{"action":"created","issue":{"url":"https://api.github.com/repos/HenrikBengtsson/aroma.affymetrix/issues/28","repository_url":"https://api.github.com/repos/HenrikBengtsson/aroma.affymetrix","labels_url":"https://api.github.com/repos/HenrikBengtsson/aroma.affymetrix/issues/28/labels{/name}","comments_url":"https://api.github.com/repos/HenrikBengtsson/aroma.affymetrix/issues/28/comments","events_url":"https://api.github.com/repos/HenrikBengtsson/aroma.affymetrix/issues/28/events","html_url":"https://github.com/HenrikBengtsson/aroma.affymetrix/issues/28","id":216224958,"number":28,"title":"Error: '%<=%' is defunct. Use '%<-%' instead.","user":{"login":"d7i1","id":3007484,"avatar_url":"https://avatars2.githubusercontent.com/u/3007484?v=3","gravatar_id":"","url":"https://api.github.com/users/d7i1","html_url":"https://github.com/d7i1","followers_url":"https://api.github.com/users/d7i1/followers","following_url":"https://api.github.com/users/d7i1/following{/other_user}","gists_url":"https://api.github.com/users/d7i1/gists{/gist_id}","starred_url":"https://api.github.com/users/d7i1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/d7i1/subscriptions","organizations_url":"https://api.github.com/users/d7i1/orgs","repos_url":"https://api.github.com/users/d7i1/repos","events_url":"https://api.github.com/users/d7i1/events{/privacy}","received_events_url":"https://api.github.com/users/d7i1/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2017-03-22T22:13:54Z","updated_at":"2017-03-23T15:04:27Z","closed_at":null,"body":"**I'm making a comeback to aroma.affymetrix after several years' absence.\r\nI reused one of my formerly-working scripts, but it fails.\r\nFWIW, it seems to fail based on a deprecation of a to-me unfamiliar operator %<=% \r\nOutput:**\r\n> **source(\"Analyse.R\")**\r\n....libraries loading....\r\n20170322 21:52:59|Background correcting data set...\r\n20170322 21:52:59| Background correcting data set...\r\n20170322 21:53:00|  Number of arrays: 24\r\n20170322 21:53:00|  Array #1 ('GSM843555_JC-110') of 24...\r\n20170322 21:53:00|   Identifying cells to be updated...\r\n20170322 21:53:10|    Number of cells: 3095094\r\n     int [1:3095094] 13 15 17 20 24 28 29 33 34 35 ...\r\n20170322 21:53:10|   Identifying cells to be updated...done\r\n**Error: '%<=%' is defunct.\r\nUse '%<-%' instead.\r\nSee help(\"Defunct\")**\r\n20170322 21:53:10|  Array #1 ('GSM843555_JC-110') of 24...done\r\n20170322 21:53:10| Background correcting data set...done\r\n20170322 21:53:10|Background correcting data set...done\r\n**script terminates here.**\r\n\r\n> **SessionInfo()**\r\nR version 3.2.3 (2015-12-10)\r\nPlatform: x86_64-pc-linux-gnu (64-bit)\r\nRunning under: Ubuntu 16.04 LTS\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] stats     graphics  grDevices utils     datasets  methods   base     \r\n\r\nother attached packages:\r\n[1] aroma.light_3.0.0      aroma.affymetrix_3.0.0 affxparser_1.42.0     \r\n[4] aroma.core_3.0.0       R.devices_2.15.1       R.filesets_2.11.0     \r\n[7] R.utils_2.5.0          R.oo_1.21.0            R.methodsS3_1.7.1     \r\n\r\nloaded via a namespace (and not attached):\r\n [1] DNAcopy_1.44.0        XVector_0.10.0        splines_3.2.3        \r\n [4] IRanges_2.4.8         BiocGenerics_0.16.1   zlibbioc_1.16.0      \r\n [7] aroma.apd_0.6.0       R.cache_0.12.0        globals_0.9.0        \r\n[10] tools_3.2.3           parallel_3.2.3        Biobase_2.30.0       \r\n[13] R.huge_0.9.0          gcrma_2.42.0          affy_1.48.0          \r\n[16] PSCBS_0.62.0          matrixStats_0.51.0    digest_0.6.12        \r\n[19] preprocessCore_1.32.0 affyio_1.40.0         R.rsp_0.40.0         \r\n[22] S4Vectors_0.8.11      base64enc_0.1-3       codetools_0.2-15     \r\n[25] BiocInstaller_1.20.3  Biostrings_2.38.4     stats4_3.2.3         \r\n[28] future_1.4.0          listenv_0.6.0        \r\n\r\n> q()\r\n\r\n **I downloaded the aroma.affymetrix 3.0.0 source package.  unzipped it and grepped for instances of %<=%**\r\n$ **grep \"%<=%\" `find . -name \"*.R\"`**\r\n./aroma.affymetrix/R/LimmaBackgroundCorrection.R:    res[[kk]] %<=% {\r\n./aroma.affymetrix/R/LimmaBackgroundCorrection.R:    } ## %<=%\r\n./aroma.affymetrix/R/AllelicCrosstalkCalibration.R:    res[[kk]] %<=% {\r\n./aroma.affymetrix/R/AllelicCrosstalkCalibration.R:    } ## %<=%\r\n./aroma.affymetrix/R/AbstractProbeSequenceNormalization.R:    res[[kk]] %<=% {\r\n./aroma.affymetrix/R/AbstractProbeSequenceNormalization.R:    } ## %<=%\r\n./aroma.affymetrix/R/OpticalBackgroundCorrection.R:    res[[ii]] %<=% {\r\n./aroma.affymetrix/R/OpticalBackgroundCorrection.R:    } ## %<=%\r\n./aroma.affymetrix/R/MatNormalization.R:    res[[ii]] %<=% {\r\n./aroma.affymetrix/R/MatNormalization.R:    } ## %<=%\r\n./aroma.affymetrix/R/UnitModel.fitCnProbes.R:    res[[kk]] %<=% {\r\n./aroma.affymetrix/R/UnitModel.fitCnProbes.R:    } # %<=%\r\n./aroma.affymetrix/R/FragmentLengthNormalization.R:    res[[kk]] %<=% {\r\n./aroma.affymetrix/R/FragmentLengthNormalization.R:    } ## %<=%\r\n./aroma.affymetrix/R/AffymetrixCelSet.NORM.R:    dataFiles[[kk]] %<=% {\r\n./aroma.affymetrix/R/AffymetrixCelSet.convertToUnique.R:      res[[kk]] %<=% {\r\n./aroma.affymetrix/R/AffymetrixCelSet.convertToUnique.R:      } ## %<=%\r\n./aroma.affymetrix/R/RmaBackgroundCorrection.R:    res[[ii]] %<=% {\r\n./aroma.affymetrix/R/RmaBackgroundCorrection.R:    } ## %<=%\r\n./aroma.affymetrix/R/GcRmaBackgroundCorrection.R:    dataFiles[[ii]] %<=% {\r\n./aroma.affymetrix/R/GcRmaBackgroundCorrection.R:    } ## %<=%\r\n\r\n**Hope this helps**\r\n"},"comment":{"url":"https://api.github.com/repos/HenrikBengtsson/aroma.affymetrix/issues/comments/288748248","html_url":"https://github.com/HenrikBengtsson/aroma.affymetrix/issues/28#issuecomment-288748248","issue_url":"https://api.github.com/repos/HenrikBengtsson/aroma.affymetrix/issues/28","id":288748248,"user":{"login":"HenrikBengtsson","id":1616850,"avatar_url":"https://avatars3.githubusercontent.com/u/1616850?v=3","gravatar_id":"","url":"https://api.github.com/users/HenrikBengtsson","html_url":"https://github.com/HenrikBengtsson","followers_url":"https://api.github.com/users/HenrikBengtsson/followers","following_url":"https://api.github.com/users/HenrikBengtsson/following{/other_user}","gists_url":"https://api.github.com/users/HenrikBengtsson/gists{/gist_id}","starred_url":"https://api.github.com/users/HenrikBengtsson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/HenrikBengtsson/subscriptions","organizations_url":"https://api.github.com/users/HenrikBengtsson/orgs","repos_url":"https://api.github.com/users/HenrikBengtsson/repos","events_url":"https://api.github.com/users/HenrikBengtsson/events{/privacy}","received_events_url":"https://api.github.com/users/HenrikBengtsson/received_events","type":"User","site_admin":false},"created_at":"2017-03-23T15:04:27Z","updated_at":"2017-03-23T15:04:27Z","body":"What is your full script up to the point of error?"}}
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