{"action":"created","issue":{"url":"https://api.github.com/repos/kendomaniac/docker4seq/issues/1","repository_url":"https://api.github.com/repos/kendomaniac/docker4seq","labels_url":"https://api.github.com/repos/kendomaniac/docker4seq/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/kendomaniac/docker4seq/issues/1/comments","events_url":"https://api.github.com/repos/kendomaniac/docker4seq/issues/1/events","html_url":"https://github.com/kendomaniac/docker4seq/issues/1","id":242328846,"number":1,"title":"Asking for Help : How to install docker4seq in windows?","user":{"login":"kagningemma","id":7575126,"avatar_url":"https://avatars2.githubusercontent.com/u/7575126?v=4","gravatar_id":"","url":"https://api.github.com/users/kagningemma","html_url":"https://github.com/kagningemma","followers_url":"https://api.github.com/users/kagningemma/followers","following_url":"https://api.github.com/users/kagningemma/following{/other_user}","gists_url":"https://api.github.com/users/kagningemma/gists{/gist_id}","starred_url":"https://api.github.com/users/kagningemma/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kagningemma/subscriptions","organizations_url":"https://api.github.com/users/kagningemma/orgs","repos_url":"https://api.github.com/users/kagningemma/repos","events_url":"https://api.github.com/users/kagningemma/events{/privacy}","received_events_url":"https://api.github.com/users/kagningemma/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2017-07-12T10:16:39Z","updated_at":"2017-07-31T03:49:02Z","closed_at":null,"body":"Thank you very much for providing this docker4seq package for R. I am a trying to learn NGS data analysis using docker4seq package but I am facing problems downloading the docker4seq package using Rstudio on windows 7 OS ( Intel Xeon CPU E5-1603 @2.8GHz, HD 1 TB, RAM 32GB). I have docker for windows installed as well as the 7 containers listed at the \"02 requirements\" section here http://rpubs.com/rcaloger/280163. \r\n\r\nI pulled+ran the images of the 7 containers, and ran the \"install_github(\"kendomaniac/docker4seq\") command in Rstudio, but it didn`t work. instead, i got the following error message in R: \r\n\r\n\r\n\r\n library(devtools)\r\nWarning message:\r\n Package 'devtools' was built under R version 3.4.1\r\n> install_github(\"kendomaniac/docker4seq\")\r\nDownloading GitHub repo kendomaniac/docker4seq@master\r\nfrom URL https://api.github.com/repos/kendomaniac/docker4seq/zipball/master\r\nInstalling docker4seq\r\n\"C:/PROGRA~1/R/R-34~1.0/bin/x64/R\" --no-site-file --no-environ --no-save  \\\r\n  --no-restore --quiet CMD INSTALL  \\\r\n  \"C:/Users/viro10/AppData/Local/Temp/RtmpOGpjw0/devtools7bc7ee232e6/kendomaniac-docker4seq-3643254\"  \\\r\n  --library=\"C:/Program Files/R/R-3.4.0/library\" --install-tests \r\n\r\n* installing *source* package 'docker4seq' ...\r\n** R\r\nWarning: 'casc.scnorm.R' (2 lines) can not be re-encoded\r\n** inst\r\n** preparing package for lazy loading\r\n** help\r\n*** installing help indices\r\n** building package indices\r\n** installing vignettes\r\n** testing if installed package can be loaded\r\n*** arch - i386\r\nError: package or namespace load failed for 'docker4seq' in namespaceExport(ns, exports):\r\n undefined exports: cascStep4\r\nError: Loading failed\r\n  Execution stopped\r\n*** arch - x64\r\nError: package or namespace load failed for 'docker4seq' in namespaceExport(ns, exports):\r\n undefined exports: cascStep4\r\n Error: Loading failed\r\n  Execution stopped\r\nERROR: loading failed for 'i386', 'x64'\r\n* removing 'C:/Program Files/R/R-3.4.0/library/docker4seq'\r\nInstallation failed: Command failed (1) \r\n\r\n\r\n\r\nplease see screenshot below\r\n[screenshot2.docx](https://github.com/kendomaniac/docker4seq/files/1141617/screenshot2.docx)\r\n \r\n\r\nI also ran the docker command: downloadContainers(group=\"docker\"), but got the same error mThank you!running the install_github(\"kendomaniac/docker4seq\") command in R. \r\nI may be mistaken, but the docker4seq downloading and installation steps listed here (http://rpubs.com/rcaloger/280163) seems to work only for linux OS.\r\nPlease can someone help ? How can i install docker4seq in windows OS ? Thanks in advance. "},"comment":{"url":"https://api.github.com/repos/kendomaniac/docker4seq/issues/comments/318960641","html_url":"https://github.com/kendomaniac/docker4seq/issues/1#issuecomment-318960641","issue_url":"https://api.github.com/repos/kendomaniac/docker4seq/issues/1","id":318960641,"user":{"login":"kagningemma","id":7575126,"avatar_url":"https://avatars2.githubusercontent.com/u/7575126?v=4","gravatar_id":"","url":"https://api.github.com/users/kagningemma","html_url":"https://github.com/kagningemma","followers_url":"https://api.github.com/users/kagningemma/followers","following_url":"https://api.github.com/users/kagningemma/following{/other_user}","gists_url":"https://api.github.com/users/kagningemma/gists{/gist_id}","starred_url":"https://api.github.com/users/kagningemma/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kagningemma/subscriptions","organizations_url":"https://api.github.com/users/kagningemma/orgs","repos_url":"https://api.github.com/users/kagningemma/repos","events_url":"https://api.github.com/users/kagningemma/events{/privacy}","received_events_url":"https://api.github.com/users/kagningemma/received_events","type":"User","site_admin":false},"created_at":"2017-07-31T03:49:02Z","updated_at":"2017-07-31T03:49:02Z","body":"Yes Sir, i did it from the docker quick start terminal.  Below is the the contents of the script.Rout file \r\n\r\n\r\n_**R version 3.4.0 (2017-04-21) -- \"You Stupid Darkness\"\r\nCopyright (C) 2017 The R Foundation for Statistical Computing\r\nPlatform: x86_64-w64-mingw32/x64 (64-bit)\r\n\r\nR is free software and comes with ABSOLUTELY NO WARRANTY.\r\nYou are welcome to redistribute it under certain conditions.\r\nType 'license()' or 'licence()' for distribution details.\r\n\r\n  Natural language support but running in an English locale\r\n\r\nR is a collaborative project with many contributors.\r\nType 'contributors()' for more information and\r\n'citation()' on how to cite R or R packages in publications.\r\n\r\nType 'demo()' for some demos, 'help()' for on-line help, or\r\n'help.start()' for an HTML browser interface to help.\r\nType 'q()' to quit R.\r\n\r\n> library(docker4seq)\r\n> \r\n> library(docker4seq)\r\n> mirnaCounts(group=\"docker\",fastq.folder=getwd(), scratch.folder=\"/data/scratch\", mirbase.id=\"hsa\",download.status=FALSE, adapter.type=\"NEB\", trimmed.fastq=FALSE)\r\n\r\n In your system the following version of Docker is installed:\r\nDocker version 17.05.0-ce, build 89658be\r\ncreating a folder in scratch folder\r\nIt seems that in  C:/Program Files/R/R-3.4.0/bin there are not fastq.gz files[1] 1\r\nWarning message:\r\nIn dir.create(file.path(scratch.folder, tmp.folder)) :\r\n  cannot create dir '\\data\\scratch\\Sat-Jul-29-18-54-49-2017', reason 'No such file or directory'\r\n> \r\n> proc.time()\r\n   user  system elapsed \r\n   0.20    0.06    0.43**_ \r\n"}}
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