{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.MedGNRyc/b1/r-bioc-basilisk_1.12.1+ds-2_i386.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.MedGNRyc/b2/r-bioc-basilisk_1.12.1+ds-2_i386.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,2 +1,2 @@\n \n- 96d59cecc795682223c8663a91d813d4 92244 gnu-r optional r-bioc-basilisk_1.12.1+ds-2_all.deb\n+ 2ec8762f2bc1f2e83fa9661c9517c08f 92180 gnu-r optional r-bioc-basilisk_1.12.1+ds-2_all.deb\n"}, {"source1": "r-bioc-basilisk_1.12.1+ds-2_all.deb", "source2": "r-bioc-basilisk_1.12.1+ds-2_all.deb", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,3 +1,3 @@\n -rw-r--r--   0        0        0        4 2023-07-21 07:22:48.000000 debian-binary\n -rw-r--r--   0        0        0     2116 2023-07-21 07:22:48.000000 control.tar.xz\n--rw-r--r--   0        0        0    89936 2023-07-21 07:22:48.000000 data.tar.xz\n+-rw-r--r--   0        0        0    89872 2023-07-21 07:22:48.000000 data.tar.xz\n"}, {"source1": "control.tar.xz", "source2": "control.tar.xz", "unified_diff": null, "details": [{"source1": "control.tar", "source2": "control.tar", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "comments": ["Files differ"], "unified_diff": null}]}]}]}, {"source1": "data.tar.xz", "source2": "data.tar.xz", "unified_diff": null, "details": [{"source1": "data.tar", "source2": "data.tar", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -15,16 +15,16 @@\n -rw-r--r--   0 root         (0) root         (0)      613 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/Meta/nsInfo.rds\n -rw-r--r--   0 root         (0) root         (0)     1225 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/Meta/package.rds\n -rw-r--r--   0 root         (0) root         (0)      200 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/Meta/vignette.rds\n -rw-r--r--   0 root         (0) root         (0)     1319 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/NAMESPACE\n -rw-r--r--   0 root         (0) root         (0)      718 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/NEWS.Rd\n drwxr-xr-x   0 root         (0) root         (0)        0 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/R/\n -rw-r--r--   0 root         (0) root         (0)     1058 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/R/basilisk\n--rw-r--r--   0 root         (0) root         (0)    33548 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/R/basilisk.rdb\n--rw-r--r--   0 root         (0) root         (0)      992 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/R/basilisk.rdx\n+-rw-r--r--   0 root         (0) root         (0)    33551 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/R/basilisk.rdb\n+-rw-r--r--   0 root         (0) root         (0)      994 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/R/basilisk.rdx\n drwxr-xr-x   0 root         (0) root         (0)        0 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/doc/\n -rw-r--r--   0 root         (0) root         (0)     1398 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/doc/index.html\n -rw-r--r--   0 root         (0) root         (0)     2120 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/doc/motivation.R\n -rw-r--r--   0 root         (0) root         (0)    19470 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/doc/motivation.Rmd\n drwxr-xr-x   0 root         (0) root         (0)        0 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/example/\n -rw-r--r--   0 root         (0) root         (0)       28 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/example/.BBSoptions\n -rw-r--r--   0 root         (0) root         (0)      434 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/example/DESCRIPTION\n@@ -44,17 +44,17 @@\n drwxr-xr-x   0 root         (0) root         (0)        0 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/example/tests/\n drwxr-xr-x   0 root         (0) root         (0)        0 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/example/tests/testthat/\n -rw-r--r--   0 root         (0) root         (0)      617 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/example/tests/testthat/test-basic.R\n -rw-r--r--   0 root         (0) root         (0)       73 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/example/tests/testthat.R\n drwxr-xr-x   0 root         (0) root         (0)        0 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/help/\n -rw-r--r--   0 root         (0) root         (0)      812 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/help/AnIndex\n -rw-r--r--   0 root         (0) root         (0)      331 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/help/aliases.rds\n--rw-r--r--   0 root         (0) root         (0)    39370 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/help/basilisk.rdb\n--rw-r--r--   0 root         (0) root         (0)      467 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/help/basilisk.rdx\n--rw-r--r--   0 root         (0) root         (0)      280 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/help/paths.rds\n+-rw-r--r--   0 root         (0) root         (0)    39420 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/help/basilisk.rdb\n+-rw-r--r--   0 root         (0) root         (0)      460 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/help/basilisk.rdx\n+-rw-r--r--   0 root         (0) root         (0)      281 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/help/paths.rds\n drwxr-xr-x   0 root         (0) root         (0)        0 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/html/\n -rw-r--r--   0 root         (0) root         (0)     4091 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/html/00Index.html\n -rw-r--r--   0 root         (0) root         (0)     1844 2023-07-21 07:22:48.000000 ./usr/lib/R/site-library/basilisk/html/R.css\n drwxr-xr-x   0 root         (0) root         (0)        0 2023-07-21 07:22:48.000000 ./usr/share/\n drwxr-xr-x   0 root         (0) root         (0)        0 2023-07-21 07:22:48.000000 ./usr/share/doc/\n drwxr-xr-x   0 root         (0) root         (0)        0 2023-07-21 07:22:48.000000 ./usr/share/doc/r-bioc-basilisk/\n -rw-r--r--   0 root         (0) root         (0)      487 2023-07-21 07:22:48.000000 ./usr/share/doc/r-bioc-basilisk/changelog.Debian.gz\n"}, {"source1": "./usr/lib/R/site-library/basilisk/R/basilisk.rdb", "source2": "./usr/lib/R/site-library/basilisk/R/basilisk.rdb", "unified_diff": null, "details": [{"source1": "Rscript --vanilla - {}", "source2": "Rscript --vanilla - {}", "unified_diff": "@@ -227,15 +227,15 @@\n     \"imports\" = \"    dir.expiry = c(unlockDirectory = \"unlockDirectory\"), methods = c(is = \"is\"), \"\n     \"imports\" = \"    parallel = c(clusterCall = \"clusterCall\"), parallel = c(makeForkCluster = \"makeForkCluster\"), \"\n     \"imports\" = \"    parallel = c(makePSOCKcluster = \"makePSOCKcluster\"), parallel = c(stopCluster = \"stopCluster\"), \"\n     \"imports\" = \"    reticulate = c(conda_install = \"conda_install\"), reticulate = c(py_available = \"py_available\"), \"\n     \"imports\" = \"    reticulate = c(py_config = \"py_config\"), reticulate = c(use_condaenv = \"use_condaenv\"), \"\n     \"imports\" = \"    utils = c(packageVersion = \"packageVersion\"))\"\n     \"lazydata\" = \"<environment>\"\n-    \"path\" = \"\"/build/1st/r-bioc-basilisk-1.12.1+ds/debian/r-bioc-basilisk/usr/lib/R/site-library/basilisk\"\"\n+    \"path\" = \"\"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/debian/r-bioc-basilisk/usr/lib/R/site-library/basilisk\"\"\n     \"spec\" = \"c(name = \"basilisk\", version = \"1.12.1\")\"\n }\n \n .__S3MethodsTable__. (environment) = \n {\n }\n \n"}]}, {"source1": "./usr/lib/R/site-library/basilisk/R/basilisk.rdx", "source2": "./usr/lib/R/site-library/basilisk/R/basilisk.rdx", "unified_diff": null, "details": [{"source1": "basilisk.rdx-content", "source2": "basilisk.rdx-content", "unified_diff": null, "details": [{"source1": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "source2": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "unified_diff": "@@ -1,187 +1,187 @@\n $variables\n $variables$.__C__BasiliskEnvironment\n [1]    0 1825\n \n $variables$.__NAMESPACE__.\n-[1] 5626   62\n+[1] 5629   62\n \n $variables$.__S3MethodsTable__.\n-[1] 5828   62\n+[1] 5831   62\n \n $variables$`.__T__.getEnvName:basilisk`\n-[1] 7489   62\n+[1] 7492   62\n \n $variables$`.__T__.getPkgName:basilisk`\n-[1] 9175   62\n+[1] 9178   62\n \n $variables$.activate_fallback\n-[1] 9237 1356\n+[1] 9240 1356\n \n $variables$.basilisk_freeze\n-[1] 10593   506\n+[1] 10596   506\n \n $variables$.check_logical\n-[1] 11099   409\n+[1] 11102   409\n \n $variables$.check_versions\n-[1] 11508   669\n+[1] 11511   669\n \n $variables$.full2pkg\n-[1] 12177   268\n+[1] 12180   268\n \n $variables$.getChannels\n-[1] 12445   356\n+[1] 12448   356\n \n $variables$.getEnvName\n-[1] 12801   420\n+[1] 12804   420\n \n $variables$.getPackages\n-[1] 13221   181\n+[1] 13224   181\n \n $variables$.getPipPackages\n-[1] 13402   177\n+[1] 13405   177\n \n $variables$.getPipPaths\n-[1] 13579   178\n+[1] 13582   178\n \n $variables$.getPkgName\n-[1] 13757   421\n+[1] 13760   421\n \n $variables$.get_env_system_dir\n-[1] 14178   372\n+[1] 14181   372\n \n $variables$.instantiate_store\n-[1] 14550   297\n+[1] 14553   297\n \n $variables$.make_globals\n-[1] 14847   896\n+[1] 14850   896\n \n $variables$.packageName\n-[1] 15743    62\n+[1] 15746    62\n \n $variables$.python_version\n-[1] 15805   614\n+[1] 15808   614\n \n $variables$.same_as_loaded\n-[1] 16419   502\n+[1] 16422   502\n \n $variables$BasiliskEnvironment\n-[1] 16921   421\n+[1] 16924   421\n \n $variables$PyPiLink\n-[1] 17342   290\n+[1] 17345   290\n \n $variables$basiliskRun\n-[1] 17632  1147\n+[1] 17635  1147\n \n $variables$basiliskStart\n-[1] 18779  2470\n+[1] 18782  2470\n \n $variables$basiliskStop\n-[1] 21249   335\n+[1] 21252   335\n \n $variables$configureBasiliskEnv\n-[1] 21584  1914\n+[1] 21587  1914\n \n $variables$createLocalBasiliskEnv\n-[1] 23498   961\n+[1] 23501   961\n \n $variables$findPersistentEnv\n-[1] 24459   275\n+[1] 24462   275\n \n $variables$getBasiliskCheckVersions\n-[1] 24734   262\n+[1] 24737   262\n \n $variables$getBasiliskForceFallback\n-[1] 24996   245\n+[1] 24999   245\n \n $variables$getBasiliskFork\n-[1] 25241   237\n+[1] 25244   237\n \n $variables$getBasiliskShared\n-[1] 25478   238\n+[1] 25481   238\n \n $variables$glibcxx_failed\n-[1] 25887    63\n+[1] 25890    63\n \n $variables$globals\n-[1] 26164   628\n+[1] 26167   628\n \n $variables$listCorePackages\n-[1] 26792   253\n+[1] 26795   253\n \n $variables$listPackages\n-[1] 27045   498\n+[1] 27048   498\n \n $variables$listPythonVersion\n-[1] 27543   323\n+[1] 27546   323\n \n $variables$obtainEnvironmentPath\n-[1] 27866  1866\n+[1] 27869  1866\n \n $variables$setBasiliskCheckVersions\n-[1] 29732   363\n+[1] 29735   363\n \n $variables$setBasiliskForceFallback\n-[1] 30095   345\n+[1] 30098   345\n \n $variables$setBasiliskFork\n-[1] 30440   338\n+[1] 30443   338\n \n $variables$setBasiliskShared\n-[1] 30778   339\n+[1] 30781   339\n \n $variables$setupBasiliskEnv\n-[1] 31117  1974\n+[1] 31120  1974\n \n $variables$useBasiliskEnv\n-[1] 33091   457\n+[1] 33094   457\n \n \n $references\n $references$`env::1`\n-[1] 2135 3491\n+[1] 2135 3494\n \n $references$`env::10`\n-[1] 8455  268\n+[1] 8458  268\n \n $references$`env::11`\n-[1] 7551  452\n+[1] 7554  452\n \n $references$`env::12`\n-[1] 8003  452\n+[1] 8006  452\n \n $references$`env::13`\n-[1] 25716   171\n+[1] 25719   171\n \n $references$`env::14`\n-[1] 25950   214\n+[1] 25953   214\n \n $references$`env::2`\n [1] 1825  140\n \n $references$`env::3`\n [1] 1965  170\n \n $references$`env::4`\n-[1] 5688  140\n+[1] 5691  140\n \n $references$`env::5`\n-[1] 7046  443\n+[1] 7049  443\n \n $references$`env::6`\n-[1] 6776  270\n+[1] 6779  270\n \n $references$`env::7`\n-[1] 5890  443\n+[1] 5893  443\n \n $references$`env::8`\n-[1] 6333  443\n+[1] 6336  443\n \n $references$`env::9`\n-[1] 8723  452\n+[1] 8726  452\n \n \n $compressed\n [1] TRUE\n \n"}]}]}, {"source1": "./usr/lib/R/site-library/basilisk/help/basilisk.rdb", "source2": "./usr/lib/R/site-library/basilisk/help/basilisk.rdb", "unified_diff": null, "details": [{"source1": "Rscript --vanilla - {}", "source2": "Rscript --vanilla - {}", "unified_diff": "@@ -43,15 +43,15 @@\n                 structure(list(structure(\"pkgname\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\"), \n                 structure(\", i.e., they are appended to the output of \", Rd_tag = \"TEXT\"), \n                 structure(list(structure(list(structure(\"system.file\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\link\")), Rd_tag = \"\\\\code\"), \n                 structure(\".\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\itemize\"), \n             structure(\"\\n\", Rd_tag = \"TEXT\"))), Rd_tag = \"\\\\section\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Aaron lun\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"BasiliskEnvironment(\\\"my_env1\\\", \\\"AaronPackage\\\", \\n\", Rd_tag = \"RCODE\"), \n-        structure(\"    packages=c(\\\"scikit-learn=1.1.1\\\", \\\"pandas=1.43.1\\\"))\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/BasiliskEnvironment-class.Rd\", class = \"Rd\", meta = list(\n+        structure(\"    packages=c(\\\"scikit-learn=1.1.1\\\", \\\"pandas=1.43.1\\\"))\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/BasiliskEnvironment-class.Rd\", class = \"Rd\", meta = list(\n     docType = \"class\"), prepared = 3L)\n \n PyPiLink (list) = structure(list(structure(list(structure(\"Link to PyPi\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n     structure(list(structure(\"PyPiLink\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n     structure(list(structure(\"PyPiLink\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Helper function to create a Markdown link to the PyPi landing page for a Python package.\\n\", Rd_tag = \"TEXT\"), \n         structure(\"Intended primarily for use inside vignettes.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n@@ -59,15 +59,15 @@\n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(list(\n         list(structure(\"package\", Rd_tag = \"TEXT\")), list(structure(\"String containing the name of the Python package.\", Rd_tag = \"TEXT\"))), Rd_tag = \"\\\\item\"), \n         structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\arguments\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"String containing a Markdown link to the package's landing page.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\value\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Aaron Lun\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"PyPiLink(\\\"pandas\\\")\\n\", Rd_tag = \"RCODE\"), \n         structure(\"PyPiLink(\\\"scikit-learn\\\")\\n\", Rd_tag = \"RCODE\"), \n-        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/PyPiLink.Rd\", class = \"Rd\", meta = list(\n+        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/PyPiLink.Rd\", class = \"Rd\", meta = list(\n     docType = character(0)), prepared = 3L)\n \n basiliskOptions (list) = structure(list(structure(list(structure(\"Options for \", Rd_tag = \"TEXT\"), \n     structure(list(structure(\"basilisk\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\pkg\")), Rd_tag = \"\\\\title\"), \n     structure(list(structure(\"getBasiliskFork\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n     structure(list(structure(\"getBasiliskFork\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n     structure(list(structure(\"setBasiliskFork\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n@@ -176,15 +176,15 @@\n             structure(\".\\n\", Rd_tag = \"TEXT\"), structure(\"This ensures that all users are creating the intended environment for greater reproducibility (and easier debugging).\\n\", Rd_tag = \"TEXT\"))), Rd_tag = \"\\\\section\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Aaron Lun\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(list(\n         structure(list(structure(\"basiliskStart\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\link\")), Rd_tag = \"\\\\code\"), \n         structure(\", where these options are used.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\seealso\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"getBasiliskFork()\\n\", Rd_tag = \"RCODE\"), \n         structure(\"getBasiliskShared()\\n\", Rd_tag = \"RCODE\"), \n-        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/basiliskOptions.Rd\", class = \"Rd\", meta = list(\n+        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/basiliskOptions.Rd\", class = \"Rd\", meta = list(\n     docType = character(0)), prepared = 3L)\n \n basiliskStart (list) = structure(list(structure(list(structure(\"Start and stop \", Rd_tag = \"TEXT\"), \n     structure(list(structure(\"basilisk\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\pkg\"), \n     structure(\"-related processes\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n     structure(list(structure(\"basiliskStart\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n     structure(list(structure(\"basiliskStart\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n@@ -590,15 +590,15 @@\n         structure(\"cl <- basiliskStart(tmploc)\\n\", Rd_tag = \"RCODE\"), \n         structure(\"basiliskRun(proc=cl, function(store) {\\n\", Rd_tag = \"RCODE\"), \n         structure(\"    store$snake.in.my.shoes <- 1\\n\", Rd_tag = \"RCODE\"), \n         structure(\"    invisible(NULL)\\n\", Rd_tag = \"RCODE\"), \n         structure(\"}, persist=TRUE)\\n\", Rd_tag = \"RCODE\"), structure(\"basiliskRun(proc=cl, function(store) {\\n\", Rd_tag = \"RCODE\"), \n         structure(\"    return(store$snake.in.my.shoes)\\n\", Rd_tag = \"RCODE\"), \n         structure(\"}, persist=TRUE)\\n\", Rd_tag = \"RCODE\"), structure(\"basiliskStop(cl)\\n\", Rd_tag = \"RCODE\"), \n-        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/basiliskStart.Rd\", class = \"Rd\", meta = list(\n+        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/basiliskStart.Rd\", class = \"Rd\", meta = list(\n     docType = character(0)), prepared = 3L)\n \n configureBasiliskEnv (list) = structure(list(structure(list(structure(\"Configure client environments\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n     structure(list(structure(\"configureBasiliskEnv\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n     structure(list(structure(\"configureBasiliskEnv\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Configure the \", Rd_tag = \"TEXT\"), \n         structure(list(structure(\"basilisk\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\pkg\"), \n@@ -655,15 +655,15 @@\n         structure(\" is invisibly returned.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\value\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Aaron Lun\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(list(\n         structure(list(structure(\"setupBasiliskEnv\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\link\")), Rd_tag = \"\\\\code\"), \n         structure(\", which does the heavy lifting of setting up the environments.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\seealso\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(list(\n         structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"configureBasiliskEnv()\\n\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\dontrun\"), \n-        structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/configureBasiliskEnv.Rd\", class = \"Rd\", meta = list(\n+        structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/configureBasiliskEnv.Rd\", class = \"Rd\", meta = list(\n     docType = character(0)), prepared = 3L)\n \n createLocalBasiliskEnv (list) = structure(list(structure(list(structure(\"Create a local conda environment manually\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n     structure(list(structure(\"createLocalBasiliskEnv\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n     structure(list(structure(\"createLocalBasiliskEnv\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Manually create a local conda environment with versioning and thread safety.\\n\", Rd_tag = \"TEXT\"), \n         structure(\"This is intended for use in analysis workflows rather than package development.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n@@ -690,15 +690,15 @@\n         structure(\".\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\value\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Aaron Lun\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"tmploc <- file.path(tempdir(), \\\"my_package_C\\\")\\n\", Rd_tag = \"RCODE\"), \n         structure(\"tmp <- createLocalBasiliskEnv(tmploc, packages=\\\"pandas==1.4.3\\\")\\n\", Rd_tag = \"RCODE\"), \n         structure(\"basiliskRun(env=tmp, fun=function() { \\n\", Rd_tag = \"RCODE\"), \n         structure(\"    X <- reticulate::import(\\\"pandas\\\"); X$`__version__` \\n\", Rd_tag = \"RCODE\"), \n         structure(\"}, testload=\\\"pandas\\\")\\n\", Rd_tag = \"RCODE\"), \n-        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/createLocalBasiliskEnv.Rd\", class = \"Rd\", meta = list(\n+        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/createLocalBasiliskEnv.Rd\", class = \"Rd\", meta = list(\n     docType = character(0)), prepared = 3L)\n \n findPersistentEnv (list) = structure(list(structure(list(structure(\"Find the persistent environment\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n     structure(list(structure(\"findPersistentEnv\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n     structure(list(structure(\"findPersistentEnv\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Previously used to find a persistent environment inside a \", Rd_tag = \"TEXT\"), \n         structure(list(structure(list(structure(\"basiliskRun\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\link\")), Rd_tag = \"\\\\code\"), \n@@ -706,15 +706,15 @@\n         structure(\"This is deprecated in favor of setting \", Rd_tag = \"TEXT\"), \n         structure(list(structure(\"persist=TRUE\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\"), \n         structure(\" in \", Rd_tag = \"TEXT\"), structure(list(structure(list(\n             structure(\"basiliskRun\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\link\")), Rd_tag = \"\\\\code\"), \n         structure(\",\\n\", Rd_tag = \"TEXT\"), structure(\"which will explicitly pass an environment in which to store persistent variables.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"findPersistentEnv()\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\usage\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"A defunct error message is raised.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\value\"), \n-    structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Aaron Lun\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\")), Rdfile = \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/findPersistentEnv.Rd\", class = \"Rd\", meta = list(\n+    structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Aaron Lun\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\")), Rdfile = \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/findPersistentEnv.Rd\", class = \"Rd\", meta = list(\n     docType = character(0)), prepared = 3L)\n \n hideOutput (NULL) = NULL\n \n listPackages (list) = structure(list(structure(list(structure(\"List packages\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n     structure(list(structure(\"listPackages\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n     structure(list(structure(\"listPackages\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n@@ -749,15 +749,15 @@\n         structure(\", the package name.\\n\", Rd_tag = \"TEXT\"), \n         structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"For \", Rd_tag = \"TEXT\"), \n         structure(list(structure(\"listPythonVersion\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\"), \n         structure(\", a string containing the default version of Python.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\value\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Aaron Lun\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"listPackages()\\n\", Rd_tag = \"RCODE\"), \n         structure(\"listPythonVersion()\\n\", Rd_tag = \"RCODE\"), \n-        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/listPackages.Rd\", class = \"Rd\", meta = list(\n+        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/listPackages.Rd\", class = \"Rd\", meta = list(\n     docType = character(0)), prepared = 3L)\n \n obtainEnvironmentPath (list) = structure(list(structure(list(structure(\"Obtain the environment path\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n     structure(list(structure(\"obtainEnvironmentPath\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n     structure(list(structure(\"obtainEnvironmentPath\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Obtain a path to a Conda environment, lazily installing it if necessary.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"obtainEnvironmentPath(env)\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\usage\"), \n@@ -782,15 +782,15 @@\n         structure(\"tmploc <- file.path(tempdir(), \\\"my_package_A\\\")\\n\", Rd_tag = \"RCODE\"), \n         structure(\"if (!file.exists(tmploc)) {\\n\", Rd_tag = \"RCODE\"), \n         structure(\"    setupBasiliskEnv(tmploc, c('pandas=1.4.3'))\\n\", Rd_tag = \"RCODE\"), \n         structure(\"}\\n\", Rd_tag = \"RCODE\"), structure(\"obtainEnvironmentPath(tmploc)\\n\", Rd_tag = \"RCODE\"), \n         structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"env <- BasiliskEnvironment(\\\"test_env\\\", \\\"basilisk\\\", \\n\", Rd_tag = \"RCODE\"), \n         structure(\"    packages=c(\\\"scikit-learn=1.1.1\\\", \\\"pandas=1.43.1\\\"))\\n\", Rd_tag = \"RCODE\"), \n         structure(list(structure(\"obtainEnvironmentPath(env)\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\dontrun\"), \n-        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/obtainEnvironmentPath.Rd\", class = \"Rd\", meta = list(\n+        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/obtainEnvironmentPath.Rd\", class = \"Rd\", meta = list(\n     docType = character(0)), prepared = 3L)\n \n safeDeparse (closure) = function (obj) \n {\n     tryCatch({\n         deparse(obj)\n     }, error = function(e) {\n@@ -930,15 +930,15 @@\n         structure(\", to list the packages in the conda environment.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\seealso\"), \n     structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(list(\n         structure(\"basilisk.utils::installConda()\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\dontshow\"), \n         structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n         structure(\"tmploc <- file.path(tempdir(), \\\"my_package_A\\\")\\n\", Rd_tag = \"RCODE\"), \n         structure(\"if (!file.exists(tmploc)) {\\n\", Rd_tag = \"RCODE\"), \n         structure(\"    setupBasiliskEnv(tmploc, c('pandas=1.4.3'))\\n\", Rd_tag = \"RCODE\"), \n-        structure(\"}\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/setupBasiliskEnv.Rd\", class = \"Rd\", meta = list(\n+        structure(\"}\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/setupBasiliskEnv.Rd\", class = \"Rd\", meta = list(\n     docType = character(0)), prepared = 3L)\n \n useBasiliskEnv (list) = structure(list(structure(list(structure(\"Use \", Rd_tag = \"TEXT\"), \n     structure(list(structure(\"basilisk\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\pkg\"), \n     structure(\" environments\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n     structure(list(structure(\"useBasiliskEnv\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n     structure(list(structure(\"useBasiliskEnv\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n@@ -985,10 +985,10 @@\n         structure(\"# has already been loaded into this R session.\\n\", Rd_tag = \"RCODE\"), \n         structure(\"try(useBasiliskEnv(tmploc))\\n\", Rd_tag = \"RCODE\"), \n         structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"# This will definitely not work, as the available Python is already set.\\n\", Rd_tag = \"RCODE\"), \n         structure(\"baseloc <- basilisk.utils::getCondaDir()\\n\", Rd_tag = \"RCODE\"), \n         structure(\"status <- try(useBasiliskEnv(baseloc))\\n\", Rd_tag = \"RCODE\"), \n         structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"# ... except on Windows, which somehow avoids tripping the error.\\n\", Rd_tag = \"RCODE\"), \n         structure(\"stopifnot(is(status, \\\"try-error\\\") || basilisk.utils::isWindows())\\n\", Rd_tag = \"RCODE\"), \n-        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/useBasiliskEnv.Rd\", class = \"Rd\", meta = list(\n+        structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/useBasiliskEnv.Rd\", class = \"Rd\", meta = list(\n     docType = character(0)), prepared = 3L)\n \n"}]}, {"source1": "./usr/lib/R/site-library/basilisk/help/basilisk.rdx", "source2": "./usr/lib/R/site-library/basilisk/help/basilisk.rdx", "unified_diff": null, "details": [{"source1": "basilisk.rdx-content", "source2": "basilisk.rdx-content", "unified_diff": null, "details": [{"source1": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "source2": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "unified_diff": "@@ -1,73 +1,73 @@\n $variables\n $variables$`BasiliskEnvironment-class`\n-[1]  289 1923\n+[1]  291 1925\n \n $variables$PyPiLink\n-[1] 2495  895\n+[1] 2501  897\n \n $variables$basiliskOptions\n-[1] 3673 4394\n+[1] 3683 4397\n \n $variables$basiliskStart\n-[1]  8346 13152\n+[1]  8362 13155\n \n $variables$configureBasiliskEnv\n-[1] 21786  2425\n+[1] 21807  2427\n \n $variables$createLocalBasiliskEnv\n-[1] 24499  1793\n+[1] 24525  1796\n \n $variables$findPersistentEnv\n-[1] 26581   930\n+[1] 26612   932\n \n $variables$listPackages\n-[1] 27795  1722\n+[1] 27830  1724\n \n $variables$obtainEnvironmentPath\n-[1] 29809  1481\n+[1] 29848  1484\n \n $variables$setupBasiliskEnv\n-[1] 31575  5239\n+[1] 31619  5241\n \n $variables$useBasiliskEnv\n-[1] 37098  2272\n+[1] 37145  2275\n \n \n $references\n $references$`env::1`\n-[1]   0 289\n+[1]   0 291\n \n $references$`env::10`\n-[1] 31290   285\n+[1] 31332   287\n \n $references$`env::11`\n-[1] 36814   284\n+[1] 36860   285\n \n $references$`env::2`\n-[1] 2212  283\n+[1] 2216  285\n \n $references$`env::3`\n-[1] 3390  283\n+[1] 3398  285\n \n $references$`env::4`\n-[1] 8067  279\n+[1] 8080  282\n \n $references$`env::5`\n-[1] 21498   288\n+[1] 21517   290\n \n $references$`env::6`\n-[1] 24211   288\n+[1] 24234   291\n \n $references$`env::7`\n-[1] 26292   289\n+[1] 26321   291\n \n $references$`env::8`\n-[1] 27511   284\n+[1] 27544   286\n \n $references$`env::9`\n-[1] 29517   292\n+[1] 29554   294\n \n \n $compressed\n [1] TRUE\n \n"}]}]}, {"source1": "./usr/lib/R/site-library/basilisk/help/paths.rds", "source2": "./usr/lib/R/site-library/basilisk/help/paths.rds", "unified_diff": null, "details": [{"source1": "paths.rds-content", "source2": "paths.rds-content", "unified_diff": null, "details": [{"source1": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "source2": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "unified_diff": "@@ -1,13 +1,13 @@\n- [1] \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/BasiliskEnvironment-class.Rd\"\n- [2] \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/PyPiLink.Rd\"                 \n- [3] \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/basiliskOptions.Rd\"          \n- [4] \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/basiliskStart.Rd\"            \n- [5] \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/configureBasiliskEnv.Rd\"     \n- [6] \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/createLocalBasiliskEnv.Rd\"   \n- [7] \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/findPersistentEnv.Rd\"        \n- [8] \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/listPackages.Rd\"             \n- [9] \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/obtainEnvironmentPath.Rd\"    \n-[10] \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/setupBasiliskEnv.Rd\"         \n-[11] \"/build/1st/r-bioc-basilisk-1.12.1+ds/man/useBasiliskEnv.Rd\"           \n+ [1] \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/BasiliskEnvironment-class.Rd\"\n+ [2] \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/PyPiLink.Rd\"                 \n+ [3] \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/basiliskOptions.Rd\"          \n+ [4] \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/basiliskStart.Rd\"            \n+ [5] \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/configureBasiliskEnv.Rd\"     \n+ [6] \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/createLocalBasiliskEnv.Rd\"   \n+ [7] \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/findPersistentEnv.Rd\"        \n+ [8] \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/listPackages.Rd\"             \n+ [9] \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/obtainEnvironmentPath.Rd\"    \n+[10] \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/setupBasiliskEnv.Rd\"         \n+[11] \"/build/2/r-bioc-basilisk-1.12.1+ds/2nd/man/useBasiliskEnv.Rd\"           \n attr(,\"first\")\n-[1] 42\n+[1] 44\n"}]}]}]}]}]}]}