbapply_1.5-0
[133] carData_3.0-5 lazyeval_0.2.2 promises_1.2.0.1
[136] doParallel_1.0.17 car_3.1-0 R.utils_2.12.0
[139] goftest_1.2-3 spatstat.utils_2.3-1 reticulate_1.25
[142] rmarkdown_2.14 cowplot_1.1.1 webshot_0.5.3
[145] Rtsne_0.16 dichromat_2.0-0.1 BSgenome_1.65.2
[148] Biobase_2.57.1 uwot_0.1.11 igraph_1.3.4
[151] HDF5Array_1.25.1 survival_3.3-1 numDeriv_2016.8-1.1
[154] yaml_2.3.5 plotrix_3.8-2 htmltools_0.5.3
[157] memoise_2.0.1 VariantAnnotation_1.43.2 profvis_0.3.7
[160] BiocIO_1.7.1 Seurat_4.1.1 seriation_1.3.6
[163] IRanges_2.31.0 quadprog_1.5-8 here_1.0.1
[166] viridisLite_0.4.0 digest_0.6.29 assertthat_0.2.1
[169] piggyback_0.1.4 mime_0.12 rappdirs_0.3.3
[172] registry_0.5-1 downloadR_0.99.3 pals_1.7
[175] RSQLite_2.2.15 yulab.utils_0.0.5 future.apply_1.9.0
[178] Exact_3.1 mapproj_1.2.8 remotes_2.4.2
[181] orthogene_1.3.1 data.table_1.14.2 urlchecker_1.0.1
[184] blob_1.2.3 S4Vectors_0.35.1 R.oo_1.25.0
[187] splines_4.2.0 Rhdf5lib_1.19.2 AnnotationHub_3.5.0
[190] RCurl_1.98-1.7 broom_1.0.0 hms_1.1.1
[193] gprofiler2_0.2.1 rhdf5_2.41.1 colorspace_2.0-3
[196] BiocManager_1.30.18 mnormt_2.1.0 shape_1.4.6
[199] GenomicRanges_1.49.0 aplot_0.1.6 GEOquery_2.65.2
[202] Rcpp_1.0.9 RANN_2.6.1 mvtnorm_1.1-3
[205] circlize_0.4.15 fansi_1.0.3 tzdb_0.3.0
[208] parallelly_1.32.1 R6_2.5.1 grid_4.2.0
[211] ggridges_0.5.3 lifecycle_1.0.1 phytools_1.0-3
[214] rootSolve_1.8.2.3 MungeSumstats_1.5.5 curl_4.3.2
[217] ggsignif_0.6.3 gdata_2.18.0.1 minqa_1.2.4
[220] leiden_0.4.2 phangorn_2.9.0 Matrix_1.4-1
[223] RcppAnnoy_0.0.19 RColorBrewer_1.1-3 iterators_1.0.14
[226] stringr_1.4.0 htmlwidgets_1.5.4 polyclip_1.10-0
[229] biomaRt_2.53.2 purrr_0.3.4 gridGraphics_0.5-1
[232] MAGMA.Celltyping_2.0.4 ComplexHeatmap_2.13.0 mgcv_1.8-40
[235] globals_0.15.1 lmom_2.9 patchwork_1.1.1
[238] spatstat.random_2.2-0 progressr_0.10.1 lubridate_1.8.0
[241] codetools_0.2-18 matrixStats_0.62.0 gtools_3.9.3
[244] EWCE_1.5.4 prettyunits_1.1.1 SingleCellExperiment_1.19.0
[247] dbplyr_2.2.1 basilisk.utils_1.9.1 R.methodsS3_1.8.2
[250] GenomeInfoDb_1.33.3 gtable_0.3.0 DBI_1.1.3
[253] stats4_4.2.0 ggfun_0.0.6 tensor_1.5
[256] httr_1.4.3 KernSmooth_2.23-20 stringi_1.7.8
[259] anndata_0.7.5.3 progress_1.2.2 reshape2_1.4.4
[262] heatmaply_1.3.0 viridis_0.6.2 ggtree_3.5.1
[265] xml2_1.3.3 combinat_0.0-8 ggdendro_0.1.23
[268] boot_1.3-28 lme4_1.1-30 restfulr_0.0.15
[271] RNOmni_1.0.0 readr_2.1.2 ggplotify_0.1.0
[274] homologene_1.4.68.19.3.27 scattermore_0.8 BiocVersion_3.16.0
[277] bit_4.0.4 MatrixGenerics_1.9.1 spatstat.data_2.2-0
[280] pkgconfig_2.0.3 babelgene_22.3 gargle_1.2.0
[283] corrplot_0.92 rstatix_0.7.0 knitr_1.39