{"action":"created","issue":{"url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/12","labels_url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/12/labels{/name}","comments_url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/12/comments","events_url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/12/events","html_url":"https://github.com/lgatto/ProteomicsAnnotationHubData/issues/12","id":102484909,"number":12,"title":"Error in makeAnnotationHubMetadataFunction","user":{"login":"lgatto","id":384198,"avatar_url":"https://avatars.githubusercontent.com/u/384198?v=3","gravatar_id":"","url":"https://api.github.com/users/lgatto","html_url":"https://github.com/lgatto","followers_url":"https://api.github.com/users/lgatto/followers","following_url":"https://api.github.com/users/lgatto/following{/other_user}","gists_url":"https://api.github.com/users/lgatto/gists{/gist_id}","starred_url":"https://api.github.com/users/lgatto/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lgatto/subscriptions","organizations_url":"https://api.github.com/users/lgatto/orgs","repos_url":"https://api.github.com/users/lgatto/repos","events_url":"https://api.github.com/users/lgatto/events{/privacy}","received_events_url":"https://api.github.com/users/lgatto/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-08-22T00:24:23Z","updated_at":"2015-08-24T22:28:37Z","closed_at":null,"body":"Yesterday, building and checking was successful. I must have updated a package a dependency, as I don't remember having changed anything, but now I get\r\n\r\n```\r\n -> % R-3.2 CMD build ProteomicsAnnotationHubData\r\n* checking for file ‘ProteomicsAnnotationHubData/DESCRIPTION’ ... OK\r\n* preparing ‘ProteomicsAnnotationHubData’:\r\n* checking DESCRIPTION meta-information ... OK\r\n* installing the package to build vignettes\r\n      -----------------------------------\r\n* installing *source* package ‘ProteomicsAnnotationHubData’ ...\r\n** R\r\n** inst\r\n** preparing package for lazy loading\r\nNote: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.\r\nerwinia_carotovora.fasta\r\nF063721.dat-mztab.txt\r\nPXD000001\r\nTMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML\r\nINFO [2015-08-22 01:18:57] Preparer Class: PXD000001FastaToAAStringSetPreparer\r\nError in makeAnnotationHubMetadataFunction(currentMetadata, justRunUnitTest = justRunUnitTest,  : \r\n  unused argument (BiocVersion)\r\nError : unable to load R code in package ‘ProteomicsAnnotationHubData’\r\nERROR: lazy loading failed for package ‘ProteomicsAnnotationHubData’\r\n* removing ‘/tmp/RtmpA1tuwQ/Rinst57b42a4453e3/ProteomicsAnnotationHubData’\r\n      -----------------------------------\r\nERROR: package installation failed\r\n```\r\nSession info:\r\n```r\r\nR version 3.2.1 Patched (2015-07-01 r68620)\r\nPlatform: x86_64-unknown-linux-gnu (64-bit)\r\nRunning under: Ubuntu 14.04.3 LTS\r\n\r\nlocale:\r\n [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              \r\n [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    \r\n [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   \r\n [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 \r\n [9] LC_ADDRESS=C               LC_TELEPHONE=C            \r\n[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       \r\n\r\nattached base packages:\r\n[1] parallel  stats4    stats     graphics  grDevices utils     datasets \r\n[8] methods   base     \r\n\r\nother attached packages:\r\n[1] AnnotationHubData_0.0.239 futile.logger_1.4.1      \r\n[3] GenomicRanges_1.21.18     GenomeInfoDb_1.5.13      \r\n[5] IRanges_2.3.18            S4Vectors_0.7.13         \r\n[7] BiocGenerics_0.15.6       AnnotationHub_2.1.39     \r\n\r\nloaded via a namespace (and not attached):\r\n [1] Rcpp_0.12.0                  plyr_1.8.3                  \r\n [3] BiocInstaller_1.19.11        XVector_0.9.2               \r\n [5] GenomicFeatures_1.21.18      bitops_1.0-6                \r\n [7] futile.options_1.0.0         tools_3.2.1                 \r\n [9] zlibbioc_1.15.0              biomaRt_2.25.1              \r\n[11] digest_0.6.8                 jsonlite_0.9.16             \r\n[13] RSQLite_1.0.0                graph_1.47.2                \r\n[15] OrganismDbi_1.11.42          GEOquery_2.35.5             \r\n[17] shiny_0.12.2                 DBI_0.3.1                   \r\n[19] rBiopaxParser_2.7.0          rtracklayer_1.29.18         \r\n[21] httr_1.0.0                   stringr_1.0.0               \r\n[23] Biostrings_2.37.6            data.table_1.9.4            \r\n[25] Biobase_2.29.1               R6_2.1.1                    \r\n[27] AnnotationDbi_1.31.17        RBGL_1.45.1                 \r\n[29] XML_3.98-1.3                 BiocParallel_1.3.50         \r\n[31] reshape2_1.4.1               lambda.r_1.1.7              \r\n[33] magrittr_1.5                 Rsamtools_1.21.15           \r\n[35] htmltools_0.2.6              GenomicAlignments_1.5.12    \r\n[37] SummarizedExperiment_0.3.3   AnnotationForge_1.11.17     \r\n[39] mime_0.3                     interactiveDisplayBase_1.7.1\r\n[41] xtable_1.7-4                 httpuv_1.3.3                \r\n[43] stringi_0.5-5                RCurl_1.95-4.7              \r\n[45] chron_2.3-47                \r\n```\r\n\r\nNote that `AnnotationHub` and `AnnotationHubData` are build from svn, at revision 107679.\r\n\r\n@sonali-bioc any idea?\r\n"},"comment":{"url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/comments/134399836","html_url":"https://github.com/lgatto/ProteomicsAnnotationHubData/issues/12#issuecomment-134399836","issue_url":"https://api.github.com/repos/lgatto/ProteomicsAnnotationHubData/issues/12","id":134399836,"user":{"login":"lgatto","id":384198,"avatar_url":"https://avatars.githubusercontent.com/u/384198?v=3","gravatar_id":"","url":"https://api.github.com/users/lgatto","html_url":"https://github.com/lgatto","followers_url":"https://api.github.com/users/lgatto/followers","following_url":"https://api.github.com/users/lgatto/following{/other_user}","gists_url":"https://api.github.com/users/lgatto/gists{/gist_id}","starred_url":"https://api.github.com/users/lgatto/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lgatto/subscriptions","organizations_url":"https://api.github.com/users/lgatto/orgs","repos_url":"https://api.github.com/users/lgatto/repos","events_url":"https://api.github.com/users/lgatto/events{/privacy}","received_events_url":"https://api.github.com/users/lgatto/received_events","type":"User","site_admin":false},"created_at":"2015-08-24T22:28:37Z","updated_at":"2015-08-24T22:28:37Z","body":"Thanks!"}}