{"action":"created","issue":{"url":"https://api.github.com/repos/tudo-r/BatchJobs/issues/58","labels_url":"https://api.github.com/repos/tudo-r/BatchJobs/issues/58/labels{/name}","comments_url":"https://api.github.com/repos/tudo-r/BatchJobs/issues/58/comments","events_url":"https://api.github.com/repos/tudo-r/BatchJobs/issues/58/events","html_url":"https://github.com/tudo-r/BatchJobs/issues/58","id":49226793,"number":58,"title":"registry sync error -- database is locked","user":{"login":"vjcitn","id":4624066,"avatar_url":"https://avatars.githubusercontent.com/u/4624066?v=3","gravatar_id":"","url":"https://api.github.com/users/vjcitn","html_url":"https://github.com/vjcitn","followers_url":"https://api.github.com/users/vjcitn/followers","following_url":"https://api.github.com/users/vjcitn/following{/other_user}","gists_url":"https://api.github.com/users/vjcitn/gists{/gist_id}","starred_url":"https://api.github.com/users/vjcitn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vjcitn/subscriptions","organizations_url":"https://api.github.com/users/vjcitn/orgs","repos_url":"https://api.github.com/users/vjcitn/repos","events_url":"https://api.github.com/users/vjcitn/events{/privacy}","received_events_url":"https://api.github.com/users/vjcitn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":21,"created_at":"2014-11-18T13:24:28Z","updated_at":"2015-02-04T23:14:16Z","closed_at":null,"body":"never ran into this before ... is there a relevant retry option?  this is occuring in a multicore\r\nsetting \r\n\r\n> fdbp = storeToFDRByProbe( mm, xprobs=c(seq(.025,.975,.025),.99))\r\nError in value[[3L]](cond) : \r\n  Error syncing registry (Error in sqliteSendQuery(con, statement, bind.data): rsqlite_query_send: could not execute1: database is locked\r\n)\r\n\r\n> sessionInfo()\r\nR Under development (unstable) (2014-11-04 r66931)\r\nPlatform: x86_64-unknown-linux-gnu (64-bit)\r\n\r\nlocale:\r\n [1] LC_CTYPE=en_US.ISO8859-1    LC_NUMERIC=C               \r\n [3] LC_TIME=en_US.ISO8859-1     LC_COLLATE=en_US.ISO8859-1 \r\n [5] LC_MONETARY=en_US.ISO8859-1 LC_MESSAGES=C              \r\n [7] LC_PAPER=C                  LC_NAME=C                  \r\n [9] LC_ADDRESS=C                LC_TELEPHONE=C             \r\n[11] LC_MEASUREMENT=C            LC_IDENTIFICATION=C        \r\n\r\nattached base packages:\r\n[1] stats     graphics  grDevices datasets  utils     tools     methods  \r\n[8] base     \r\n\r\nother attached packages:\r\n[1] eqtlStore_0.1.7      BatchJobs_1.5        BBmisc_1.8          \r\n[4] BiocParallel_1.0.0   knitr_1.8            weaver_1.32.0       \r\n[7] codetools_0.2-9      digest_0.6.4         BiocInstaller_1.16.1\r\n\r\nloaded via a namespace (and not attached):\r\n [1] acepack_1.3-3.3          annotate_1.44.0          AnnotationDbi_1.28.1    \r\n [4] base64enc_0.1-2          biglm_0.9-1              Biobase_2.26.0          \r\n [7] BiocGenerics_0.12.1      biomaRt_2.22.0           Biostrings_2.34.0       \r\n[10] biovizBase_1.14.0        bit_1.1-12               bitops_1.0-6            \r\n[13] brew_1.0-6               BSgenome_1.34.0          caTools_1.17.1          \r\n[16] checkmate_1.5.0          chron_2.3-45             cluster_1.15.3          \r\n[19] colorspace_1.2-4         data.table_1.9.4         DBI_0.3.1               \r\n[22] dichromat_2.0-0          evaluate_0.5.5           fail_1.2                \r\n[25] fastmatch_1.0-4          ff_2.2-13                ffbase_0.11.3           \r\n[28] foreach_1.4.2            foreign_0.8-61           formatR_1.0             \r\n[31] Formula_1.1-2            gdata_2.13.3             genefilter_1.48.1       \r\n[34] GenomeInfoDb_1.2.3       GenomicAlignments_1.2.1  GenomicFeatures_1.18.2  \r\n[37] GenomicRanges_1.18.1     GGBase_3.28.0            ggplot2_1.0.0           \r\n[40] GGtools_5.3.9            gplots_2.14.2            grid_3.2.0              \r\n[43] gtable_0.1.2             gtools_3.4.1             Gviz_1.10.2             \r\n[46] hexbin_1.27.0            Hmisc_3.14-5             IRanges_2.0.0           \r\n[49] iterators_1.0.7          KernSmooth_2.23-13       lattice_0.20-29         \r\n[52] latticeExtra_0.6-26      MASS_7.3-35              Matrix_1.1-4            \r\n[55] matrixStats_0.10.3       munsell_0.4.2            nnet_7.3-8              \r\n[58] parallel_3.2.0           plyr_1.8.1               proto_0.3-10            \r\n[61] RColorBrewer_1.0-5       Rcpp_0.11.3              RCurl_1.95-4.3          \r\n[64] reshape2_1.4             R.methodsS3_1.6.1        ROCR_1.0-5              \r\n[67] rpart_4.1-8              Rsamtools_1.18.2         RSQLite_1.0.0           \r\n[70] rtracklayer_1.26.2       S4Vectors_0.4.0          scales_0.2.4            \r\n[73] sendmailR_1.2-1          snpStats_1.16.0          splines_3.2.0           \r\n[76] stats4_3.2.0             stringr_0.6.2            survival_2.37-7         \r\n[79] VariantAnnotation_1.12.4 XML_3.98-1.1             xtable_1.7-4            \r\n[82] XVector_0.6.0            zlibbioc_1.12.0         \r\n"},"comment":{"url":"https://api.github.com/repos/tudo-r/BatchJobs/issues/comments/72960964","html_url":"https://github.com/tudo-r/BatchJobs/issues/58#issuecomment-72960964","issue_url":"https://api.github.com/repos/tudo-r/BatchJobs/issues/58","id":72960964,"user":{"login":"mllg","id":1260920,"avatar_url":"https://avatars.githubusercontent.com/u/1260920?v=3","gravatar_id":"","url":"https://api.github.com/users/mllg","html_url":"https://github.com/mllg","followers_url":"https://api.github.com/users/mllg/followers","following_url":"https://api.github.com/users/mllg/following{/other_user}","gists_url":"https://api.github.com/users/mllg/gists{/gist_id}","starred_url":"https://api.github.com/users/mllg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mllg/subscriptions","organizations_url":"https://api.github.com/users/mllg/orgs","repos_url":"https://api.github.com/users/mllg/repos","events_url":"https://api.github.com/users/mllg/events{/privacy}","received_events_url":"https://api.github.com/users/mllg/received_events","type":"User","site_admin":false},"created_at":"2015-02-04T23:14:16Z","updated_at":"2015-02-04T23:14:16Z","body":"Note that we still access the DB on the nodes in ro mode which should result in a shared lock. This might still have an impact on the master which tries to get a reserved (or exclusive?) lock, but at least should not influence other slave processes.\r\n\r\nAs far as I understand this issue by combining all the reports (thanks guys!), the exception occurs in this scenario:\r\n\r\nslave processes query the DB while the master process tries to writes in either `submitJobs` or `waitForJobs`/`syncRegistry`. IMHO we cannot avoid a lock here, but we really should catch such errors on the master and retry. Lets hope my last commit is working."}}