{"action":"created","issue":{"url":"https://api.github.com/repos/Bioconductor/BiocManager/issues/4","repository_url":"https://api.github.com/repos/Bioconductor/BiocManager","labels_url":"https://api.github.com/repos/Bioconductor/BiocManager/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/Bioconductor/BiocManager/issues/4/comments","events_url":"https://api.github.com/repos/Bioconductor/BiocManager/issues/4/events","html_url":"https://github.com/Bioconductor/BiocManager/issues/4","id":331982886,"node_id":"MDU6SXNzdWUzMzE5ODI4ODY=","number":4,"title":"BiocManager::valid() not working within reprex::reprex()","user":{"login":"PeteHaitch","id":1049741,"node_id":"MDQ6VXNlcjEwNDk3NDE=","avatar_url":"https://avatars0.githubusercontent.com/u/1049741?v=4","gravatar_id":"","url":"https://api.github.com/users/PeteHaitch","html_url":"https://github.com/PeteHaitch","followers_url":"https://api.github.com/users/PeteHaitch/followers","following_url":"https://api.github.com/users/PeteHaitch/following{/other_user}","gists_url":"https://api.github.com/users/PeteHaitch/gists{/gist_id}","starred_url":"https://api.github.com/users/PeteHaitch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PeteHaitch/subscriptions","organizations_url":"https://api.github.com/users/PeteHaitch/orgs","repos_url":"https://api.github.com/users/PeteHaitch/repos","events_url":"https://api.github.com/users/PeteHaitch/events{/privacy}","received_events_url":"https://api.github.com/users/PeteHaitch/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-06-13T12:57:08Z","updated_at":"2018-07-09T21:44:41Z","closed_at":null,"author_association":"NONE","body":"Running from a new R session:\r\n\r\n```R\r\n> BiocManager::valid()\r\n\r\n* sessionInfo()\r\n\r\nR version 3.5.0 (2018-04-23)\r\nPlatform: x86_64-apple-darwin15.6.0 (64-bit)\r\nRunning under: macOS Sierra 10.12.6\r\n\r\nMatrix products: default\r\nBLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib\r\nLAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib\r\n\r\nlocale:\r\n[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8\r\n\r\nattached base packages:\r\n[1] stats     graphics  grDevices utils     datasets  methods  \r\n[7] base     \r\n\r\nother attached packages:\r\n[1] repete_0.0.0.9011 devtools_1.13.5  \r\n\r\nloaded via a namespace (and not attached):\r\n [1] Rcpp_0.12.17           lobstr_0.0.0.9000     \r\n [3] XVector_0.21.2         magrittr_1.5          \r\n [5] GenomicRanges_1.33.6   BiocGenerics_0.27.0   \r\n [7] zlibbioc_1.27.0        IRanges_2.15.14       \r\n [9] munsell_0.5.0          colorspace_1.3-2      \r\n[11] rlang_0.2.1            stringr_1.3.1         \r\n[13] GenomeInfoDb_1.17.1    plyr_1.8.4            \r\n[15] tools_3.5.0            parallel_3.5.0        \r\n[17] withr_2.1.2            fortunes_1.5-4        \r\n[19] yaml_2.1.19            digest_0.6.15         \r\n[21] GenomeInfoDbData_1.1.0 BiocManager_1.29.45   \r\n[23] pryr_0.1.4             S4Vectors_0.19.12     \r\n[25] bitops_1.0-6           codetools_0.2-15      \r\n[27] RCurl_1.95-4.10        memoise_1.1.0         \r\n[29] stringi_1.2.3          compiler_3.5.0        \r\n[31] scales_0.5.0           stats4_3.5.0          \r\n\r\nBioconductor version '3.8'\r\n\r\n  * 0 packages out-of-date\r\n  * 2 packages too new\r\n\r\ncreate a valid installation with\r\n\r\n  BiocManager::install(c(\r\n    \"hms\", \"reprex\"\r\n  ), update = TRUE, ask = FALSE)\r\n\r\nWarning message:\r\n0 packages out-of-date; 2 packages too new \r\n```\r\n\r\nRunning as `reprex::reprex(x = BiocManager::valid())`:\r\n\r\n``` r\r\nBiocManager::valid()\r\n#> Error in repos[[\"CRAN\"]]: subscript out of bounds\r\n```\r\n\r\nCreated on 2018-06-13 by the [reprex package](http://reprex.tidyverse.org) (v0.2.0).\r\n\r\nAny ideas? The combo of `reprex::reprex()` and `BiocManager::valid()` will be valuable when asking for minimal bug reports."},"comment":{"url":"https://api.github.com/repos/Bioconductor/BiocManager/issues/comments/403630328","html_url":"https://github.com/Bioconductor/BiocManager/issues/4#issuecomment-403630328","issue_url":"https://api.github.com/repos/Bioconductor/BiocManager/issues/4","id":403630328,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMzYzMDMyOA==","user":{"login":"jennybc","id":599454,"node_id":"MDQ6VXNlcjU5OTQ1NA==","avatar_url":"https://avatars3.githubusercontent.com/u/599454?v=4","gravatar_id":"","url":"https://api.github.com/users/jennybc","html_url":"https://github.com/jennybc","followers_url":"https://api.github.com/users/jennybc/followers","following_url":"https://api.github.com/users/jennybc/following{/other_user}","gists_url":"https://api.github.com/users/jennybc/gists{/gist_id}","starred_url":"https://api.github.com/users/jennybc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jennybc/subscriptions","organizations_url":"https://api.github.com/users/jennybc/orgs","repos_url":"https://api.github.com/users/jennybc/repos","events_url":"https://api.github.com/users/jennybc/events{/privacy}","received_events_url":"https://api.github.com/users/jennybc/received_events","type":"User","site_admin":false},"created_at":"2018-07-09T21:44:41Z","updated_at":"2018-07-09T21:44:41Z","author_association":"NONE","body":"Maybe the names are being lost here:\r\n\r\nhttps://github.com/cran/callr/blob/d591dfee954a3a87cdf690c5e4953c4782ec17cb/R/check.R#L27\r\n\r\nSmall demo:\r\n\r\n``` r\r\n(x <- c(getOption(\"repos\"), c(CRAN = \"whatever\")))\r\n#>                                                             \r\n#>    \"https://cran.rstudio.org\" \"https://cloud.r-project.org\" \r\n#>                          CRAN \r\n#>                    \"whatever\"\r\nas.character(x)\r\n#> [1] \"https://cran.rstudio.org\"    \"https://cloud.r-project.org\"\r\n#> [3] \"whatever\"\r\n```\r\n\r\nCreated on 2018-07-10 by the [reprex package](http://reprex.tidyverse.org) (v0.2.0.9000)."}}
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