{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.gmPZWCsG/b1/r-cran-treescape_1.10.18+dfsg-2_arm64.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.gmPZWCsG/b2/r-cran-treescape_1.10.18+dfsg-2_arm64.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,3 +1,3 @@\n \n- c980c74cd1853171d4d5d53c9072681c 233876 debug optional r-cran-treescape-dbgsym_1.10.18+dfsg-2_arm64.deb\n- 983b3a300f4ffa661c099c3759ab6f59 1115628 gnu-r optional r-cran-treescape_1.10.18+dfsg-2_arm64.deb\n+ cb66b71a99babcd46c8a70d1f735db2f 233888 debug optional r-cran-treescape-dbgsym_1.10.18+dfsg-2_arm64.deb\n+ 84564f1e220a078afaaf77a15f98a8a7 1115820 gnu-r optional r-cran-treescape_1.10.18+dfsg-2_arm64.deb\n"}, {"source1": "r-cran-treescape_1.10.18+dfsg-2_arm64.deb", "source2": "r-cran-treescape_1.10.18+dfsg-2_arm64.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 2020-05-22 06:51:07.000000 debian-binary\n -rw-r--r-- 0 0 0 2108 2020-05-22 06:51:07.000000 control.tar.xz\n--rw-r--r-- 0 0 0 1113328 2020-05-22 06:51:07.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 1113520 2020-05-22 06:51:07.000000 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": "@@ -14,15 +14,15 @@\n -rw-r--r-- 0 root (0) root (0) 382 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/Meta/links.rds\n -rw-r--r-- 0 root (0) root (0) 808 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/Meta/nsInfo.rds\n -rw-r--r-- 0 root (0) root (0) 1460 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/Meta/package.rds\n -rw-r--r-- 0 root (0) root (0) 310 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/Meta/vignette.rds\n -rw-r--r-- 0 root (0) root (0) 1590 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/NAMESPACE\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/R/\n -rw-r--r-- 0 root (0) root (0) 1058 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/R/treescape\n--rw-r--r-- 0 root (0) root (0) 51502 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/R/treescape.rdb\n+-rw-r--r-- 0 root (0) root (0) 51505 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/R/treescape.rdb\n -rw-r--r-- 0 root (0) root (0) 542 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/R/treescape.rdx\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/data/\n -rw-r--r-- 0 root (0) root (0) 850392 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/data/Rdata.rdb\n -rw-r--r-- 0 root (0) root (0) 141 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/data/Rdata.rds\n -rw-r--r-- 0 root (0) root (0) 232 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/data/Rdata.rdx\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/\n -rw-r--r-- 0 root (0) root (0) 8869 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/DengueVignette.R\n@@ -31,17 +31,17 @@\n -rw-r--r-- 0 root (0) root (0) 8024 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/TransmissionTreesVignette.Rmd\n -rw-r--r-- 0 root (0) root (0) 2682 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/index.html\n -rw-r--r-- 0 root (0) root (0) 5345 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/treescape.R\n -rw-r--r-- 0 root (0) root (0) 16607 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/treescape.Rmd\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/\n -rw-r--r-- 0 root (0) root (0) 468 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/AnIndex\n -rw-r--r-- 0 root (0) root (0) 257 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/aliases.rds\n--rw-r--r-- 0 root (0) root (0) 316 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/paths.rds\n--rw-r--r-- 0 root (0) root (0) 50773 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/treescape.rdb\n--rw-r--r-- 0 root (0) root (0) 624 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/treescape.rdx\n+-rw-r--r-- 0 root (0) root (0) 318 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/paths.rds\n+-rw-r--r-- 0 root (0) root (0) 50853 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/treescape.rdb\n+-rw-r--r-- 0 root (0) root (0) 628 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/treescape.rdx\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/html/\n -rw-r--r-- 0 root (0) root (0) 3597 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/html/00Index.html\n -rw-r--r-- 0 root (0) root (0) 1844 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/html/R.css\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/libs/\n -rw-r--r-- 0 root (0) root (0) 68552 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/libs/treescape.so\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/shiny/\n -rw-r--r-- 0 root (0) root (0) 36496 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/shiny/server.R\n"}, {"source1": "./usr/lib/R/site-library/treescape/R/treescape.rdb", "source2": "./usr/lib/R/site-library/treescape/R/treescape.rdb", "unified_diff": null, "details": [{"source1": "Rscript --vanilla - {}", "source2": "Rscript --vanilla - {}", "unified_diff": "@@ -261,15 +261,15 @@\n \"imports\" = \" phangorn = c(Descendants = \"Descendants\"), phangorn = c(KF.dist = \"KF.dist\"), \"\n \"imports\" = \" phangorn = c(RF.dist = \"RF.dist\"), phangorn = c(path.dist = \"path.dist\"), \"\n \"imports\" = \" phangorn = c(wRF.dist = \"wRF.dist\"), rgl = c(writeWebGL = \"writeWebGL\"), \"\n \"imports\" = \" shinyBS = c(bsTooltip = \"bsTooltip\"), stats = c(as.dist = \"as.dist\"), \"\n \"imports\" = \" stats = c(cutree = \"cutree\"), stats = c(dist = \"dist\"), stats = c(hclust = \"hclust\"), \"\n \"imports\" = \" utils = c(packageDescription = \"packageDescription\"))\"\n \"lazydata\" = \"\"\n- \"path\" = \"\"/build/1st/r-cran-treescape-1.10.18+dfsg/debian/r-cran-treescape/usr/lib/R/site-library/treescape\"\"\n+ \"path\" = \"\"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/debian/r-cran-treescape/usr/lib/R/site-library/treescape\"\"\n \"spec\" = \"c(name = \"treescape\", version = \"1.10.18\")\"\n }\n \n .__S3MethodsTable__. (environment) = \n {\n }\n \n"}]}, {"source1": "./usr/lib/R/site-library/treescape/R/treescape.rdx", "source2": "./usr/lib/R/site-library/treescape/R/treescape.rdx", "unified_diff": null, "details": [{"source1": "treescape.rdx-content", "source2": "treescape.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": "@@ -1,82 +1,82 @@\n $variables\n $variables$.__NAMESPACE__.\n-[1] 5694 60\n+[1] 5697 60\n \n $variables$.__S3MethodsTable__.\n-[1] 5893 60\n+[1] 5896 60\n \n $variables$.packageName\n-[1] 5953 62\n+[1] 5956 62\n \n $variables$.render.server.info\n-[1] 6015 746\n+[1] 6018 746\n \n $variables$findGroves\n-[1] 6761 2312\n+[1] 6764 2312\n \n $variables$findMRCIs\n-[1] 9073 4199\n+[1] 9076 4199\n \n $variables$linearMrca\n-[1] 13272 2105\n+[1] 13275 2105\n \n $variables$medTree\n-[1] 15377 5405\n+[1] 15380 5405\n \n $variables$multiDist\n-[1] 20782 3462\n+[1] 20785 3462\n \n $variables$plotGroves\n-[1] 24244 3454\n+[1] 24247 3454\n \n $variables$plotGrovesD3\n-[1] 27698 1123\n+[1] 27701 1123\n \n $variables$plotTreeDiff\n-[1] 28821 2662\n+[1] 28824 2662\n \n $variables$refTreeDist\n-[1] 31483 2681\n+[1] 31486 2681\n \n $variables$tipDiff\n-[1] 34164 2382\n+[1] 34167 2382\n \n $variables$treeDist\n-[1] 36546 1245\n+[1] 36549 1245\n \n $variables$treeVec\n-[1] 37791 6965\n+[1] 37794 6965\n \n $variables$treescape\n-[1] 44756 3769\n+[1] 44759 3769\n \n $variables$treescapeServer\n-[1] 48525 329\n+[1] 48528 329\n \n $variables$updateDistancesWithCombinations\n-[1] 48854 438\n+[1] 48857 438\n \n $variables$wiwMedTree\n-[1] 49292 1384\n+[1] 49295 1384\n \n $variables$wiwTreeDist\n-[1] 50676 826\n+[1] 50679 826\n \n \n $references\n $references$`env::1`\n-[1] 309 5385\n+[1] 309 5388\n \n $references$`env::2`\n [1] 0 139\n \n $references$`env::3`\n [1] 139 170\n \n $references$`env::4`\n-[1] 5754 139\n+[1] 5757 139\n \n \n $compressed\n [1] TRUE\n \n"}]}]}, {"source1": "./usr/lib/R/site-library/treescape/help/paths.rds", "source2": "./usr/lib/R/site-library/treescape/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": "@@ -1,23 +1,23 @@\n- [1] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueBEASTMCC.Rd\" \n- [2] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueSeqs.Rd\" \n- [3] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueTrees.Rd\" \n- [4] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/findGroves.Rd\" \n- [5] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/findMRCIs.Rd\" \n- [6] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/fluTrees.Rd\" \n- [7] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/linearMrca.Rd\" \n- [8] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/medTree.Rd\" \n- [9] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/multiDist.Rd\" \n-[10] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/plotGroves.Rd\" \n-[11] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/plotGrovesD3.Rd\" \n-[12] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/plotTreeDiff.Rd\" \n-[13] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/refTreeDist.Rd\" \n-[14] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/tipDiff.Rd\" \n-[15] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treeDist.Rd\" \n-[16] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treeVec.Rd\" \n-[17] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treescape.Rd\" \n-[18] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treescapeServer.Rd\"\n-[19] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/wiwMedTree.Rd\" \n-[20] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/wiwTreeDist.Rd\" \n-[21] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/woodmiceTrees.Rd\" \n+ [1] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueBEASTMCC.Rd\" \n+ [2] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueSeqs.Rd\" \n+ [3] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueTrees.Rd\" \n+ [4] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/findGroves.Rd\" \n+ [5] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/findMRCIs.Rd\" \n+ [6] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/fluTrees.Rd\" \n+ [7] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/linearMrca.Rd\" \n+ [8] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/medTree.Rd\" \n+ [9] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/multiDist.Rd\" \n+[10] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotGroves.Rd\" \n+[11] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotGrovesD3.Rd\" \n+[12] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotTreeDiff.Rd\" \n+[13] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/refTreeDist.Rd\" \n+[14] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/tipDiff.Rd\" \n+[15] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treeDist.Rd\" \n+[16] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treeVec.Rd\" \n+[17] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treescape.Rd\" \n+[18] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treescapeServer.Rd\"\n+[19] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/wiwMedTree.Rd\" \n+[20] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/wiwTreeDist.Rd\" \n+[21] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/woodmiceTrees.Rd\" \n attr(,\"first\")\n-[1] 46\n+[1] 48\n"}]}]}, {"source1": "./usr/lib/R/site-library/treescape/help/treescape.rdb", "source2": "./usr/lib/R/site-library/treescape/help/treescape.rdb", "unified_diff": null, "details": [{"source1": "Rscript --vanilla - {}", "source2": "Rscript --vanilla - {}", "unified_diff": "@@ -13,15 +13,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Drummond, A. J., and Rambaut, A. (2007) \\n\", Rd_tag = \"TEXT\"), \n structure(\"BEAST: Bayesian evolutionary analysis by sampling trees.\\n\", Rd_tag = \"TEXT\"), \n structure(list(structure(\"BMC Evolutionary Biology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n structure(\", 7(1), 214.\\n\", Rd_tag = \"TEXT\"), structure(\"\\n\", Rd_tag = \"TEXT\"), \n structure(\"Lanciotti, R. S., Gubler, D. J., and Trent, D. W. (1997)\\n\", Rd_tag = \"TEXT\"), \n structure(\"Molecular evolution and phylogeny of dengue-4 viruses.\\n\", Rd_tag = \"TEXT\"), \n structure(list(structure(\"Journal of General Virology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n- structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueBEASTMCC.Rd\", class = \"Rd\", meta = list(\n+ structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueBEASTMCC.Rd\", class = \"Rd\", meta = list(\n docType = \"data\"), prepared = 3L)\n \n DengueSeqs (list) = structure(list(structure(list(structure(\"Dengue fever sequences\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"DengueSeqs\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"DengueSeqs\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"datasets\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\keyword\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"17 dengue virus serotype 4 sequences from Lanciotti et al. (1997)\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n@@ -29,15 +29,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Michelle Kendall \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"michelle.louise.kendall@gmail.com\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\email\"), \n structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-214\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\source\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Lanciotti, R. S., Gubler, D. J., and Trent, D. W. (1997)\\n\", Rd_tag = \"TEXT\"), \n structure(\"Molecular evolution and phylogeny of dengue-4 viruses.\\n\", Rd_tag = \"TEXT\"), \n structure(list(structure(\"Journal of General Virology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n- structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueSeqs.Rd\", class = \"Rd\", meta = list(\n+ structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueSeqs.Rd\", class = \"Rd\", meta = list(\n docType = \"data\"), prepared = 3L)\n \n DengueTrees (list) = structure(list(structure(list(structure(\"BEAST analysis of Dengue fever\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"DengueTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"DengueTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"datasets\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\keyword\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"These trees were created using one of the \", Rd_tag = \"TEXT\"), \n@@ -57,15 +57,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Drummond, A. J., and Rambaut, A. (2007) \\n\", Rd_tag = \"TEXT\"), \n structure(\"BEAST: Bayesian evolutionary analysis by sampling trees.\\n\", Rd_tag = \"TEXT\"), \n structure(list(structure(\"BMC Evolutionary Biology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n structure(\", 7(1), 214.\\n\", Rd_tag = \"TEXT\"), structure(\"\\n\", Rd_tag = \"TEXT\"), \n structure(\"Lanciotti, R. S., Gubler, D. J., and Trent, D. W. (1997)\\n\", Rd_tag = \"TEXT\"), \n structure(\"Molecular evolution and phylogeny of dengue-4 viruses.\\n\", Rd_tag = \"TEXT\"), \n structure(list(structure(\"Journal of General Virology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n- structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueTrees.Rd\", class = \"Rd\", meta = list(\n+ structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueTrees.Rd\", class = \"Rd\", meta = list(\n docType = \"data\"), prepared = 3L)\n \n findGroves (list) = structure(list(structure(list(structure(\"Identify clusters of similar trees\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"findGroves\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"findGroves\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"This function uses hierarchical clustering on principal components output by \", Rd_tag = \"TEXT\"), \n structure(list(structure(list(structure(\"treescape\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\link\")), Rd_tag = \"\\\\code\"), \n@@ -125,15 +125,15 @@\n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## run findGroves: treescape+clustering\\n\", Rd_tag = \"RCODE\"), \n structure(\"res <- findGroves(woodmiceTrees, nf=5, nclust=6)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## plot results on first 2 axes\\n\", Rd_tag = \"RCODE\"), \n structure(\"PCs <- res$treescape$pco$li\\n\", Rd_tag = \"RCODE\"), \n structure(\"s.class(PCs, fac=res$groups, col=funky(6))\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## using plotGroves\\n\", Rd_tag = \"RCODE\"), \n structure(\"plotGroves(res)\\n\", Rd_tag = \"RCODE\"), structure(\"}\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/findGroves.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/findGroves.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n findMRCIs (list) = structure(list(structure(list(structure(\"Find MRCIs\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"findMRCIs\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"findMRCIs\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Function to find the most recent common infector (MRCI) matrix from \\\"who infected whom\\\" information.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"findMRCIs(wiw)\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\usage\"), \n@@ -154,15 +154,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Michelle Kendall \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"michelle.louise.kendall@gmail.com\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\email\"), \n structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## a simple who infected whom matrix:\\n\", Rd_tag = \"RCODE\"), \n structure(\"tree1 <- cbind(Infector=1:5,Infectee=2:6) \\n\", Rd_tag = \"RCODE\"), \n structure(\"findMRCIs(tree1)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/findMRCIs.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/findMRCIs.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n fluTrees (list) = structure(list(structure(list(structure(\"BEAST analysis of seasonal influenza (A/H3N2)\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"fluTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"fluTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"datasets\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\keyword\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"These trees were created using BEAST on hemagglutinin (HA) segments\\n\", Rd_tag = \"TEXT\"), \n@@ -170,15 +170,15 @@\n structure(\"http://beast.bio.ed.ac.uk/tutorials\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"A multiPhylo object containing 200 trees, each with 165 tips\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\format\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Only the first 200 trees (out of 10,000) were retained.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\details\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Thibaut Jombart \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"thibautjombart@gmail.com\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\email\"), \n structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"http://beast.bio.ed.ac.uk/tutorials\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\source\"), \n- structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"http://beast.bio.ed.ac.uk/tutorials\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/fluTrees.Rd\", class = \"Rd\", meta = list(\n+ structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"http://beast.bio.ed.ac.uk/tutorials\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/fluTrees.Rd\", class = \"Rd\", meta = list(\n docType = \"data\"), prepared = 3L)\n \n hideOutput (NULL) = NULL\n \n linearMrca (list) = structure(list(structure(list(structure(\"Linear MRCA function\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"linearMrca\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"linearMrca\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n@@ -197,15 +197,15 @@\n structure(list(structure(\"michelle.louise.kendall@gmail.com\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\email\"), \n structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## generate a random tree\\n\", Rd_tag = \"RCODE\"), \n structure(\"x <- rtree(6)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## create matrix of MRCAs: entry (i,j) is the node number of the MRCA of tips i and j\\n\", Rd_tag = \"RCODE\"), \n structure(\"linearMrca(x,6)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/linearMrca.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/linearMrca.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n medTree (list) = structure(list(structure(list(structure(\"Geometric median tree function\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"medTree\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"medTree\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Finds the geometric median of a set of trees according to the Kendall Colijn metric.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"medTree(x, groups = NULL, lambda = 0, weights = NULL,\\n\", Rd_tag = \"RCODE\"), \n@@ -290,15 +290,15 @@\n structure(\"names(res.with.grp)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## get the first median of each\\n\", Rd_tag = \"RCODE\"), \n structure(\"med.trees <- lapply(res.with.grp, function(e) ladderize(e$trees[[1]]))\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## plot trees\\n\", Rd_tag = \"RCODE\"), \n structure(\"par(mfrow=c(2,3))\\n\", Rd_tag = \"RCODE\"), structure(\"for(i in 1:length(med.trees)) plot(med.trees[[i]], main=paste(\\\"cluster\\\",i))\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## highlight the differences between a pair of median trees\\n\", Rd_tag = \"RCODE\"), \n structure(\"plotTreeDiff(med.trees[[1]],med.trees[[5]])\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/medTree.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/medTree.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n multiDist (list) = structure(list(structure(list(structure(\"Metric function for \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"multiPhylo\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\"), \n structure(\" input\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"multiDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"multiDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n@@ -350,15 +350,15 @@\n structure(\"multiDist(trees)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## pairwise distance matrix as a function of lambda:\\n\", Rd_tag = \"RCODE\"), \n structure(\"m <- multiDist(trees, return.lambda.function=TRUE)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## evaluate at lambda=0. Equivalent to multiDist(trees).\\n\", Rd_tag = \"RCODE\"), \n structure(\"m0 <- m(0)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## save memory by recomputing each tree vector for each pairwise tree comparison (for fixed lambda):\\n\", Rd_tag = \"RCODE\"), \n structure(\"m0.5 <- multiDist(trees,0.5,save.memory=TRUE)\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/multiDist.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/multiDist.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n plotGroves (list) = structure(list(structure(list(structure(\"Scatterplot of groups of trees\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"plotGroves\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"plotGroves\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"This function displays the scatterplot of the Multidimensional\\n\", Rd_tag = \"TEXT\"), \n structure(\"Scaling (MDS) output by treescape, superimposing group information\\n\", Rd_tag = \"TEXT\"), \n@@ -455,15 +455,15 @@\n structure(\"plotGroves(res, type=\\\"ellipse\\\", lab.show=TRUE,\\n\", Rd_tag = \"VERB\"), \n structure(\"lab.optim=FALSE, scree.size=.35)\\n\", Rd_tag = \"VERB\"), \n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"## example with no group information\\n\", Rd_tag = \"VERB\"), \n structure(\"plotGroves(res$treescape$pco)\\n\", Rd_tag = \"VERB\"), \n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"## adding labels\\n\", Rd_tag = \"VERB\"), \n structure(\"plotGroves(res$treescape$pco, lab.show=TRUE, lab.cex=2)\\n\", Rd_tag = \"VERB\"), \n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"}\\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-cran-treescape-1.10.18+dfsg/man/plotGroves.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotGroves.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n plotGrovesD3 (list) = structure(list(structure(list(structure(\"Scatterplot of groups of trees using \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"scatterD3\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"plotGrovesD3\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"plotGrovesD3\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"This function displays the scatterplot of the Multidimensional\\n\", Rd_tag = \"TEXT\"), \n@@ -532,15 +532,15 @@\n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"## adding tree labels\\n\", Rd_tag = \"VERB\"), \n structure(\"plotGrovesD3(res, treeNames=1:201)\\n\", Rd_tag = \"VERB\"), \n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"## customizing: vary the colour and the symbol by group\\n\", Rd_tag = \"VERB\"), \n structure(\"plotGrovesD3(res, symbol_var=res$groups)\\n\", Rd_tag = \"VERB\"), \n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"## example with no group information\\n\", Rd_tag = \"VERB\"), \n structure(\"plotGrovesD3(res$treescape$pco)\\n\", Rd_tag = \"VERB\"), \n structure(\"}\\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-cran-treescape-1.10.18+dfsg/man/plotGrovesD3.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotGrovesD3.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n plotTreeDiff (list) = structure(list(structure(list(structure(\"Plot tree differences\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"plotTreeDiff\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"plotTreeDiff\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Highlight the topologicial differences between two trees, plotted side by side. \\n\", Rd_tag = \"TEXT\"), \n structure(\"This function is useful for comparing representative \\\"median\\\" trees - see \", Rd_tag = \"TEXT\"), \n@@ -651,15 +651,15 @@\n structure(\"plotTreeDiff(woodmiceTrees[[1]],woodmiceTrees[[2]], tipDiff=wmTipDiff,\\n\", Rd_tag = \"RCODE\"), \n structure(\" baseCol=\\\"grey2\\\", col1=\\\"cyan\\\", col2=\\\"navy\\\", \\n\", Rd_tag = \"RCODE\"), \n structure(\" edge.width=2, type=\\\"radial\\\", cex=0.5, font=2)\\n\", Rd_tag = \"RCODE\"), \n structure(\"## use colour palette from adegenet:\\n\", Rd_tag = \"RCODE\"), \n structure(\"plotTreeDiff(woodmiceTrees[[1]],woodmiceTrees[[2]], tipDiff=wmTipDiff,\\n\", Rd_tag = \"RCODE\"), \n structure(\" baseCol=\\\"black\\\", colourMethod=\\\"palette\\\", \\n\", Rd_tag = \"RCODE\"), \n structure(\" edge.width=2, type=\\\"cladogram\\\", cex=0.5, font=2) \\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/plotTreeDiff.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotTreeDiff.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n refTreeDist (list) = structure(list(structure(list(structure(\"Metric function for comparing a reference \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"phylo\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\"), \n structure(\" to \", Rd_tag = \"TEXT\"), structure(list(structure(\"multiPhylo\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\"), \n structure(\" input\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"refTreeDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n@@ -703,15 +703,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## generate a single reference tree with 6 tips\\n\", Rd_tag = \"RCODE\"), \n structure(\"refTree <- rtree(6)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## generate 10 random trees, each with 6 tips\\n\", Rd_tag = \"RCODE\"), \n structure(\"trees <- rmtree(10,6)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## find the distances from each of the 10 random trees to the single reference tree\\n\", Rd_tag = \"RCODE\"), \n structure(\"refTreeDist(refTree,trees)\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/refTreeDist.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/refTreeDist.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@@ -760,15 +760,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## simple example on trees with five tips:\\n\", Rd_tag = \"RCODE\"), \n structure(\"tr1 <- read.tree(text=\\\"((A:1,B:1):1,((C:1,D:1):1,E:1):1):1;\\\")\\n\", Rd_tag = \"RCODE\"), \n structure(\"tr2 <- read.tree(text=\\\"((A:1,B:1):1,(C:1,(D:1,E:1):1):1):1;\\\")\\n\", Rd_tag = \"RCODE\"), \n structure(\"tipDiff(tr1,tr2)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## example on larger woodmice trees\\n\", Rd_tag = \"RCODE\"), \n structure(\"data(woodmiceTrees)\\n\", Rd_tag = \"RCODE\"), \n structure(\"tipDiff(woodmiceTrees[[1]],woodmiceTrees[[2]])\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/tipDiff.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/tipDiff.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n treeDist (list) = structure(list(structure(list(structure(\"Metric function\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"treeDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"treeDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Comparison of two trees using the Kendall Colijn metric\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"treeDist(tree.a, tree.b, lambda = 0, return.lambda.function = FALSE,\\n\", Rd_tag = \"RCODE\"), \n@@ -817,15 +817,15 @@\n structure(\"dist.func <- treeDist(tree.a,tree.b,return.lambda.function=TRUE) # distance as a function of lambda\\n\", Rd_tag = \"RCODE\"), \n structure(\"dist.func(0) # evaluate at lambda=0. Equivalent to treeDist(tree.a,tree.b).\\n\", Rd_tag = \"RCODE\"), \n structure(\"## We can see how the distance changes when moving from focusing on topology to length:\\n\", Rd_tag = \"RCODE\"), \n structure(\"plot(sapply(seq(0,1,length.out=100), function(x) dist.func(x)), type=\\\"l\\\",ylab=\\\"\\\",xlab=\\\"\\\")\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## The distance may also change if we emphasise the position of certain tips:\\n\", Rd_tag = \"RCODE\"), \n structure(\"plot(sapply(tree.a$tip.label, function(x) treeDist(tree.a,tree.b,emphasise.tips=x)),\\n\", Rd_tag = \"RCODE\"), \n structure(\" xlab=\\\"Tip number\\\",ylab=\\\"Distance when vector entries corresponding to tip are doubled\\\")\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treeDist.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treeDist.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n treeVec (list) = structure(list(structure(list(structure(\"Tree vector function\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"treeVec\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"treeVec\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Function which takes an object of class phylo and outputs the vector for the Kendall Colijn metric.\\n\", Rd_tag = \"TEXT\"), \n structure(\"The elements of the vector are numeric if \", Rd_tag = \"TEXT\"), \n@@ -866,15 +866,15 @@\n structure(\"## generate a random tree\\n\", Rd_tag = \"RCODE\"), \n structure(\"tree <- rtree(6)\\n\", Rd_tag = \"RCODE\"), structure(\"## topological vector of mrca distances from root:\\n\", Rd_tag = \"RCODE\"), \n structure(\"treeVec(tree)\\n\", Rd_tag = \"RCODE\"), structure(\"## vector of mrca distances from root when lambda=0.5:\\n\", Rd_tag = \"RCODE\"), \n structure(\"treeVec(tree,0.5)\\n\", Rd_tag = \"RCODE\"), structure(\"## vector of mrca distances as a function of lambda:\\n\", Rd_tag = \"RCODE\"), \n structure(\"vecAsFunction <- treeVec(tree,return.lambda.function=TRUE)\\n\", Rd_tag = \"RCODE\"), \n structure(\"## evaluate the vector at lambda=0.5:\\n\", Rd_tag = \"RCODE\"), \n structure(\"vecAsFunction(0.5)\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treeVec.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treeVec.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n treescape (list) = structure(list(structure(list(structure(\"Phylogenetic tree exploration\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"treescape\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"treescape\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Compares phylogenetic trees and maps them into a small number of dimensions for easy visualisation and identification of clusters.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"treescape(x, method = \\\"treeVec\\\", nf = NULL, return.tree.vectors = FALSE,\\n\", Rd_tag = \"RCODE\"), \n@@ -979,15 +979,15 @@\n structure(\"xlab(\\\"\\\") + ylab(\\\"\\\") + theme_bw(base_family=\\\"\\\") # remove axis labels and grey background\\n\", Rd_tag = \"RCODE\"), \n structure(\"}\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(list(structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"if(require(rgl)){\\n\", Rd_tag = \"VERB\"), \n structure(\"plot3d(woodmicedf[,1], woodmicedf[,2], woodmicedf[,3], type=\\\"s\\\", size=1.5,\\n\", Rd_tag = \"VERB\"), \n structure(\"col=\\\"navy\\\", alpha=0.5, xlab=\\\"\\\", ylab=\\\"\\\", zlab=\\\"\\\")\\n\", Rd_tag = \"VERB\"), \n structure(\"}\\n\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\dontrun\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treescape.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treescape.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n treescapeServer (list) = structure(list(structure(list(structure(\"Web-based tree explorer\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"treescapeServer\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"treescapeServer\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"This function opens up an application in a web browser for an interactive exploration of the diversity in a set of trees.\\n\", Rd_tag = \"TEXT\"), \n structure(\"For further details please see the \\\"help\\\" tab within the application.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n@@ -999,15 +999,15 @@\n structure(\"michelle.louise.kendall@gmail.com\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\email\"), \n structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"For convenience, \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"treescapeServer\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\"), \n structure(\" is also available as a separate web app which can be used from any browser (it is not necessary to have \", Rd_tag = \"TEXT\"), \n structure(list(), Rd_tag = \"\\\\R\"), structure(\" installed): \", Rd_tag = \"TEXT\"), \n structure(list(structure(list(structure(\"http://shiny.imperial-stats-experimental.co.uk/users/mlkendal/treescape/\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\url\")), Rd_tag = \"LIST\"), \n- structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\seealso\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treescapeServer.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\seealso\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treescapeServer.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n wiwMedTree (list) = structure(list(structure(list(structure(\"Median transmission tree\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"wiwMedTree\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"wiwMedTree\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Function to find the median of a list of transmission scenarios\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"wiwMedTree(matList, sampled = NULL, weights = NULL)\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\usage\"), \n@@ -1050,15 +1050,15 @@\n structure(\"tree3 <- cbind(Infector=c(2,2,3,4,5),Infectee=c(1,3,4,5,6)) \\n\", Rd_tag = \"RCODE\"), \n structure(\"# create list of the MRCI depth matrices:\\n\", Rd_tag = \"RCODE\"), \n structure(\"matList <- lapply(list(tree1,tree2,tree3), function(x) findMRCIs(x)$mrciDepths)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"# median tree, assuming all cases are sampled:\\n\", Rd_tag = \"RCODE\"), \n structure(\"wiwMedTree(matList)\\n\", Rd_tag = \"RCODE\"), \n structure(\"# median tree when cases 1, 2 and 4 are sampled:\\n\", Rd_tag = \"RCODE\"), \n structure(\"wiwMedTree(matList, sampled=c(1,2,4))\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/wiwMedTree.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/wiwMedTree.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n wiwTreeDist (list) = structure(list(structure(list(structure(\"Transmission tree distance\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"wiwTreeDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"wiwTreeDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Function to find the distance between transmission trees by comparing their MRCI depth matrices; to be precise, by finding the Euclidean distance between the tree vectors, restricted to their sampled node entries.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"wiwTreeDist(matList, sampled = NULL)\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\usage\"), \n@@ -1081,15 +1081,15 @@\n structure(\"tree3 <- cbind(Infector=c(2,2,3,4,5),Infectee=c(1,3,4,5,6)) \\n\", Rd_tag = \"RCODE\"), \n structure(\"# create list of the MRCI depth matrices:\\n\", Rd_tag = \"RCODE\"), \n structure(\"matList <- lapply(list(tree1,tree2,tree3), function(x) findMRCIs(x)$mrciDepths)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"# transmission tree distance, assuming all cases are sampled:\\n\", Rd_tag = \"RCODE\"), \n structure(\"wiwTreeDist(matList)\\n\", Rd_tag = \"RCODE\"), \n structure(\"# transmission tree distance when cases 1, 2 and 4 are sampled:\\n\", Rd_tag = \"RCODE\"), \n structure(\"wiwTreeDist(matList, sampled=c(1,2,4))\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/wiwTreeDist.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/wiwTreeDist.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n woodmiceTrees (list) = structure(list(structure(list(structure(\"Bootstrap trees from woodmouse dataset\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"woodmiceTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"woodmiceTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"datasets\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\keyword\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"These trees were created using the neighbour-joining and bootstrapping\\n\", Rd_tag = \"TEXT\"), \n@@ -1102,10 +1102,10 @@\n structure(\"woodmouse (Apodemus sylvaticus) which is a subset of the data analysed by\\n\", Rd_tag = \"TEXT\"), \n structure(\"Michaux et al. (2003). The full data set is available through GenBank\\n\", Rd_tag = \"TEXT\"), \n structure(\"(accession numbers AJ511877 to AJ511987)\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\source\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Michaux, J. R., Magnanou, E., Paradis, E., Nieberding, C. and\\n\", Rd_tag = \"TEXT\"), \n structure(\"Libois, R. (2003) Mitochondrial phylogeography of the Woodmouse (Apodemus\\n\", Rd_tag = \"TEXT\"), \n structure(\"sylvaticus) in the Western Palearctic region. \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"Molecular Ecology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n- structure(\", 12,\\n\", Rd_tag = \"TEXT\"), structure(\"685-697\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/woodmiceTrees.Rd\", class = \"Rd\", meta = list(\n+ structure(\", 12,\\n\", Rd_tag = \"TEXT\"), structure(\"685-697\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/woodmiceTrees.Rd\", class = \"Rd\", meta = list(\n docType = \"data\"), prepared = 3L)\n \n"}]}, {"source1": "./usr/lib/R/site-library/treescape/help/treescape.rdx", "source2": "./usr/lib/R/site-library/treescape/help/treescape.rdx", "unified_diff": null, "details": [{"source1": "treescape.rdx-content", "source2": "treescape.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": "@@ -1,133 +1,133 @@\n $variables\n $variables$DengueBEASTMCC\n-[1] 292 1207\n+[1] 294 1208\n \n $variables$DengueSeqs\n-[1] 1786 1015\n+[1] 1791 1018\n \n $variables$DengueTrees\n-[1] 3087 1619\n+[1] 3097 1622\n \n $variables$findGroves\n-[1] 4992 2583\n+[1] 5007 2586\n \n $variables$findMRCIs\n-[1] 7861 1528\n+[1] 7881 1531\n \n $variables$fluTrees\n-[1] 9673 1036\n+[1] 9698 1037\n \n $variables$linearMrca\n-[1] 10995 1197\n+[1] 11023 1200\n \n $variables$medTree\n-[1] 12475 3698\n+[1] 12508 3701\n \n $variables$multiDist\n-[1] 16458 2553\n+[1] 16496 2556\n \n $variables$plotGroves\n-[1] 19298 3447\n+[1] 19340 3449\n \n $variables$plotGrovesD3\n-[1] 23034 2822\n+[1] 23080 2823\n \n $variables$plotTreeDiff\n-[1] 26144 3963\n+[1] 26192 3965\n \n $variables$refTreeDist\n-[1] 30394 2192\n+[1] 30445 2194\n \n $variables$tipDiff\n-[1] 32870 1874\n+[1] 32924 1875\n \n $variables$treeDist\n-[1] 35027 2356\n+[1] 35084 2358\n \n $variables$treeVec\n-[1] 37666 2135\n+[1] 37726 2137\n \n $variables$treescape\n-[1] 40082 3623\n+[1] 40146 3624\n \n $variables$treescapeServer\n-[1] 43990 1153\n+[1] 44056 1156\n \n $variables$wiwMedTree\n-[1] 45430 1962\n+[1] 45501 1964\n \n $variables$wiwTreeDist\n-[1] 47678 1548\n+[1] 47754 1549\n \n $variables$woodmiceTrees\n-[1] 49514 1259\n+[1] 49592 1261\n \n \n $references\n $references$`env::1`\n-[1] 0 292\n+[1] 0 294\n \n $references$`env::10`\n-[1] 19011 287\n+[1] 19052 288\n \n $references$`env::11`\n-[1] 22745 289\n+[1] 22789 291\n \n $references$`env::12`\n-[1] 25856 288\n+[1] 25903 289\n \n $references$`env::13`\n-[1] 30107 287\n+[1] 30157 288\n \n $references$`env::14`\n-[1] 32586 284\n+[1] 32639 285\n \n $references$`env::15`\n-[1] 34744 283\n+[1] 34799 285\n \n $references$`env::16`\n-[1] 37383 283\n+[1] 37442 284\n \n $references$`env::17`\n-[1] 39801 281\n+[1] 39863 283\n \n $references$`env::18`\n-[1] 43705 285\n+[1] 43770 286\n \n $references$`env::19`\n-[1] 45143 287\n+[1] 45212 289\n \n $references$`env::2`\n-[1] 1499 287\n+[1] 1502 289\n \n $references$`env::20`\n-[1] 47392 286\n+[1] 47465 289\n \n $references$`env::21`\n-[1] 49226 288\n+[1] 49303 289\n \n $references$`env::3`\n-[1] 2801 286\n+[1] 2809 288\n \n $references$`env::4`\n-[1] 4706 286\n+[1] 4719 288\n \n $references$`env::5`\n-[1] 7575 286\n+[1] 7593 288\n \n $references$`env::6`\n-[1] 9389 284\n+[1] 9412 286\n \n $references$`env::7`\n-[1] 10709 286\n+[1] 10735 288\n \n $references$`env::8`\n-[1] 12192 283\n+[1] 12223 285\n \n $references$`env::9`\n-[1] 16173 285\n+[1] 16209 287\n \n \n $compressed\n [1] TRUE\n \n"}]}]}, {"source1": "./usr/lib/R/site-library/treescape/libs/treescape.so", "source2": "./usr/lib/R/site-library/treescape/libs/treescape.so", "comments": ["File has been modified after NT_GNU_BUILD_ID has been applied."], "unified_diff": null, "details": [{"source1": "readelf --wide --notes {}", "source2": "readelf --wide --notes {}", "unified_diff": "@@ -1,4 +1,4 @@\n \n Displaying notes found in: .note.gnu.build-id\n Owner Data size \tDescription\n- GNU 0x00000014\tNT_GNU_BUILD_ID (unique build ID bitstring)\t Build ID: a23b92ce4057f9223d2e9c402582653b74f8600b\n+ GNU 0x00000014\tNT_GNU_BUILD_ID (unique build ID bitstring)\t Build ID: cd60d39de5d6bdd3bed373c463c0b2e59c20b5b2\n"}, {"source1": "objdump --line-numbers --disassemble --demangle --reloc --no-show-raw-insn --section=.text {}", "source2": "objdump --line-numbers --disassemble --demangle --reloc --no-show-raw-insn --section=.text {}", "unified_diff": "@@ -30,31 +30,31 @@\n \tmov\tx19, x1\n \tbl\t5020 <__cxa_free_exception@plt>\n \tmov\tx0, x19\n \tbl\t5390 <_Unwind_Resume@plt>\n \tnop\n \tnop\n _GLOBAL__sub_I_CPP_update_combinations.cpp():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:31\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:31\n \tstp\tx29, x30, [sp, #-80]!\n \tmov\tx29, sp\n \tstp\tx19, x20, [sp, #16]\n /usr/include/c++/12/iostream:74\n \tadrp\tx20, 20000 \n \tadd\tx19, x20, #0x3e0\n \tmov\tx0, x19\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:31\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:31\n \tstp\tx21, x22, [sp, #32]\n /usr/include/c++/12/iostream:74\n \tadrp\tx22, 20000 \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:31\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:31\n \tstp\tx23, x24, [sp, #48]\n /usr/include/c++/12/bits/basic_ios.h:462\n \tadd\tx23, x19, #0x58\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:31\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:31\n \tstr\tx25, [sp, #64]\n /usr/include/c++/12/iostream:74\n \tbl\t52c0 \n \tadrp\tx0, 1f000 \n \tldr\tx0, [x0, #4064]\n \tmov\tx1, x19\n \tadd\tx2, x22, #0x3a0\n@@ -177,23 +177,23 @@\n \tadd\tx3, x3, #0x10\n /usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:90\n \tmov\tx2, x22\n /usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:34\n \tstr\tx3, [x20, #360]\n /usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:90\n \tbl\t5180 <__cxa_atexit@plt>\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:31\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:31\n \tldp\tx23, x24, [sp, #48]\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tmov\tx2, x22\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:31\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:31\n \tldp\tx21, x22, [sp, #32]\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tadd\tx1, x20, #0x2b0\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:31\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:31\n \tldp\tx19, x20, [sp, #16]\n \tldr\tx25, [sp, #64]\n \tldp\tx29, x30, [sp], #80\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tadrp\tx0, 1f000 \n \tldr\tx0, [x0, #3960]\n \tb\t5180 <__cxa_atexit@plt>\n@@ -216,35 +216,35 @@\n \tadd\tx1, x1, #0x10\n \tstr\tx1, [x20, #424]\n \tbl\t4e60 \n \tmov\tx0, x19\n \tbl\t5390 <_Unwind_Resume@plt>\n \tnop\n _GLOBAL__sub_I_RcppExports.cpp():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:23\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:23\n \tstp\tx29, x30, [sp, #-80]!\n \tmov\tx29, sp\n \tstp\tx19, x20, [sp, #16]\n /usr/include/c++/12/iostream:74\n \tadrp\tx19, 20000 \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:23\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:23\n \tstp\tx21, x22, [sp, #32]\n __static_initialization_and_destruction_0():\n /usr/include/c++/12/iostream:74\n \tadd\tx21, x19, #0x6a0\n \tadd\tx20, x21, #0x38\n \tmov\tx0, x20\n _GLOBAL__sub_I_RcppExports.cpp():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:23\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:23\n \tstp\tx23, x24, [sp, #48]\n __static_initialization_and_destruction_0():\n /usr/include/c++/12/iostream:74\n \tadrp\tx22, 20000 \n _GLOBAL__sub_I_RcppExports.cpp():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:23\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:23\n \tstr\tx25, [sp, #64]\n __static_initialization_and_destruction_0():\n /usr/include/c++/12/iostream:74\n \tbl\t52c0 \n \tadrp\tx0, 1f000 \n \tldr\tx0, [x0, #4064]\n \tmov\tx1, x20\n@@ -411,27 +411,27 @@\n Rcpp::Rstreambuf::Rstreambuf():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:34\n \tstr\tx3, [x19, #408]\n __static_initialization_and_destruction_0():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:90\n \tbl\t5180 <__cxa_atexit@plt>\n _GLOBAL__sub_I_RcppExports.cpp():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:23\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:23\n \tldp\tx23, x24, [sp, #48]\n __static_initialization_and_destruction_0():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tmov\tx2, x22\n _GLOBAL__sub_I_RcppExports.cpp():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:23\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:23\n \tldp\tx21, x22, [sp, #32]\n __static_initialization_and_destruction_0():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tadd\tx1, x19, #0x2e0\n _GLOBAL__sub_I_RcppExports.cpp():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:23\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:23\n \tldp\tx19, x20, [sp, #16]\n \tldr\tx25, [sp, #64]\n \tldp\tx29, x30, [sp], #80\n __static_initialization_and_destruction_0():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tadrp\tx0, 1f000 \n \tldr\tx0, [x0, #3960]\n@@ -522,104 +522,104 @@\n \tb\t5920 , std::allocator > const&)@@Base+0x4b0>\n \tnop\n \tnop\n \tnop\n \n 00000000000059c0 &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@@Base>:\n updateDistancesWithCombinations(Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int):\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:13\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:13\n \tstp\tx29, x30, [sp, #-96]!\n \tmov\tx29, sp\n \tstp\tx19, x20, [sp, #16]\n \tmov\tx19, x2\n \tstp\tx23, x24, [sp, #48]\n \tmov\tx24, x0\n \tmov\tx23, x1\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/Vector.h:276\n \tldr\tx0, [x19]\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:13\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:13\n \tstr\td8, [sp, #88]\n \tfmov\td8, d0\n \tstp\tx21, x22, [sp, #32]\n \tmov\tx22, x4\n \tmov\tw21, w5\n \tstp\tx25, x26, [sp, #64]\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:15\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:15\n \tmov\tx25, #0x0 \t// #0\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:13\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:13\n \tstr\tx27, [sp, #80]\n \tmov\tx27, x3\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/Vector.h:276\n \tbl\t51b0 \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:15\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:15\n \tcmp\tx0, x25\n \tb.le\t5a90 &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@@Base+0xd0>\n \tlsl\tx20, x25, #2\n \tmov\tx26, #0x0 \t// #0\n \tb\t5a6c &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@@Base+0xac>\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:18\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:18\n \tldr\tx1, [x27, #16]\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:28\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:28\n \tscvtf\td1, w21\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:17\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:17\n \tldr\tx0, [x19, #16]\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:18\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:18\n \tldr\tw6, [x1, x26, lsl #2]\n \tadd\tx26, x26, #0x1\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:25\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:25\n \tldr\tx3, [x22, #16]\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:17\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:17\n \tldr\tw0, [x0, x20]\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:27\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:27\n \tldr\tx2, [x24, #16]\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:20\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:20\n \tcmp\tw0, w6\n \tcsel\tw1, w0, w6, le\n \tcsel\tw6, w6, w0, le\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:25\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:25\n \tsub\tw4, w1, #0x1\n \tsub\tw6, w6, w1\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:28\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:28\n \tldr\tx0, [x23, #16]\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:25\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:25\n \tldr\tw1, [x3, w4, sxtw #2]\n \tadd\tw6, w6, w1\n \tsub\tw6, w6, #0x1\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/traits.h:46\n \tsxtw\tx6, w6\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:27\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:27\n \tstr\td8, [x2, x6, lsl #3]\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:28\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:28\n \tstr\td1, [x0, x6, lsl #3]\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/Vector.h:276 (discriminator 1)\n \tldr\tx0, [x27]\n \tbl\t51b0 \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:16 (discriminator 1)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:16 (discriminator 1)\n \tcmp\tx0, x26\n \tb.gt\t5a1c &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@@Base+0x5c>\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/Vector.h:276 (discriminator 2)\n \tldr\tx0, [x19]\n \tadd\tx25, x25, #0x1\n \tbl\t51b0 \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:15 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:15 (discriminator 2)\n \tcmp\tx0, x25\n \tb.gt\t5a10 &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@@Base+0x50>\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:31\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:31\n \tldp\tx19, x20, [sp, #16]\n \tldp\tx21, x22, [sp, #32]\n \tldp\tx23, x24, [sp, #48]\n \tldp\tx25, x26, [sp, #64]\n \tldr\tx27, [sp, #80]\n \tldr\td8, [sp, #88]\n \tldp\tx29, x30, [sp], #96\n \tret\n \n 0000000000005ab0 :\n Rcpp::internal::NamedPlaceHolder::~NamedPlaceHolder():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:53\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:53\n \tret\n \tnop\n \tnop\n \tnop\n \n 0000000000005ac0 ::xsputn(char const*, long)@@Base>:\n Rcpp::Rstreambuf::xsputn(char const*, long):\n@@ -2194,46 +2194,46 @@\n Rcpp::Vector<13, Rcpp::PreserveStorage>::Vector(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/Vector.h:74\n \tmov\tx19, x0\n \tb\t6b1c ::~Rostream()@@Base+0x9ec>\n \n 0000000000006ba0 :\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:10\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:10\n \tstp\tx29, x30, [sp, #-272]!\n \tadrp\tx8, 1f000 \n \tldr\tx8, [x8, #3784]\n \tmov\tx29, sp\n \tstp\tx19, x20, [sp, #16]\n \tmov\tx20, x5\n \tmov\tx19, x6\n \tstp\tx21, x22, [sp, #32]\n \tmov\tx22, x3\n \tmov\tx21, x4\n \tstp\tx23, x24, [sp, #48]\n \tmov\tx24, x1\n \tmov\tx23, x2\n \tstp\tx25, x26, [sp, #64]\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:11\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:11\n \tadrp\tx26, 20000 \n \tadd\tx7, x26, #0x6a0\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:10\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:10\n \tstp\tx27, x28, [sp, #80]\n \tmov\tx25, x0\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:11\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:11\n \tadd\tx0, x7, #0x28\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:10\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:10\n \tstr\td8, [sp, #96]\n \tldr\tx1, [x8]\n \tstr\tx1, [sp, #264]\n \tmov\tx1, #0x0 \t// #0\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:11\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:11\n \tldar\tx1, [x0]\n \ttbnz\tw1, #0, 6c0c \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:11 (discriminator 1)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:11 (discriminator 1)\n \tbl\t53c0 <__cxa_guard_acquire@plt>\n \tcbnz\tw0, 6ef8 \n Rcpp::internal::enterRNGScope():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:93 (discriminator 2)\n \tadrp\tx27, 20000 \n \tadd\tx0, x27, #0x9f8\n \tldar\tx1, [x0]\n@@ -2272,37 +2272,37 @@\n \tbl\t4f30 (SEXPREC*)@plt>\n \tfmov\td8, d0\n int Rcpp::internal::as(SEXPREC*, Rcpp::traits::r_type_primitive_tag):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/as.h:44\n \tmov\tx0, x19\n \tbl\t5100 (SEXPREC*)@plt>\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:20\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:20\n \tfmov\td0, d8\n \tmov\tw5, w0\n \tmov\tx4, x22\n \tmov\tx3, x23\n \tmov\tx2, x24\n \tmov\tx1, x25\n \tmov\tx0, x27\n \tbl\t5240 &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@plt>\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:21\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:21\n \tadrp\tx1, 1f000 \n \tldr\tx1, [x1, #3760]\n Rcpp::Rcpp_precious_remove(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:159\n \tadrp\tx20, 20000 \n Rcpp::PreserveStorage >::~PreserveStorage():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/storage/PreserveStorage.h:34\n \tldr\tx22, [sp, #216]\n Rcpp::Rcpp_precious_remove(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:159\n \tadd\tx0, x20, #0x9c8\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:21\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:21\n \tldr\tx21, [x1]\n Rcpp::Rcpp_precious_remove(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:159\n \tldar\tx1, [x0]\n \tadrp\tx19, 20000 \n \ttbz\tw1, #0, 6e98 \n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:160\n@@ -2368,15 +2368,15 @@\n \tldar\tx1, [x0]\n \tadrp\tx19, 20000 \n \ttbz\tw1, #0, 6da8 \n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:100\n \tldr\tx0, [x19, #2544]\n \tblr\tx0\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:23\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:23\n \tadrp\tx0, 1f000 \n \tldr\tx0, [x0, #3784]\n \tldr\tx2, [sp, #264]\n \tldr\tx1, [x0]\n \tsubs\tx2, x2, x1\n \tmov\tx1, #0x0 \t// #0\n \tb.ne\t6f1c // b.any\n@@ -2476,25 +2476,25 @@\n \tbl\t50c0 \n \tmov\tx1, x0\n \tadd\tx0, x27, #0x9f8\n \tstr\tx1, [x28, #2560]\n \tbl\t4fc0 <__cxa_guard_release@plt>\n \tb\t6c20 \n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:11 (discriminator 3)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:11 (discriminator 3)\n \tadrp\tx0, b000 , std::allocator > tinyformat::format(char const*, char const* const&, char const* const&)@@Base+0x190>\n \tadd\tx0, x0, #0xdb8\n \tbl\t4fd0 \n \tmov\tx2, x0\n \tadd\tx1, x26, #0x6a0\n \tadd\tx0, x1, #0x28\n \tstr\tx2, [x1, #48]\n \tbl\t4fc0 <__cxa_guard_release@plt>\n \tb\t6c0c \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:23\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:23\n \tbl\t4e70 <__stack_chk_fail@plt>\n Rcpp::internal::exitRNGScope():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:99\n \tadd\tx0, x20, #0x9e8\n \tbl\t4fb0 <__cxa_guard_abort@plt>\n treescape_updateDistancesWithCombinations():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/RNGScope.h:30\n@@ -2515,46 +2515,46 @@\n \tmov\tx19, x0\n \tmov\tx20, x1\n \tadd\tx0, x27, #0x9f8\n \tbl\t4fb0 <__cxa_guard_abort@plt>\n \tmov\tx0, x19\n \tmov\tx1, x20\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22\n \tcmp\tx1, #0x4\n \tb.eq\t70ac // b.none\n \tb.gt\t6f84 \n \tcmp\tx1, #0x3\n \tb.eq\t7130 // b.none\n \tcmp\tx1, #0x1\n \tb.eq\t7154 // b.none\n \tcmp\tx1, #0x2\n \tb.eq\t7168 // b.none\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 19)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 19)\n \tbl\t4eb0 <__cxa_begin_catch@plt>\n \tadd\tx20, sp, #0xe8\n \tadrp\tx1, b000 , std::allocator > tinyformat::format(char const*, char const* const&, char const* const&)@@Base+0x190>\n \tmov\tx0, x20\n \tadd\tx1, x1, #0xde0\n \tbl\t6290 ::~Rostream()@@Base+0x160>\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 33)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 33)\n \tmov\tx0, x20\n \tbl\t52f0 , std::allocator > const&)@plt>\n \tbl\t4ff0 \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 35)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 35)\n \tmov\tx19, x0\n std::__cxx11::basic_string, std::allocator >::~basic_string():\n /usr/include/c++/12/bits/basic_string.h:795 (discriminator 35)\n \tmov\tx0, x20\n \tbl\t51e0 , std::allocator >::_M_dispose()@plt>\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 35)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 35)\n \tbl\t5320 <__cxa_end_catch@plt>\n \tb\t70c4 \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:11\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:11\n \tadd\tx26, x26, #0x6a0\n \tmov\tx19, x0\n \tadd\tx0, x26, #0x28\n \tbl\t4fb0 <__cxa_guard_abort@plt>\n \tmov\tx0, x19\n \tbl\t5390 <_Unwind_Resume@plt>\n Rcpp::Rcpp_PreciousRelease(SEXPREC*):\n@@ -2617,82 +2617,82 @@\n Rcpp::internal::exitRNGScope():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:99\n \tmov\tx21, x0\n \tmov\tx22, x1\n \tb\t700c \n \tb\t6f60 \n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 18)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 18)\n \tbl\t4eb0 <__cxa_begin_catch@plt>\n exception_to_r_condition(std::exception const&):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:353 (discriminator 18)\n \tmov\tw1, #0x1 \t// #1\n \tbl\t4da0 (std::exception const&, bool)@plt>\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 18)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 18)\n \tbl\t4ff0 \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22\n \tmov\tx19, x0\n \tbl\t5320 <__cxa_end_catch@plt>\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 9)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 9)\n \tadd\tx26, x26, #0x6a0\n \tmov\tx1, x19\n \tldr\tx0, [x26, #48]\n \tbl\t4d40 \n \tbl\t4ff0 \n \tadrp\tx1, 1f000 \n \tldr\tx1, [x1, #4000]\n \tldr\tx1, [x1]\n \tbl\t5090 \n \tmov\tw0, #0x2 \t// #2\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 14)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 14)\n \tbl\t4ef0 \n \tadrp\tx0, 1f000 \n \tldr\tx0, [x0, #3760]\n \tldr\tx21, [x0]\n \tb\t6d68 \n std::__cxx11::basic_string, std::allocator >::~basic_string():\n /usr/include/c++/12/bits/basic_string.h:795\n \tmov\tx19, x0\n \tmov\tx0, x20\n \tbl\t51e0 , std::allocator >::_M_dispose()@plt>\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 32)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 32)\n \tbl\t5320 <__cxa_end_catch@plt>\n \tmov\tx0, x19\n \tbl\t5390 <_Unwind_Resume@plt>\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22\n \tmov\tx19, x0\n \tb\t710c \n \tmov\tx19, x0\n \tbl\t5320 <__cxa_end_catch@plt>\n \tmov\tx0, x19\n \tbl\t5390 <_Unwind_Resume@plt>\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 17)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 17)\n \tbl\t4eb0 <__cxa_begin_catch@plt>\n \tmov\tx19, x0\n rcpp_exception_to_r_condition(Rcpp::exception const&):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:348 (discriminator 17)\n \tbl\t4dd0 \n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:349\n \tldrb\tw1, [x19, #40]\n \tmov\tx0, x19\n \tbl\t5430 (Rcpp::exception const&, bool)@plt>\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22\n \tbl\t4ff0 \n \tb\t70bc \n \tb\t7120 \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 15)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 15)\n \tbl\t4eb0 <__cxa_begin_catch@plt>\n \tbl\t5320 <__cxa_end_catch@plt>\n \tbl\t51d0 \n \tmov\tw0, #0x0 \t// #0\n \tb\t70ec \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 16)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 16)\n \tbl\t4eb0 <__cxa_begin_catch@plt>\n \tldr\tx19, [x0]\n \tbl\t5320 <__cxa_end_catch@plt>\n Rcpp::internal::isLongjumpSentinel(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:139 (discriminator 16)\n \tadrp\tx1, b000 , std::allocator > tinyformat::format(char const*, char const* const&, char const* const&)@@Base+0x190>\n \tadd\tx1, x1, #0xe20\n@@ -2727,15 +2727,15 @@\n \tbl\t4f10 \n treescape_updateDistancesWithCombinations():\n \tnop\n \tnop\n \n 00000000000071d0 ::do_widen(char) const@@Base>:\n std::ctype::do_widen(char) const:\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:1093\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:1093\n \tmov\tw0, w1\n \tret\n \tnop\n \tnop\n \n 00000000000071e0 :\n Rcpp::exception::what() const:\n"}, {"source1": "readelf --wide --decompress --hex-dump=.gnu_debuglink {}", "source2": "readelf --wide --decompress --hex-dump=.gnu_debuglink {}", "comments": ["error from `readelf --wide --decompress --hex-dump=.gnu_debuglink {}`:", "readelf: Error: no .dynamic section in the dynamic segment"], "unified_diff": "@@ -1,7 +1,7 @@\n \n Hex dump of section '.gnu_debuglink':\n- 0x00000000 33623932 63653430 35376639 32323364 3b92ce4057f9223d\n- 0x00000010 32653963 34303235 38323635 33623734 2e9c402582653b74\n- 0x00000020 66383630 30622e64 65627567 00000000 f8600b.debug....\n- 0x00000030 74b11be8 t...\n+ 0x00000000 36306433 39646535 64366264 64336265 60d39de5d6bdd3be\n+ 0x00000010 64333733 63343633 63306232 65353963 d373c463c0b2e59c\n+ 0x00000020 32306235 62322e64 65627567 00000000 20b5b2.debug....\n+ 0x00000030 a3e2d980 ....\n \n"}]}]}]}]}, {"source1": "r-cran-treescape-dbgsym_1.10.18+dfsg-2_arm64.deb", "source2": "r-cran-treescape-dbgsym_1.10.18+dfsg-2_arm64.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 2020-05-22 06:51:07.000000 debian-binary\n--rw-r--r-- 0 0 0 544 2020-05-22 06:51:07.000000 control.tar.xz\n--rw-r--r-- 0 0 0 233140 2020-05-22 06:51:07.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 548 2020-05-22 06:51:07.000000 control.tar.xz\n+-rw-r--r-- 0 0 0 233148 2020-05-22 06:51:07.000000 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": "./control", "source2": "./control", "unified_diff": "@@ -5,8 +5,8 @@\n Architecture: arm64\n Maintainer: Debian R Packages Maintainers \n Installed-Size: 255\n Depends: r-cran-treescape (= 1.10.18+dfsg-2)\n Section: debug\n Priority: optional\n Description: debug symbols for r-cran-treescape\n-Build-Ids: a23b92ce4057f9223d2e9c402582653b74f8600b\n+Build-Ids: cd60d39de5d6bdd3bed373c463c0b2e59c20b5b2\n"}, {"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": 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169\t(udata)\t0\t(line_strp)\t(offset: 0x8c3): \n \n Line Number Statements:\n [0x0000100f] Set column to 7\n [0x00001011] Extended opcode 2: set Address to 0x71d0\n [0x0000101c] Advance Line by 1091 to 1092\n [0x0000101f] Copy\n [0x00001020] Set column to 9\n"}, {"source1": "readelf --wide --debug-dump=info {}", "source2": "readelf --wide --debug-dump=info {}", "unified_diff": "@@ -4,15 +4,15 @@\n Length: 0x6d63 (32-bit)\n Version: 5\n Unit Type: DW_UT_partial (3)\n Abbrev Offset: 0\n Pointer Size: 8\n <0>: Abbrev Number: 71 (DW_TAG_partial_unit)\n DW_AT_stmt_list : (sec_offset) 0\n- <11> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/1st/r-cran-treescape-1.10.18+dfsg/src\n+ <11> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/2/r-cran-treescape-1.10.18+dfsg/2nd/src\n <1><15>: Abbrev Number: 24 (DW_TAG_base_type)\n <16> DW_AT_byte_size : (data1) 8\n <17> DW_AT_encoding : (data1) 4\t(float)\n <18> DW_AT_name : (strp) (offset: 0x1348f): double\n <1><1c>: Abbrev Number: 9 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DW_AT_name : (strp) (offset: 0x1348f): double\n@@ -48921,16 +48921,16 @@\n Version: 5\n Unit Type: DW_UT_compile (1)\n Abbrev Offset: 0x16b3\n Pointer Size: 8\n <0><126ef>: Abbrev Number: 276 (DW_TAG_compile_unit)\n <126f1> DW_AT_producer : (strp) (offset: 0x22f14): GNU C++17 12.2.0 -mlittle-endian -mabi=lp64 -g -O2 -std=gnu++17 -fPIC -fstack-protector-strong -fasynchronous-unwind-tables\n <126f5> DW_AT_language : (data1) 33\t(C++14)\n- <126f6> DW_AT_name : (line_strp) (offset: 0x9d9): RcppExports.cpp\n- <126fa> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/1st/r-cran-treescape-1.10.18+dfsg/src\n+ <126f6> DW_AT_name : (line_strp) (offset: 0x9db): RcppExports.cpp\n+ <126fa> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/2/r-cran-treescape-1.10.18+dfsg/2nd/src\n <126fe> DW_AT_ranges : (sec_offset) 0x484b\n <12702> DW_AT_low_pc : (addr) 0\n <1270a> DW_AT_stmt_list : (sec_offset) 0xc18\n <1><1270e>: Abbrev Number: 1 (DW_TAG_base_type)\n <1270f> DW_AT_byte_size : (data1) 8\n 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c41] wrap_type_traits.h\n+ [ c54] enable_if.h\n+ [ c60] Interrupt.h\n+ [ c6c] execinfo.h\n+ [ c77] GraphicsDevice.h\n \n"}]}]}]}]}]}