Open ZheFrench opened 2 years ago
Happening again on 4.1.3. Was working well until now... Any idea would be more thant welcome.
`ensembl <- useEnsembl(biomart = "ensembl")`
or biomartCacheInfo()
Error in lock(.sql_lock_path(dbfile), exclusive = FALSE) :
Cannot lock file: '/home/villemin/.cache/biomaRt/BiocFileCache.sqlite.LOCK': Aucun verrou disponible
Appels : findOrthologs ... 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
Here is not working : sessionInfo()
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=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=Cattached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
Here from windows, it's working for same version of R.
R version 4.1.3 (2022-03-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 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 LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=Cattached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] biomaRt_2.48.3
loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 prettyunits_1.1.1 png_0.1-7 ps_1.6.0 Biostrings_2.60.2 utf8_1.2.2 assertthat_0.2.1
[8] rprojroot_2.0.3 digest_0.6.29 foreach_1.5.2 BiocFileCache_2.0.0 R6_2.5.1 GenomeInfoDb_1.28.4 stats4_4.1.3
[15] RSQLite_2.2.12 pillar_1.7.0 httr_1.4.2 zlibbioc_1.38.0 rlang_1.0.2 progress_1.2.2 curl_4.3.2
[22] rstudioapi_0.13 callr_3.7.0 blob_1.2.3 S4Vectors_0.30.2 desc_1.4.1 devtools_2.4.3 stringr_1.4.0
[29] RCurl_1.98-1.6 bit_4.0.4 tinytex_0.38 compiler_4.1.3 xfun_0.30 pkgconfig_2.0.3 BiocGenerics_0.38.0
[36] pkgbuild_1.3.1 tidyselect_1.1.2 KEGGREST_1.32.0 tibble_3.1.6 GenomeInfoDbData_1.2.6 IRanges_2.26.0 codetools_0.2-18
[43] XML_3.99-0.9 fansi_1.0.3 dplyr_1.0.8 dbplyr_2.1.1 crayon_1.5.1 withr_2.5.0 rappdirs_0.3.3
[50] bitops_1.0-7 brio_1.1.3 lifecycle_1.0.1 DBI_1.1.2 magrittr_2.0.3 cli_3.2.0 stringi_1.7.6
[57] cachem_1.0.6 XVector_0.32.0 fs_1.5.2 remotes_2.4.2 testthat_3.1.3 xml2_1.3.3 filelock_1.0.2
[64] generics_0.1.2 ellipsis_0.3.2 vctrs_0.4.1 iterators_1.0.14 tools_4.1.3 bit64_4.0.5 Biobase_2.52.0
[71] glue_1.6.2 purrr_0.3.4 hms_1.1.1 processx_3.5.3 pkgload_1.2.4 parallel_4.1.3 fastmap_1.1.0
[78] AnnotationDbi_1.54.1 sessioninfo_1.2.2 memoise_2.0.1 usethis_2.1.5
https://support.bioconductor.org/p/9143445/ This was posted in multiple places -- did this get resolved by moving the cache location?
I removed the directory and reinstall biomartR several times. Didn't work. Any idea would be more than welcome.
By the way, It works with this environment.