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grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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Lock error in 4.1.1 not in 4.03 #55

Open ZheFrench opened 2 years ago

ZheFrench commented 2 years ago

I removed the directory and reinstall biomartR several times. Didn't work. Any idea would be more than welcome.

Erreur dans lock(.sql_lock_path(dbfile)) :
Cannot lock file: '/home/villemin/.cache/biomaRt/BiocFileCache.sqlite.LOCK': Aucun verrou disponible
Appels : getBM ... tryCatch -> tryCatchList -> .sql_connect_RW -> lock
Erreur dans h(simpleError(msg, call)) :
erreur d'�valuation de l'argument 'conn' lors de la s�lection d'une m�thode pour la fonction 'dbDisconnect' : objet 'info' introuvable
Appels : getBM ... .sql_disconnect -> dbDisconnect -> .handleSimpleError -> h

R version 4.1.1 (2021-08-10)
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/lib/libopenblasp-r0.3.17.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=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] optparse_1.7.1 plyr_1.8.6 biomaRt_2.48.3
[4] GenomicFeatures_1.44.2 AnnotationDbi_1.54.1 Biobase_2.52.0
[7] GenomicRanges_1.44.0 GenomeInfoDb_1.28.4 IRanges_2.26.0
[10] S4Vectors_0.30.2 BiocGenerics_0.38.0 reshape2_1.4.4
[13] data.table_1.14.2

loaded via a namespace (and not attached):
[1] Rcpp_1.0.8 lattice_0.20-45
[3] prettyunits_1.1.1 png_0.1-7
[5] Rsamtools_2.8.0 Biostrings_2.60.2
[7] assertthat_0.2.1 digest_0.6.29
[9] utf8_1.2.2 BiocFileCache_2.0.0
[11] R6_2.5.1 RSQLite_2.2.9
[13] httr_1.4.2 pillar_1.7.0
[15] zlibbioc_1.38.0 rlang_1.0.1
[17] progress_1.2.2 curl_4.3.2
[19] blob_1.2.2 Matrix_1.4-0
[21] BiocParallel_1.26.2 stringr_1.4.0
[23] RCurl_1.98-1.6 bit_4.0.4
[25] DelayedArray_0.18.0 compiler_4.1.1
[27] rtracklayer_1.52.1 pkgconfig_2.0.3
[29] SummarizedExperiment_1.22.0 tidyselect_1.1.1
[31] KEGGREST_1.32.0 tibble_3.1.6
[33] GenomeInfoDbData_1.2.6 matrixStats_0.61.0
[35] XML_3.99-0.7 fansi_1.0.2
[37] crayon_1.5.0 dplyr_1.0.8
[39] dbplyr_2.1.1 GenomicAlignments_1.28.0
[41] bitops_1.0-7 rappdirs_0.3.3
[43] grid_4.1.1 lifecycle_1.0.1
[45] DBI_1.1.2 magrittr_2.0.2
[47] cli_3.2.0 stringi_1.7.4
[49] cachem_1.0.6 XVector_0.32.0
[51] getopt_1.20.3 xml2_1.3.3
[53] ellipsis_0.3.2 filelock_1.0.2
[55] generics_0.1.2 vctrs_0.3.8
[57] rjson_0.2.21 restfulr_0.0.13
[59] tools_4.1.1 bit64_4.0.5
[61] glue_1.6.1 purrr_0.3.4
[63] MatrixGenerics_1.4.3 hms_1.1.1
[65] fastmap_1.1.0 yaml_2.2.2
[67] memoise_2.0.1 BiocIO_1.2.0

By the way, It works with this environment.

R version 4.0.3 (2020-10-10)
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-base/lib/libopenblasp-r0.3.12.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=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] optparse_1.6.6 plyr_1.8.6 biomaRt_2.46.3
[4] GenomicFeatures_1.42.3 AnnotationDbi_1.52.0 Biobase_2.50.0
[7] GenomicRanges_1.42.0 GenomeInfoDb_1.26.7 IRanges_2.24.1
[10] S4Vectors_0.28.1 BiocGenerics_0.36.0 reshape2_1.4.4
[13] data.table_1.14.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 lattice_0.20-44
[3] prettyunits_1.1.1 Rsamtools_2.6.0
[5] Biostrings_2.58.0 assertthat_0.2.1
[7] utf8_1.2.1 BiocFileCache_1.14.0
[9] R6_2.5.1 RSQLite_2.2.5
[11] httr_1.4.2 pillar_1.7.0
[13] zlibbioc_1.36.0 rlang_1.0.1
[15] progress_1.2.2 curl_4.3
[17] rstudioapi_0.13 blob_1.2.1
[19] Matrix_1.3-4 BiocParallel_1.24.1
[21] stringr_1.4.0 RCurl_1.98-1.3
[23] bit_4.0.4 DelayedArray_0.16.3
[25] compiler_4.0.3 rtracklayer_1.50.0
[27] pkgconfig_2.0.3 askpass_1.1
[29] openssl_1.4.3 tidyselect_1.1.1
[31] SummarizedExperiment_1.20.0 tibble_3.1.6
[33] GenomeInfoDbData_1.2.4 matrixStats_0.58.0
[35] XML_3.99-0.6 fansi_0.4.2
[37] crayon_1.4.1 dplyr_1.0.7
[39] dbplyr_2.1.0 GenomicAlignments_1.26.0
[41] bitops_1.0-6 rappdirs_0.3.3
[43] grid_4.0.3 lifecycle_1.0.1
[45] DBI_1.1.1 magrittr_2.0.2
[47] cli_3.2.0 stringi_1.5.3
[49] cachem_1.0.4 XVector_0.30.0
[51] getopt_1.20.3 xml2_1.3.2
[53] ellipsis_0.3.2 generics_0.1.0
[55] vctrs_0.3.8 tools_4.0.3
[57] bit64_4.0.5 glue_1.6.1
[59] purrr_0.3.4 hms_1.0.0
[61] MatrixGenerics_1.2.1 fastmap_1.1.0
[63] memoise_2.0.0
ZheFrench commented 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
ZheFrench commented 2 years ago

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=C

attached 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=C

attached 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

lshep commented 2 years ago

https://support.bioconductor.org/p/9143445/ This was posted in multiple places -- did this get resolved by moving the cache location?