{"action":"created","issue":{"url":"https://api.github.com/repos/conda/conda/issues/1405","labels_url":"https://api.github.com/repos/conda/conda/issues/1405/labels{/name}","comments_url":"https://api.github.com/repos/conda/conda/issues/1405/comments","events_url":"https://api.github.com/repos/conda/conda/issues/1405/events","html_url":"https://github.com/conda/conda/issues/1405","id":92426996,"number":1405,"title":"Trouble updating Bioconductor R packages","user":{"login":"olgabot","id":806256,"avatar_url":"https://avatars.githubusercontent.com/u/806256?v=3","gravatar_id":"","url":"https://api.github.com/users/olgabot","html_url":"https://github.com/olgabot","followers_url":"https://api.github.com/users/olgabot/followers","following_url":"https://api.github.com/users/olgabot/following{/other_user}","gists_url":"https://api.github.com/users/olgabot/gists{/gist_id}","starred_url":"https://api.github.com/users/olgabot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/olgabot/subscriptions","organizations_url":"https://api.github.com/users/olgabot/orgs","repos_url":"https://api.github.com/users/olgabot/repos","events_url":"https://api.github.com/users/olgabot/events{/privacy}","received_events_url":"https://api.github.com/users/olgabot/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2015-07-01T16:26:31Z","updated_at":"2015-07-01T17:24:01Z","closed_at":null,"body":"Ultimately, I want to be able to run [this](http://www.bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf) vignette on using SVA (surrogate variable analysis). I'm having trouble installing the packages' dependencies. I get an `IOError: [Errno 2] No such file or directory: '/Users/olga/anaconda/envs/r/conda-meta/r-nlme-3.1_119-r3.0.0_2.json'`, and if I add `r-nlme` to my package list, the install goes smoothly. I'm not sure exactly what's happening, and as an observer it seems like something in the dependency graph isn't getting drawn correctly. here's the full error output and `conda info`.\r\n\r\n```\r\n(r)➜  ~  conda install -c asmeurer r-recommended r-survival r-matrix r-kernsmooth r-foreign r-codetools r-base r-mass\r\nFetching package metadata: ......\r\nSolving package specifications: ...........\r\nWarning: 4 possible package resolutions (only showing differing packages):\r\n\t[u'r-cluster-2.0.1-r3.2.0_1.tar.bz2', u'r-mass-7.3_40-r3.2.0_0.tar.bz2'],\r\n\t[u'r-cluster-2.0.1-r3.2.0_1.tar.bz2', u'r-mass-7.3_40-0.tar.bz2'],\r\n\t[u'r-cluster-2.0.1-r2.15.0_1.tar.bz2', u'r-mass-7.3_40-0.tar.bz2'],\r\n\t[u'r-cluster-2.0.1-r2.15.0_1.tar.bz2', u'r-mass-7.3_40-r3.2.0_0.tar.bz2'],\r\n\r\nPackage plan for installation in environment /Users/olga/anaconda/envs/r:\r\n\r\nThe following NEW packages will be INSTALLED:\r\n\r\n    libtiff:       4.0.3-0         \r\n    ncurses:       5.9-1           \r\n    pcre:          8.36-0          \r\n    r:             3.2.0-0         \r\n    r-base:        3.2.0-0         \r\n    r-boot:        1.3_16-r3.2.0_0 \r\n    r-class:       7.3_13-r3.2.0_0 \r\n    r-cluster:     2.0.1-r3.2.0_1  \r\n    r-codetools:   0.2_11-r3.2.0_0 \r\n    r-foreign:     0.8_63-r3.2.0_0 \r\n    r-kernsmooth:  2.23_14-r3.2.0_0\r\n    r-lattice:     0.20_31-r3.2.0_0\r\n    r-mass:        7.3_40-r3.2.0_0 \r\n\r\nThe following packages will be UPDATED:\r\n\r\n    r-matrix:      1.1_5-r2.15.2_2  --> 1.1_5-0         \r\n    r-mgcv:        1.8_4-r2.14.0_2  --> 1.8_6-r3.2.0_0  \r\n    r-nlme:        3.1_119-r3.0.0_2 --> 3.1_120-r3.2.0_0\r\n    r-nnet:        7.3_8-r2.14.0_2  --> 7.3_9-r3.2.0_0  \r\n    r-recommended: 3.1.3-0          --> 3.2.0-r3.2.0_0  \r\n    r-rpart:       4.1_8-r2.15.0_2  --> 4.1_9-r3.2.0_0  \r\n    r-spatial:     7.3_8-r3.0.0_2   --> 7.3_9-r3.2.0_0  \r\n    r-survival:    2.37_7-1         --> 2.38_2-r3.2.0_0 \r\n    readline:      6.2-2            --> 6.2.5-1         \r\n\r\nProceed ([y]/n)? y\r\n\r\nUnlinking packages ...\r\nAn unexpected error has occurred, please consider sending the                                                                                                             |  22%\r\nfollowing traceback to the conda GitHub issue tracker at:\r\n\r\n    https://github.com/conda/conda/issues\r\n\r\nInclude the output of the command 'conda info' in your report.\r\n\r\n\r\nTraceback (most recent call last):\r\n  File \"/Users/olga/anaconda/envs/r/bin/conda\", line 5, in <module>\r\n    sys.exit(main())\r\n  File \"/Users/olga/anaconda/lib/python2.7/site-packages/conda/cli/main.py\", line 201, in main\r\n    args_func(args, p)\r\n  File \"/Users/olga/anaconda/lib/python2.7/site-packages/conda/cli/main.py\", line 208, in args_func\r\n    args.func(args, p)\r\n  File \"/Users/olga/anaconda/lib/python2.7/site-packages/conda/cli/common.py\", line 612, in inner\r\n    return func(args, parser)\r\n  File \"/Users/olga/anaconda/lib/python2.7/site-packages/conda/cli/main_install.py\", line 46, in execute\r\n    install.install(args, parser, 'install')\r\n  File \"/Users/olga/anaconda/lib/python2.7/site-packages/conda/cli/install.py\", line 413, in install\r\n    plan.execute_actions(actions, index, verbose=not args.quiet)\r\n  File \"/Users/olga/anaconda/lib/python2.7/site-packages/conda/plan.py\", line 527, in execute_actions\r\n    inst.execute_instructions(plan, index, verbose)\r\n  File \"/Users/olga/anaconda/lib/python2.7/site-packages/conda/instructions.py\", line 148, in execute_instructions\r\n    cmd(state, arg)\r\n  File \"/Users/olga/anaconda/lib/python2.7/site-packages/conda/instructions.py\", line 95, in UNLINK_CMD\r\n    install.unlink(state['prefix'], arg)\r\n  File \"/Users/olga/anaconda/lib/python2.7/site-packages/conda/install.py\", line 671, in unlink\r\n    with open(meta_path) as fi:\r\nIOError: [Errno 2] No such file or directory: '/Users/olga/anaconda/envs/r/conda-meta/r-nlme-3.1_119-r3.0.0_2.json'\r\n```\r\n\r\nOutput from `conda info`:\r\n\r\n```\r\nCurrent conda install:\r\n\r\n             platform : osx-64\r\n        conda version : 3.13.0\r\n  conda-build version : 1.8.2\r\n       python version : 2.7.10.final.0\r\n     requests version : 2.7.0\r\n     root environment : /Users/olga/anaconda  (writable)\r\n  default environment : /Users/olga/anaconda/envs/r\r\n     envs directories : /Users/olga/anaconda/envs\r\n        package cache : /Users/olga/anaconda/pkgs\r\n         channel URLs : https://repo.continuum.io/pkgs/free/osx-64/\r\n                        https://repo.continuum.io/pkgs/free/noarch/\r\n                        https://repo.continuum.io/pkgs/pro/osx-64/\r\n                        https://repo.continuum.io/pkgs/pro/noarch/\r\n          config file : None\r\n    is foreign system : False\r\n```"},"comment":{"url":"https://api.github.com/repos/conda/conda/issues/comments/117757470","html_url":"https://github.com/conda/conda/issues/1405#issuecomment-117757470","issue_url":"https://api.github.com/repos/conda/conda/issues/1405","id":117757470,"user":{"login":"asmeurer","id":71486,"avatar_url":"https://avatars.githubusercontent.com/u/71486?v=3","gravatar_id":"","url":"https://api.github.com/users/asmeurer","html_url":"https://github.com/asmeurer","followers_url":"https://api.github.com/users/asmeurer/followers","following_url":"https://api.github.com/users/asmeurer/following{/other_user}","gists_url":"https://api.github.com/users/asmeurer/gists{/gist_id}","starred_url":"https://api.github.com/users/asmeurer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/asmeurer/subscriptions","organizations_url":"https://api.github.com/users/asmeurer/orgs","repos_url":"https://api.github.com/users/asmeurer/repos","events_url":"https://api.github.com/users/asmeurer/events{/privacy}","received_events_url":"https://api.github.com/users/asmeurer/received_events","type":"User","site_admin":false},"created_at":"2015-07-01T17:24:01Z","updated_at":"2015-07-01T17:24:01Z","body":"I probably need to update the conda package for r-xml. "}}