{"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":25,"created_at":"2014-11-18T13:24:28Z","updated_at":"2015-02-04T23:57:26Z","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/72966840","html_url":"https://github.com/tudo-r/BatchJobs/issues/58#issuecomment-72966840","issue_url":"https://api.github.com/repos/tudo-r/BatchJobs/issues/58","id":72966840,"user":{"login":"berndbischl","id":1225974,"avatar_url":"https://avatars.githubusercontent.com/u/1225974?v=3","gravatar_id":"","url":"https://api.github.com/users/berndbischl","html_url":"https://github.com/berndbischl","followers_url":"https://api.github.com/users/berndbischl/followers","following_url":"https://api.github.com/users/berndbischl/following{/other_user}","gists_url":"https://api.github.com/users/berndbischl/gists{/gist_id}","starred_url":"https://api.github.com/users/berndbischl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/berndbischl/subscriptions","organizations_url":"https://api.github.com/users/berndbischl/orgs","repos_url":"https://api.github.com/users/berndbischl/repos","events_url":"https://api.github.com/users/berndbischl/events{/privacy}","received_events_url":"https://api.github.com/users/berndbischl/received_events","type":"User","site_admin":false},"created_at":"2015-02-04T23:57:26Z","updated_at":"2015-02-04T23:57:26Z","body":"Ah, i am going to bed, I am only writing idiotic stuff.\r\n\r\n EC2 is definitely useful.\r\n\r\n1) If you reproduce the bug on EC2 we can create our own account, copy your example and debug it\r\n\r\n2) An EC2 demo, how to use BJ with it, should be written anyway.\r\n\r\n(I used BJ on Azure a couple of weeks ago, but that was so simple i did not even think about writing it up. Maybe I still should have)"}}