{"action":"created","issue":{"url":"https://api.github.com/repos/fgeorgatos/easybuild.experimental/issues/16","repository_url":"https://api.github.com/repos/fgeorgatos/easybuild.experimental","labels_url":"https://api.github.com/repos/fgeorgatos/easybuild.experimental/issues/16/labels{/name}","comments_url":"https://api.github.com/repos/fgeorgatos/easybuild.experimental/issues/16/comments","events_url":"https://api.github.com/repos/fgeorgatos/easybuild.experimental/issues/16/events","html_url":"https://github.com/fgeorgatos/easybuild.experimental/issues/16","id":166333876,"number":16,"title":"generateEasyConfig aborting","user":{"login":"verdurin","id":12435,"avatar_url":"https://avatars.githubusercontent.com/u/12435?v=3","gravatar_id":"","url":"https://api.github.com/users/verdurin","html_url":"https://github.com/verdurin","followers_url":"https://api.github.com/users/verdurin/followers","following_url":"https://api.github.com/users/verdurin/following{/other_user}","gists_url":"https://api.github.com/users/verdurin/gists{/gist_id}","starred_url":"https://api.github.com/users/verdurin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/verdurin/subscriptions","organizations_url":"https://api.github.com/users/verdurin/orgs","repos_url":"https://api.github.com/users/verdurin/repos","events_url":"https://api.github.com/users/verdurin/events{/privacy}","received_events_url":"https://api.github.com/users/verdurin/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-07-19T13:40:21Z","updated_at":"2016-07-19T15:39:26Z","closed_at":null,"body":"I've followed the procedure outlined by @pescobar in https://github.com/hpcugent/easybuild-easyconfigs/pull/3079.\r\n\r\nIn my case, I want to install *all* the Bioconductor packages and generate an EasyConfig for that.\r\n\r\nWhen I run the script, I see this error:\r\n\r\n```\r\n./generateEasyConfig.R --tc foss/2016b --od $TMPDIR -ll DEBUG\r\n2016-07-19 14:13:30 INFO::Log level set to INFO.\r\n2016-07-19 14:13:30 INFO::Will store EasyConfig in /home/camp/huffmaa/tmp/R-3.3.1-foss-2016b.eb\r\nBioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help\r\n2016-07-19 14:25:22 CRITICAL::Package  is not installed. Aborting!\r\n\r\nDescription:\r\n    Generates an EasyBuild EasyConfig file from an existing R environment.\r\n    Optionally you can first load a specific version of R using module load before generating the *.eb EasyConfig\r\n\r\nExample usage:\r\n    module load EasyBuild\r\n    module load R\r\n    generateEasyConfig.R  --tc  goolf/1.7.20 \\\r\n                          --od  /path/to/my/EasyConfigs/r/R/ \\\r\n                          --ll  WARNING\r\n\r\nExplanation of options:\r\n    --tc toolchain/version  EasyBuild ToolChain (required).\r\n                               To get a list of available toolchains (may or may not be already installed):\r\n                                   module load EasyBuild\r\n                                   eb --list-toolchains\r\n                               To check if a toolchain is already installed and if yes which version is the default:\r\n                                   module -r -t avail -d '^name_of_toolchain$'\r\n    --od path               Output Directory where the generated *.eb EasyConfig file will be stored (optional).\r\n                               Will default to the current working directory as determined with getwd().\r\n                               Name of the output file follows strict rules\r\n                               and is automatically generated based on R version and toolchain.\r\n    --ll LEVEL              Log level (optional).\r\n                               One of FINEST, FINER, FINE, DEBUG, INFO (default), WARNING, ERROR or CRITICAL.\r\n```\r\n\r\nNote that the request to see the logging level to `DEBUG` doesn't work either."},"comment":{"url":"https://api.github.com/repos/fgeorgatos/easybuild.experimental/issues/comments/233673494","html_url":"https://github.com/fgeorgatos/easybuild.experimental/issues/16#issuecomment-233673494","issue_url":"https://api.github.com/repos/fgeorgatos/easybuild.experimental/issues/16","id":233673494,"user":{"login":"verdurin","id":12435,"avatar_url":"https://avatars.githubusercontent.com/u/12435?v=3","gravatar_id":"","url":"https://api.github.com/users/verdurin","html_url":"https://github.com/verdurin","followers_url":"https://api.github.com/users/verdurin/followers","following_url":"https://api.github.com/users/verdurin/following{/other_user}","gists_url":"https://api.github.com/users/verdurin/gists{/gist_id}","starred_url":"https://api.github.com/users/verdurin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/verdurin/subscriptions","organizations_url":"https://api.github.com/users/verdurin/orgs","repos_url":"https://api.github.com/users/verdurin/repos","events_url":"https://api.github.com/users/verdurin/events{/privacy}","received_events_url":"https://api.github.com/users/verdurin/received_events","type":"User","site_admin":false},"created_at":"2016-07-19T15:39:26Z","updated_at":"2016-07-19T15:39:26Z","body":"Thanks, @pescobar - commenting out that check worked for me:\r\n\r\n```\r\n2016-07-19 15:42:12 INFO::Log level set to INFO.\r\n2016-07-19 15:42:12 INFO::Will store EasyConfig in /home/camp/huffmaa/tmp/R-3.3.1-foss-2016b.eb\r\nBioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help\r\n2016-07-19 16:11:24 WARNING::Failed to determine repo origin for package NA .\r\n2016-07-19 16:11:24 WARNING::Failed to determine repo origin for 1 package!\r\n2016-07-19 16:11:24 INFO::===========================================================================\r\n2016-07-19 16:11:24 INFO::: Total R packages processed:                                1938\r\n2016-07-19 16:11:24 INFO:::  * Resolved packages    (will be added to EasyConfig):     1937  ( 99.95%)\r\n2016-07-19 16:11:24 INFO:::  * Unavailable packages (missing from EasyConfig):            1  (  0.05%)\r\n2016-07-19 16:11:24 INFO::===========================================================================\r\n2016-07-19 16:11:24 INFO::Finished!\r\n```\r\n\r\nWould be nice to know which is the miscreant package..."}}
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