{"action":"created","issue":{"url":"https://api.github.com/repos/nicholasjcooper/plumbCNV/issues/3","repository_url":"https://api.github.com/repos/nicholasjcooper/plumbCNV","labels_url":"https://api.github.com/repos/nicholasjcooper/plumbCNV/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/nicholasjcooper/plumbCNV/issues/3/comments","events_url":"https://api.github.com/repos/nicholasjcooper/plumbCNV/issues/3/events","html_url":"https://github.com/nicholasjcooper/plumbCNV/issues/3","id":390798400,"node_id":"MDU6SXNzdWUzOTA3OTg0MDA=","number":3,"title":"unable to find an inherited method for function ‘universe<-’ for signature ‘\"CompressedIRangesList\"’","user":{"login":"rdauria","id":10660664,"node_id":"MDQ6VXNlcjEwNjYwNjY0","avatar_url":"https://avatars1.githubusercontent.com/u/10660664?v=4","gravatar_id":"","url":"https://api.github.com/users/rdauria","html_url":"https://github.com/rdauria","followers_url":"https://api.github.com/users/rdauria/followers","following_url":"https://api.github.com/users/rdauria/following{/other_user}","gists_url":"https://api.github.com/users/rdauria/gists{/gist_id}","starred_url":"https://api.github.com/users/rdauria/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rdauria/subscriptions","organizations_url":"https://api.github.com/users/rdauria/orgs","repos_url":"https://api.github.com/users/rdauria/repos","events_url":"https://api.github.com/users/rdauria/events{/privacy}","received_events_url":"https://api.github.com/users/rdauria/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-12-13T18:12:05Z","updated_at":"2018-12-13T18:48:07Z","closed_at":null,"author_association":"NONE","body":"Hello, \r\n\r\nI have installed the dependencies for your plumbCNV pipeline but some packages are more recent than what you had available when last pushing an update to your code. It is possible that the error I get is connected with the newer version of humarray (but I was not able to install the version you provided).\r\n\r\nWhen running the run_example.R I get:\r\n\r\n`Retrieving Plate/Well information from lookup table:\r\n taking id, plate from columns: id, plate \r\n file preview:\r\n  V1             V2        V3\r\n1  1 chr1_171422483 171422483\r\n2 11 chr11_76048775  76048775\r\n3 11 chr11_76048907  76048907\r\n4 11 chr11_76049066  76049066\r\n\r\nError in (function (classes, fdef, mtable)  : \r\n  unable to find an inherited method for function ‘universe<-’ for signature ‘\"CompressedIRangesList\"’\r\nIn addition: There were 15 warnings (use warnings() to see them)\r\n`\r\n\r\nCould you please give suggestions?\r\n\r\nPlease find below the output of sessionInfo() on my R prompt.\r\n\r\nThanks in advance!\r\n\r\nRD\r\n\r\n`> sessionInfo()\r\nR version 3.5.1 (2018-07-02)\r\nPlatform: x86_64-pc-linux-gnu (64-bit)\r\nRunning under: CentOS release 6.9 (Final)\r\n\r\nMatrix products: default\r\nBLAS: /u/local/apps/R/3.5.1/gcc-4.9.3_MKL-2018/lib64/R/lib/libRblas.so\r\nLAPACK: /u/local/apps/R/3.5.1/gcc-4.9.3_MKL-2018/lib64/R/lib/libRlapack.so\r\n\r\nlocale:\r\n [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              \r\n [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    \r\n [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   \r\n [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 \r\n [9] LC_ADDRESS=C               LC_TELEPHONE=C            \r\n[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       \r\n\r\nattached base packages:\r\n [1] compiler  stats4    parallel  stats     graphics  grDevices utils    \r\n [8] datasets  methods   base     \r\n\r\nother attached packages:\r\n [1] irlba_2.3.2                 genoset_1.38.0             \r\n [3] SummarizedExperiment_1.12.0 DelayedArray_0.8.0         \r\n [5] BiocParallel_1.16.2         matrixStats_0.54.0         \r\n [7] Biobase_2.42.0              lattice_0.20-38            \r\n [9] annotSnpStats_1.1           snpStats_1.32.0            \r\n[11] survival_2.43-3             Matrix_1.2-15              \r\n[13] humarray_1.2                GenomicRanges_1.34.0       \r\n[15] GenomeInfoDb_1.18.1         IRanges_2.16.0             \r\n[17] S4Vectors_0.20.1            BiocGenerics_0.28.0        \r\n[19] bigpca_1.0.3                biganalytics_1.1.14        \r\n[21] biglm_0.9-1                 DBI_1.0.0                  \r\n[23] foreach_1.4.4               bigmemory_4.5.33           \r\n[25] reader_1.0.6                NCmisc_1.1.6               \r\n\r\nloaded via a namespace (and not attached):\r\n [1] progress_1.2.0           splines_3.5.1            rtracklayer_1.42.1      \r\n [4] GenomicFeatures_1.34.1   blob_1.1.1               XML_3.98-1.16           \r\n [7] rlang_0.3.0.1            bit64_0.9-7              GenomeInfoDbData_1.2.0  \r\n[10] stringr_1.3.1            zlibbioc_1.28.0          Biostrings_2.50.1       \r\n[13] codetools_0.2-15         memoise_1.1.0            biomaRt_2.38.0          \r\n[16] BiocInstaller_1.32.1     AnnotationDbi_1.44.0     Rcpp_1.0.0              \r\n[19] XVector_0.22.0           bit_1.1-14               Rsamtools_1.34.0        \r\n[22] hms_0.4.2                digest_0.6.18            stringi_1.2.4           \r\n[25] proftools_0.99-2         grid_3.5.1               tools_3.5.1             \r\n[28] bitops_1.0-6             magrittr_1.5             RCurl_1.95-4.11         \r\n[31] RSQLite_2.1.1            crayon_1.3.4             bigmemory.sri_0.1.3     \r\n[34] pkgconfig_2.0.2          prettyunits_1.0.2        assertthat_0.2.0        \r\n[37] httr_1.4.0               iterators_1.0.10         R6_2.3.0                \r\n[40] GenomicAlignments_1.18.0\r\n`"},"comment":{"url":"https://api.github.com/repos/nicholasjcooper/plumbCNV/issues/comments/447077513","html_url":"https://github.com/nicholasjcooper/plumbCNV/issues/3#issuecomment-447077513","issue_url":"https://api.github.com/repos/nicholasjcooper/plumbCNV/issues/3","id":447077513,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NzA3NzUxMw==","user":{"login":"rdauria","id":10660664,"node_id":"MDQ6VXNlcjEwNjYwNjY0","avatar_url":"https://avatars1.githubusercontent.com/u/10660664?v=4","gravatar_id":"","url":"https://api.github.com/users/rdauria","html_url":"https://github.com/rdauria","followers_url":"https://api.github.com/users/rdauria/followers","following_url":"https://api.github.com/users/rdauria/following{/other_user}","gists_url":"https://api.github.com/users/rdauria/gists{/gist_id}","starred_url":"https://api.github.com/users/rdauria/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rdauria/subscriptions","organizations_url":"https://api.github.com/users/rdauria/orgs","repos_url":"https://api.github.com/users/rdauria/repos","events_url":"https://api.github.com/users/rdauria/events{/privacy}","received_events_url":"https://api.github.com/users/rdauria/received_events","type":"User","site_admin":false},"created_at":"2018-12-13T18:48:07Z","updated_at":"2018-12-13T18:48:07Z","author_association":"NONE","body":"Hello Nick,\r\n\r\nThanks for your prompt reply. I wonder whether, to expedite the process, you would not mind to share the output of your:\r\n\r\nsessionInfo()\r\n\r\nin an R session after your have loaded all the needed packages to run run_example.R?\r\n\r\nThanks,\r\nRD"}}
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