{"action":"created","issue":{"url":"https://api.github.com/repos/pkimes/sigclust2/issues/7","repository_url":"https://api.github.com/repos/pkimes/sigclust2","labels_url":"https://api.github.com/repos/pkimes/sigclust2/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/pkimes/sigclust2/issues/7/comments","events_url":"https://api.github.com/repos/pkimes/sigclust2/issues/7/events","html_url":"https://github.com/pkimes/sigclust2/issues/7","id":378504918,"node_id":"MDU6SXNzdWUzNzg1MDQ5MTg=","number":7,"title":"Installation issue","user":{"login":"idc9","id":906398,"node_id":"MDQ6VXNlcjkwNjM5OA==","avatar_url":"https://avatars2.githubusercontent.com/u/906398?v=4","gravatar_id":"","url":"https://api.github.com/users/idc9","html_url":"https://github.com/idc9","followers_url":"https://api.github.com/users/idc9/followers","following_url":"https://api.github.com/users/idc9/following{/other_user}","gists_url":"https://api.github.com/users/idc9/gists{/gist_id}","starred_url":"https://api.github.com/users/idc9/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/idc9/subscriptions","organizations_url":"https://api.github.com/users/idc9/orgs","repos_url":"https://api.github.com/users/idc9/repos","events_url":"https://api.github.com/users/idc9/events{/privacy}","received_events_url":"https://api.github.com/users/idc9/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-11-07T22:55:12Z","updated_at":"2018-11-08T16:58:51Z","closed_at":null,"author_association":"NONE","body":"When I install the package using the provided instructions I encounter an error.\r\n\r\n```R\r\n> devtools::install_github(\"pkimes/sigclust2\")\r\nDownloading GitHub repo pkimes/sigclust2@master\r\nfrom URL https://api.github.com/repos/pkimes/sigclust2/zipball/master\r\nInstalling sigclust2\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/dplyr_0.7.7.tgz'\r\nContent type 'application/x-gzip' length 5198161 bytes (5.0 MB)\r\n==================================================\r\ndownloaded 5.0 MB\r\n\r\nInstalling dplyr\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/glue_1.3.0.tgz'\r\nContent type 'application/x-gzip' length 93367 bytes (91 KB)\r\n==================================================\r\ndownloaded 91 KB\r\n\r\nInstalling glue\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a6a61d1ea/glue'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘glue’ ...\r\n* DONE (glue)\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/pkgconfig_2.0.2.tgz'\r\nContent type 'application/x-gzip' length 15456 bytes (15 KB)\r\n==================================================\r\ndownloaded 15 KB\r\n\r\nInstalling pkgconfig\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a49c2c4c/pkgconfig'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘pkgconfig’ ...\r\n* DONE (pkgconfig)\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/R6_2.3.0.tgz'\r\nContent type 'application/x-gzip' length 34492 bytes (33 KB)\r\n==================================================\r\ndownloaded 33 KB\r\n\r\nInstalling R6\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a3f45b26/R6'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘R6’ ...\r\n* DONE (R6)\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/Rcpp_0.12.19.tgz'\r\nContent type 'application/x-gzip' length 4429794 bytes (4.2 MB)\r\n==================================================\r\ndownloaded 4.2 MB\r\n\r\nInstalling Rcpp\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a7285bc43/Rcpp'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘Rcpp’ ...\r\n* DONE (Rcpp)\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/rlang_0.3.0.1.tgz'\r\nContent type 'application/x-gzip' length 1074663 bytes (1.0 MB)\r\n==================================================\r\ndownloaded 1.0 MB\r\n\r\nInstalling rlang\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a78473bd6/rlang'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘rlang’ ...\r\n* DONE (rlang)\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/tidyselect_0.2.5.tgz'\r\nContent type 'application/x-gzip' length 294992 bytes (288 KB)\r\n==================================================\r\ndownloaded 288 KB\r\n\r\nInstalling tidyselect\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a3171858a/tidyselect'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘tidyselect’ ...\r\n* DONE (tidyselect)\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a1344b4cb/dplyr'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘dplyr’ ...\r\n* DONE (dplyr)\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/ggdendro_0.1-20.tgz'\r\nContent type 'application/x-gzip' length 132139 bytes (129 KB)\r\n==================================================\r\ndownloaded 129 KB\r\n\r\nInstalling ggdendro\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/ggplot2_3.1.0.tgz'\r\nContent type 'application/x-gzip' length 3179264 bytes (3.0 MB)\r\n==================================================\r\ndownloaded 3.0 MB\r\n\r\nInstalling ggplot2\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/digest_0.6.18.tgz'\r\nContent type 'application/x-gzip' length 166752 bytes (162 KB)\r\n==================================================\r\ndownloaded 162 KB\r\n\r\nInstalling digest\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a7ce7e9c/digest'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘digest’ ...\r\n* DONE (digest)\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/scales_1.0.0.tgz'\r\nContent type 'application/x-gzip' length 590050 bytes (576 KB)\r\n==================================================\r\ndownloaded 576 KB\r\n\r\nInstalling scales\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a628434f4/scales'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘scales’ ...\r\n* DONE (scales)\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a107752db/ggplot2'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘ggplot2’ ...\r\n* DONE (ggplot2)\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a9f50133/ggdendro'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘ggdendro’ ...\r\n* DONE (ggdendro)\r\nSkipping install of 'ggplot2' from a cran remote, the SHA1 (3.1.0) has not changed since last install.\r\n  Use `force = TRUE` to force installation\r\ntrying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/ggthemes_4.0.1.tgz'\r\nContent type 'application/x-gzip' length 334081 bytes (326 KB)\r\n==================================================\r\ndownloaded 326 KB\r\n\r\nInstalling ggthemes\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a7a815897/ggthemes'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\n* installing *binary* package ‘ggthemes’ ...\r\n* DONE (ggthemes)\r\nSkipping install of 'Rcpp' from a cran remote, the SHA1 (0.12.19) has not changed since last install.\r\n  Use `force = TRUE` to force installation\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \\\r\n  --no-save --no-restore --quiet CMD INSTALL  \\\r\n  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a4a3a386/pkimes-sigclust2-f5b57f0'  \\\r\n  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \\\r\n  --install-tests\r\n\r\nERROR: dependencies ‘Rclusterpp’, ‘WGCNA’ are not available for package ‘sigclust2’\r\n* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/sigclust2’\r\nInstallation failed: Command failed (1)\r\n\r\n```\r\n\r\nMy R/computer setup is as follows\r\n```R\r\n> R.Version()\r\n$platform\r\n[1] \"x86_64-apple-darwin15.6.0\"\r\n\r\n$arch\r\n[1] \"x86_64\"\r\n\r\n$os\r\n[1] \"darwin15.6.0\"\r\n\r\n$system\r\n[1] \"x86_64, darwin15.6.0\"\r\n\r\n$status\r\n[1] \"\"\r\n\r\n$major\r\n[1] \"3\"\r\n\r\n$minor\r\n[1] \"4.3\"\r\n\r\n$year\r\n[1] \"2017\"\r\n\r\n$month\r\n[1] \"11\"\r\n\r\n$day\r\n[1] \"30\"\r\n\r\n$`svn rev`\r\n[1] \"73796\"\r\n\r\n$language\r\n[1] \"R\"\r\n\r\n$version.string\r\n[1] \"R version 3.4.3 (2017-11-30)\"\r\n\r\n$nickname\r\n[1] \"Kite-Eating Tree\"\r\n\r\n\r\n```"},"comment":{"url":"https://api.github.com/repos/pkimes/sigclust2/issues/comments/437076491","html_url":"https://github.com/pkimes/sigclust2/issues/7#issuecomment-437076491","issue_url":"https://api.github.com/repos/pkimes/sigclust2/issues/7","id":437076491,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNzA3NjQ5MQ==","user":{"login":"pkimes","id":3516025,"node_id":"MDQ6VXNlcjM1MTYwMjU=","avatar_url":"https://avatars1.githubusercontent.com/u/3516025?v=4","gravatar_id":"","url":"https://api.github.com/users/pkimes","html_url":"https://github.com/pkimes","followers_url":"https://api.github.com/users/pkimes/followers","following_url":"https://api.github.com/users/pkimes/following{/other_user}","gists_url":"https://api.github.com/users/pkimes/gists{/gist_id}","starred_url":"https://api.github.com/users/pkimes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pkimes/subscriptions","organizations_url":"https://api.github.com/users/pkimes/orgs","repos_url":"https://api.github.com/users/pkimes/repos","events_url":"https://api.github.com/users/pkimes/events{/privacy}","received_events_url":"https://api.github.com/users/pkimes/received_events","type":"User","site_admin":false},"created_at":"2018-11-08T16:58:51Z","updated_at":"2018-11-08T16:58:51Z","author_association":"OWNER","body":"Hi @idc9 - just got a chance to look at this. I think root of your problem is:\r\n\r\n1. `Rclusterpp` is [no longer available on CRAN](https://cran.r-project.org/web/packages/Rclusterpp/index.html) and needs to be installed from [this GitHub repo].(https://github.com/nolanlab/Rclusterpp)\r\n2. `WGCNA` depends on some packages on Bioconductor (`‘AnnotationDbi’, ‘GO.db’, ‘impute’, ‘preprocessCore’`) and not CRAN.\r\n\r\nI'll add a note to the README about `Rclusterpp` for now, and try to update the package to remove this deprecated dependency when I get a chance. \r\n\r\nThanks for reporting this. \r\nLet me know if the above solves your problems!"}}
{"actor":{"display_login":"pkimes"}}