{"action":"created","issue":{"url":"https://api.github.com/repos/r-lib/conflicted/issues/8","repository_url":"https://api.github.com/repos/r-lib/conflicted","labels_url":"https://api.github.com/repos/r-lib/conflicted/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/r-lib/conflicted/issues/8/comments","events_url":"https://api.github.com/repos/r-lib/conflicted/issues/8/events","html_url":"https://github.com/r-lib/conflicted/issues/8","id":329497726,"node_id":"MDU6SXNzdWUzMjk0OTc3MjY=","number":8,"title":"R session terminates with conflicted and GEOquery (Bioconductor package)","user":{"login":"sraorao","id":12804083,"node_id":"MDQ6VXNlcjEyODA0MDgz","avatar_url":"https://avatars1.githubusercontent.com/u/12804083?v=4","gravatar_id":"","url":"https://api.github.com/users/sraorao","html_url":"https://github.com/sraorao","followers_url":"https://api.github.com/users/sraorao/followers","following_url":"https://api.github.com/users/sraorao/following{/other_user}","gists_url":"https://api.github.com/users/sraorao/gists{/gist_id}","starred_url":"https://api.github.com/users/sraorao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sraorao/subscriptions","organizations_url":"https://api.github.com/users/sraorao/orgs","repos_url":"https://api.github.com/users/sraorao/repos","events_url":"https://api.github.com/users/sraorao/events{/privacy}","received_events_url":"https://api.github.com/users/sraorao/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2018-06-05T15:01:11Z","updated_at":"2018-06-06T01:17:26Z","closed_at":null,"author_association":"NONE","body":"When a function in GEOquery Bioconductor package is run after loading the conflicted package, R session terminates. As I couldn't see any error messages before R terminated in Rstudio, I ran the same lines at the command line. \r\n\r\n```\r\n> library(conflicted)\r\n> library(GEOquery)\r\nLoading required package: Biobase\r\nLoading required package: BiocGenerics\r\nLoading required package: parallel\r\n\r\nAttaching package: ‘BiocGenerics’\r\n\r\nThe following objects are masked from ‘package:parallel’:\r\n\r\n    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\r\n    clusterExport, clusterMap, parApply, parCapply, parLapply,\r\n    parLapplyLB, parRapply, parSapply, parSapplyLB\r\n\r\nThe following objects are masked from ‘package:stats’:\r\n\r\n    IQR, mad, sd, var, xtabs\r\n\r\nThe following objects are masked from ‘package:base’:\r\n\r\n    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,\r\n    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\r\n    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,\r\n    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\r\n    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,\r\n    table, tapply, union, unique, unsplit, which, which.max, which.min\r\n\r\nWelcome to Bioconductor\r\n\r\n    Vignettes contain introductory material; view with\r\n    'browseVignettes()'. To cite Bioconductor, see\r\n    'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\r\n\r\nSetting options('download.file.method.GEOquery'='auto')\r\nSetting options('GEOquery.inmemory.gpl'=FALSE)\r\n> gset <- getGEO(\"GSE39549\", GSEMatrix =TRUE, AnnotGPL=FALSE, destdir = \".\")\r\nterminate called after throwing an instance of 'Rcpp::eval_error'\r\n  what():  Evaluation error: evalq found in 2 packages. You must indicate which one you want with ::\r\n * BiocGenerics::evalq\r\n * base::evalq.\r\nAborted (core dumped)\r\n```\r\nSession info after loading the packages but before running getGEO()\r\n\r\n```\r\n> sessionInfo()\r\nR version 3.4.4 (2018-03-15)\r\nPlatform: x86_64-pc-linux-gnu (64-bit)\r\nRunning under: Ubuntu 16.04.4 LTS\r\n\r\nMatrix products: default\r\nBLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0\r\nLAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0\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  stats     graphics  grDevices utils     datasets  methods  \r\n[8] base     \r\n\r\nother attached packages:\r\n[1] GEOquery_2.46.15    Biobase_2.38.0      BiocGenerics_0.24.0\r\n[4] conflicted_0.1.0   \r\n\r\nloaded via a namespace (and not attached):\r\n [1] Rcpp_0.12.17     tidyr_0.8.1      crayon_1.3.4     dplyr_0.7.5     \r\n [5] assertthat_0.2.0 R6_2.2.2         magrittr_1.5     pillar_1.2.2    \r\n [9] rlang_0.2.0.9001 bindrcpp_0.2.2   limma_3.34.9     xml2_1.2.0      \r\n[13] readr_1.1.1      glue_1.2.0       purrr_0.2.4      hms_0.4.2       \r\n[17] compiler_3.4.4   pkgconfig_2.0.1  tidyselect_0.2.4 bindr_0.1.1     \r\n[21] tibble_1.4.2    \r\n\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/r-lib/conflicted/issues/comments/394909074","html_url":"https://github.com/r-lib/conflicted/issues/8#issuecomment-394909074","issue_url":"https://api.github.com/repos/r-lib/conflicted/issues/8","id":394909074,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NDkwOTA3NA==","user":{"login":"hpages","id":8810451,"node_id":"MDQ6VXNlcjg4MTA0NTE=","avatar_url":"https://avatars1.githubusercontent.com/u/8810451?v=4","gravatar_id":"","url":"https://api.github.com/users/hpages","html_url":"https://github.com/hpages","followers_url":"https://api.github.com/users/hpages/followers","following_url":"https://api.github.com/users/hpages/following{/other_user}","gists_url":"https://api.github.com/users/hpages/gists{/gist_id}","starred_url":"https://api.github.com/users/hpages/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hpages/subscriptions","organizations_url":"https://api.github.com/users/hpages/orgs","repos_url":"https://api.github.com/users/hpages/repos","events_url":"https://api.github.com/users/hpages/events{/privacy}","received_events_url":"https://api.github.com/users/hpages/received_events","type":"User","site_admin":false},"created_at":"2018-06-06T01:17:26Z","updated_at":"2018-06-06T01:17:26Z","author_association":"NONE","body":"When B depends on (or imports) A and B exports a symbol that masks a symbol already exported by A, shouldn't conflicted assume that the masking is intended so not see it as a conflict? Promotion to S4 generic and the replacement of `base::evalq()` with `BiocGenerics::evalq()` are both particular cases of this more general situation."}}
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