Cannot lock file
Closed this issue · 2 comments
ZheFrench commented
Initially from biomart ` ensembl <- useEnsembl(biomart = "ensembl") but due to biocfileCache ?
biomartCacheInfo() give the same error.
`
I deleted /home/villemin/.cache/biomaRt. No sucess
Error in lock(.sql_lock_path(dbfile), exclusive = FALSE) :
Cannot lock file: '/home/villemin/.cache/biomaRt/BiocFileCache.sqlite.LOCK': Aucun verrou disponible
Appels : biomartCacheInfo ... tryCatch -> tryCatchList -> .sql_connect_RW -> lock
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'conn' in selecting a method for function 'dbDisconnect': object 'info' not found
Calls: <Anonymous> ... .sql_disconnect -> dbDisconnect -> .handleSimpleError -> h
Execution halted
R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS
Matrix products: default
BLAS/LAPACK: /data/USERS/villemin/anaconda3/envs/r4.1.3/lib/libopenblasp-r0.3.20.so
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=fr_FR.UTF-8
[9] LC_ADDRESS=fr_FR.UTF-8 LC_TELEPHONE=fr_FR.UTF-8
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=fr_FR.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BulkSignalR_0.0.9 BiocFileCache_2.2.1 dbplyr_2.1.1
[4] stringi_1.7.6 rjson_0.2.21 biomaRt_2.50.3
[7] ggrepel_0.9.1 ggridges_0.5.3 viridis_0.6.2
[10] viridisLite_0.4.0 stringr_1.4.0 doParallel_1.0.17
[13] iterators_1.0.14 foreach_1.5.2 paxtoolsr_1.28.0
[16] XML_3.99-0.9 rJava_1.0-6 tidyr_1.2.0
[19] dplyr_1.0.8 ggplot2_3.3.5 igraph_1.3.0
[22] devtools_2.4.3 usethis_2.1.5 data.table_1.14.2
[25] glue_1.6.2
loaded via a namespace (and not attached):
[1] matrixStats_0.61.0 bitops_1.0-7 fs_1.5.2
[4] bit64_4.0.5 RColorBrewer_1.1-3 filelock_1.0.2
[7] progress_1.2.2 httr_1.4.2 rprojroot_2.0.3
[10] GenomeInfoDb_1.30.1 tools_4.1.3 utf8_1.2.2
[13] R6_2.5.1 DBI_1.1.2 BiocGenerics_0.40.0
[16] colorspace_2.0-3 GetoptLong_1.0.5 withr_2.5.0
[19] tidyselect_1.1.2 gridExtra_2.3 prettyunits_1.1.1
[22] processx_3.5.3 curl_4.3.2 bit_4.0.4
[25] compiler_4.1.3 cli_3.2.0 Biobase_2.54.0
[28] xml2_1.3.3 desc_1.4.1 scales_1.1.1
[31] readr_2.1.2 callr_3.7.0 rappdirs_0.3.3
[34] digest_0.6.29 R.utils_2.11.0 XVector_0.34.0
[37] pkgconfig_2.0.3 sessioninfo_1.2.2 fastmap_1.1.0
[40] GlobalOptions_0.1.2 rlang_1.0.2 RSQLite_2.2.12
[43] shape_1.4.6 generics_0.1.2 jsonlite_1.8.0
[46] R.oo_1.24.0 RCurl_1.98-1.6 magrittr_2.0.3
[49] GenomeInfoDbData_1.2.7 Rcpp_1.0.8.3 munsell_0.5.0
[52] S4Vectors_0.32.4 fansi_1.0.3 lifecycle_1.0.1
[55] R.methodsS3_1.8.1 zlibbioc_1.40.0 brio_1.1.3
[58] pkgbuild_1.3.1 plyr_1.8.7 grid_4.1.3
[61] blob_1.2.3 crayon_1.5.1 Biostrings_2.62.0
[64] circlize_0.4.14 hms_1.1.1 KEGGREST_1.34.0
[67] ComplexHeatmap_2.10.0 ps_1.6.0 pillar_1.7.0
[70] codetools_0.2-18 stats4_4.1.3 pkgload_1.2.4
[73] remotes_2.4.2 vctrs_0.4.0 png_0.1-7
[76] tzdb_0.3.0 testthat_3.1.3 gtable_0.3.0
[79] purrr_0.3.4 clue_0.3-60 assertthat_0.2.1
[82] cachem_1.0.6 tibble_3.1.6 AnnotationDbi_1.56.2
[85] memoise_2.0.1 IRanges_2.28.0 cluster_2.1.3
[88] ellipsis_0.3.2
lshep commented
https://support.bioconductor.org/p/9143445/
This was posted in multiple places -- did this get resolved by moving the cache location?
ZheFrench commented
Yes i was resolved by moving the cache location. Thanks.