{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.RPLzerDz/b1/r-cran-treescape_1.10.18+dfsg-2_i386.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.RPLzerDz/b2/r-cran-treescape_1.10.18+dfsg-2_i386.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,3 +1,3 @@\n \n- e6e86935103f530ccf5a7490cc6d20df 224800 debug optional r-cran-treescape-dbgsym_1.10.18+dfsg-2_i386.deb\n- 9ed6b022c9f8a30985cc29ac751484a7 1118352 gnu-r optional r-cran-treescape_1.10.18+dfsg-2_i386.deb\n+ 3f84167a25564bb73adab508a0ca28e2 224804 debug optional r-cran-treescape-dbgsym_1.10.18+dfsg-2_i386.deb\n+ e61f5c083d90b23757a006df0b478935 1118592 gnu-r optional r-cran-treescape_1.10.18+dfsg-2_i386.deb\n"}, {"source1": "r-cran-treescape_1.10.18+dfsg-2_i386.deb", "source2": "r-cran-treescape_1.10.18+dfsg-2_i386.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 2112 2020-05-22 06:51:07.000000 control.tar.xz\n--rw-r--r-- 0 0 0 1116048 2020-05-22 06:51:07.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 1116288 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": "@@ -14,16 +14,16 @@\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) 1452 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) 51527 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+-rw-r--r-- 0 root (0) root (0) 51529 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) 544 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) 850400 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) 143 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) 234 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 -rw-r--r-- 0 root (0) root (0) 12557 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/DengueVignette.Rmd\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) 255 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) 317 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) 51021 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+-rw-r--r-- 0 root (0) root (0) 319 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) 51103 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) 623 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) 1735 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) 67408 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": "@@ -266,15 +266,15 @@\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\" = \"<environment>\"\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] 5679 62\n+[1] 5681 62\n \n $variables$.__S3MethodsTable__.\n-[1] 5881 62\n+[1] 5883 62\n \n $variables$.packageName\n-[1] 5943 63\n+[1] 5945 63\n \n $variables$.render.server.info\n-[1] 6006 748\n+[1] 6008 748\n \n $variables$findGroves\n-[1] 6754 2316\n+[1] 6756 2316\n \n $variables$findMRCIs\n-[1] 9070 4201\n+[1] 9072 4201\n \n $variables$linearMrca\n-[1] 13271 2107\n+[1] 13273 2107\n \n $variables$medTree\n-[1] 15378 5407\n+[1] 15380 5407\n \n $variables$multiDist\n-[1] 20785 3463\n+[1] 20787 3463\n \n $variables$plotGroves\n-[1] 24248 3456\n+[1] 24250 3456\n \n $variables$plotGrovesD3\n-[1] 27704 1125\n+[1] 27706 1125\n \n $variables$plotTreeDiff\n-[1] 28829 2664\n+[1] 28831 2664\n \n $variables$refTreeDist\n-[1] 31493 2683\n+[1] 31495 2683\n \n $variables$tipDiff\n-[1] 34176 2384\n+[1] 34178 2384\n \n $variables$treeDist\n-[1] 36560 1247\n+[1] 36562 1247\n \n $variables$treeVec\n-[1] 37807 6966\n+[1] 37809 6966\n \n $variables$treescape\n-[1] 44773 3771\n+[1] 44775 3771\n \n $variables$treescapeServer\n-[1] 48544 331\n+[1] 48546 331\n \n $variables$updateDistancesWithCombinations\n-[1] 48875 439\n+[1] 48877 439\n \n $variables$wiwMedTree\n-[1] 49314 1385\n+[1] 49316 1385\n \n $variables$wiwTreeDist\n-[1] 50699 828\n+[1] 50701 828\n \n \n $references\n $references$`env::1`\n-[1] 311 5368\n+[1] 311 5370\n \n $references$`env::2`\n [1] 0 140\n \n $references$`env::3`\n [1] 140 171\n \n $references$`env::4`\n-[1] 5741 140\n+[1] 5743 140\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] 304 1208\n+[1] 305 1208\n \n $variables$DengueSeqs\n-[1] 1810 1016\n+[1] 1813 1019\n \n $variables$DengueTrees\n-[1] 3124 1619\n+[1] 3132 1623\n \n $variables$findGroves\n-[1] 5042 2584\n+[1] 5056 2586\n \n $variables$findMRCIs\n-[1] 7925 1528\n+[1] 7943 1530\n \n $variables$fluTrees\n-[1] 9748 1036\n+[1] 9770 1037\n \n $variables$linearMrca\n-[1] 11082 1197\n+[1] 11107 1200\n \n $variables$medTree\n-[1] 12574 3699\n+[1] 12603 3700\n \n $variables$multiDist\n-[1] 16569 2553\n+[1] 16602 2556\n \n $variables$plotGroves\n-[1] 19420 3447\n+[1] 19458 3449\n \n $variables$plotGrovesD3\n-[1] 23168 2821\n+[1] 23210 2823\n \n $variables$plotTreeDiff\n-[1] 26289 3964\n+[1] 26334 3966\n \n $variables$refTreeDist\n-[1] 30552 2191\n+[1] 30601 2193\n \n $variables$tipDiff\n-[1] 33038 1874\n+[1] 33091 1875\n \n $variables$treeDist\n-[1] 35207 2354\n+[1] 35263 2357\n \n $variables$treeVec\n-[1] 37855 2133\n+[1] 37916 2136\n \n $variables$treescape\n-[1] 40281 3622\n+[1] 40347 3624\n \n $variables$treescapeServer\n-[1] 44200 1153\n+[1] 44269 1156\n \n $variables$wiwMedTree\n-[1] 45652 1962\n+[1] 45726 1964\n \n $variables$wiwTreeDist\n-[1] 47913 1549\n+[1] 47991 1550\n \n $variables$woodmiceTrees\n-[1] 49762 1259\n+[1] 49842 1261\n \n \n $references\n $references$`env::1`\n-[1] 0 304\n+[1] 0 305\n \n $references$`env::10`\n-[1] 19122 298\n+[1] 19158 300\n \n $references$`env::11`\n-[1] 22867 301\n+[1] 22907 303\n \n $references$`env::12`\n-[1] 25989 300\n+[1] 26033 301\n \n $references$`env::13`\n-[1] 30253 299\n+[1] 30300 301\n \n $references$`env::14`\n-[1] 32743 295\n+[1] 32794 297\n \n $references$`env::15`\n-[1] 34912 295\n+[1] 34966 297\n \n $references$`env::16`\n-[1] 37561 294\n+[1] 37620 296\n \n $references$`env::17`\n-[1] 39988 293\n+[1] 40052 295\n \n $references$`env::18`\n-[1] 43903 297\n+[1] 43971 298\n \n $references$`env::19`\n-[1] 45353 299\n+[1] 45425 301\n \n $references$`env::2`\n-[1] 1512 298\n+[1] 1513 300\n \n $references$`env::20`\n-[1] 47614 299\n+[1] 47690 301\n \n $references$`env::21`\n-[1] 49462 300\n+[1] 49541 301\n \n $references$`env::3`\n-[1] 2826 298\n+[1] 2832 300\n \n $references$`env::4`\n-[1] 4743 299\n+[1] 4755 301\n \n $references$`env::5`\n-[1] 7626 299\n+[1] 7642 301\n \n $references$`env::6`\n-[1] 9453 295\n+[1] 9473 297\n \n $references$`env::7`\n-[1] 10784 298\n+[1] 10807 300\n \n $references$`env::8`\n-[1] 12279 295\n+[1] 12307 296\n \n $references$`env::9`\n-[1] 16273 296\n+[1] 16303 299\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: cb2b0be3ea0f581e758ac0c4cf828df06f3f10eb\n+ GNU 0x00000014\tNT_GNU_BUILD_ID (unique build ID bitstring)\t Build ID: a7486f5f6fd57c04a23173ac9517f3f2b984982c\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": "@@ -284,53 +284,53 @@\n \tsub $0xc,%esp\n \tpush -0x94(%ebp)\n \tmov %edi,%ebx\n \tcall 4250 <__cxa_guard_abort@plt>\n \tmov -0x7c(%ebp),%eax\n \tadd $0x10,%esp\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 $0x4,%eax\n \tje 4a8d <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x385>\n \tjg 4985 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x27d>\n \tcmp $0x3,%eax\n \tje 4b14 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x40c>\n \tcmp $0x1,%eax\n \tje 4b8b <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x483>\n \tcmp $0x2,%eax\n \tje 4baa <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x4a2>\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 \tsub $0xc,%esp\n \tmov %edi,%ebx\n \tpush %esi\n \tcall 4150 <__cxa_begin_catch@plt>\n \tlea -0x34(%ebp),%eax\n \tadd $0x10,%esp\n \tlea -0x3f50(%edi),%edx\n \tmov %eax,-0x7c(%ebp)\n \tcall 5a50 <virtual thunk to Rcpp::Rostream<false>::~Rostream()@@Base+0x130>\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 \tsub $0xc,%esp\n \tpush -0x7c(%ebp)\n \tcall 4540 <string_to_try_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@plt>\n \tmov %eax,(%esp)\n \tcall 4280 <Rf_protect@plt>\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 %eax,%esi\n \tpop %eax\n std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string():\n /usr/include/c++/12/bits/basic_string.h:795 (discriminator 35)\n \tpush -0x7c(%ebp)\n \tcall 4440 <std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_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 \tadd $0x10,%esp\n \tcall 4580 <__cxa_end_catch@plt>\n \tjmp 4ab4 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x3ac>\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:11 (discriminator 4)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:11 (discriminator 4)\n \tsub $0xc,%esp\n \tpush -0x94(%ebp)\n \tmov %edi,%ebx\n \tcall 4250 <__cxa_guard_abort@plt>\n \tmov %esi,(%esp)\n \tcall 4600 <_Unwind_Resume@plt>\n Rcpp::Rcpp_PreciousRelease(SEXPREC*):\n@@ -383,35 +383,35 @@\n \tadd $0x10,%esp\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:100\n \tcall *0x5a4(%edi)\n \tmov -0x7c(%ebp),%esi\n \tmov -0x80(%ebp),%eax\n \tjmp 495f <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x257>\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 \tsub $0xc,%esp\n \tmov %edi,%ebx\n \tpush %esi\n \tcall 4150 <__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 \tpop %edx\n \tpop %ecx\n \tpush $0x1\n \tpush %eax\n \tcall 40a0 <SEXPREC* exception_to_condition_template<std::exception>(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 \tmov %eax,(%esp)\n \tcall 4280 <Rf_protect@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 \tadd $0x10,%esp\n \tmov %eax,%esi\n \tcall 4580 <__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 \tpush %eax\n \tmov %edi,%ebx\n \tpush %eax\n \tpush %esi\n \tpush 0x394(%edi)\n \tcall 4040 <Rf_lang2@plt>\n \tmov %eax,(%esp)\n@@ -420,77 +420,77 @@\n \tmov -0x20(%edi),%edx\n \tpop %ecx\n \tpush (%edx)\n \tpush %eax\n \tcall 4340 <Rf_eval@plt>\n \tadd $0x10,%esp\n \tmov $0x2,%eax\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 \tsub $0xc,%esp\n \tmov %edi,%ebx\n \tpush %eax\n \tcall 4190 <Rf_unprotect@plt>\n \tmov -0x90(%edi),%eax\n \tadd $0x10,%esp\n \tmov (%eax),%eax\n \tmov %eax,-0x80(%ebp)\n \tjmp 6620 <treescape_updateDistancesWithCombinations@@Base+0x210>\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 %edi,%ebx\n \tmov %eax,%esi\n \tcall 4580 <__cxa_end_catch@plt>\n \tsub $0xc,%esp\n \tpush %esi\n \tcall 4600 <_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 \tsub $0xc,%esp\n \tmov %edi,%ebx\n \tpush %esi\n \tcall 4150 <__cxa_begin_catch@plt>\n rcpp_exception_to_r_condition(Rcpp::exception const&):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:348 (discriminator 17)\n \tmov %eax,(%esp)\n treescape_updateDistancesWithCombinations():\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 \tmov %eax,%esi\n rcpp_exception_to_r_condition(Rcpp::exception const&):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:348 (discriminator 17)\n \tcall 40c0 <Rcpp::exception::copy_stack_trace_to_r() const@plt>\n \tpop %eax\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:349 (discriminator 17)\n \tmovzbl 0x1c(%esi),%eax\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:348 (discriminator 17)\n \tpop %edx\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:349 (discriminator 17)\n \tpush %eax\n \tpush %esi\n \tcall 4690 <SEXPREC* exception_to_condition_template<Rcpp::exception>(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 \tmov %eax,(%esp)\n \tcall 4280 <Rf_protect@plt>\n \tjmp 4aaa <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x3a2>\n std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string():\n /usr/include/c++/12/bits/basic_string.h:795\n \tsub $0xc,%esp\n \tpush -0x7c(%ebp)\n \tmov %edi,%ebx\n \tmov %eax,%esi\n \tcall 4440 <std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_dispose()@plt>\n std::__new_allocator<char>::~__new_allocator():\n /usr/include/c++/12/bits/new_allocator.h:90\n \tadd $0x10,%esp\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 \tmov %edi,%ebx\n \tcall 4580 <__cxa_end_catch@plt>\n \tsub $0xc,%esp\n \tpush %esi\n \tcall 4600 <_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 %eax,%esi\n \tjmp 4b55 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x44d>\n \tmov %edi,%ebx\n \tmov %eax,%esi\n \tcall 4580 <__cxa_end_catch@plt>\n \tsub $0xc,%esp\n \tpush %esi\n@@ -500,25 +500,25 @@\n \tsub $0xc,%esp\n \tmov %edi,%ebx\n \tpush %esi\n \tcall 4250 <__cxa_guard_abort@plt>\n treescape_updateDistancesWithCombinations():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/RNGScope.h:30\n \tcall 40d0 <std::terminate()@plt>\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 \tsub $0xc,%esp\n \tmov %edi,%ebx\n \tpush %esi\n \tcall 4150 <__cxa_begin_catch@plt>\n \tcall 4580 <__cxa_end_catch@plt>\n \tadd $0x10,%esp\n \tcall 4430 <Rf_onintr@plt>\n \txor %eax,%eax\n \tjmp 4ae4 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x3dc>\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 \tsub $0xc,%esp\n \tmov %edi,%ebx\n \tpush %esi\n \tcall 4150 <__cxa_begin_catch@plt>\n \tmov (%eax),%esi\n \tcall 4580 <__cxa_end_catch@plt>\n Rcpp::internal::isLongjumpSentinel(SEXPREC*):\n@@ -589,15 +589,15 @@\n \tadd $0x8,%eax\n \tmov %eax,0x3f0(%esi)\n \tpush -0x1c(%ebp)\n \tcall 4100 <std::ios_base::~ios_base()@plt>\n \tmov %edi,(%esp)\n \tcall 4600 <_Unwind_Resume@plt>\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 \tpush %ebp\n \tmov %esp,%ebp\n \tpush %edi\n \tpush %esi\n \tcall 5995 <virtual thunk to Rcpp::Rostream<false>::~Rostream()@@Base+0x75>\n \tadd $0xc38a,%esi\n \tpush %ebx\n@@ -760,30 +760,30 @@\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tadd $0xc,%esp\n \tlea 0x1ec(%esi),%eax\n \tpush %edi\n \tpush %eax\n \tpush -0x34(%esi)\n \tcall 4290 <__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 \tadd $0x10,%esp\n \tlea -0xc(%ebp),%esp\n \tpop %ebx\n \tpop %esi\n \tpop %edi\n \tpop %ebp\n \tret\n /usr/include/c++/12/bits/basic_ios.h:282\n \tmov %eax,%edi\n \tjmp 46c0 <__cxa_finalize@plt+0x10>\n \tmov %eax,%edi\n \tjmp 46e4 <__cxa_finalize@plt+0x34>\n \txchg %ax,%ax\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 \tpush %ebp\n \tmov %esp,%ebp\n \tpush %edi\n \tpush %esi\n \tcall 5995 <virtual thunk to Rcpp::Rostream<false>::~Rostream()@@Base+0x75>\n \tadd $0xc10a,%esi\n \tpush %ebx\n@@ -980,15 +980,15 @@\n \tadd $0xc,%esp\n \tlea 0x3bc(%esi),%eax\n \tpush %edi\n \tpush %eax\n \tpush -0x34(%esi)\n \tcall 4290 <__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 \tadd $0x10,%esp\n \tlea -0xc(%ebp),%esp\n \tpop %ebx\n \tpop %esi\n \tpop %edi\n \tpop %ebp\n \tret\n@@ -1091,117 +1091,117 @@\n \txchg %ax,%ax\n \txchg %ax,%ax\n \txchg %ax,%ax\n \tnop\n \n 00005260 <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)@@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:15\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:15\n \tcall 5991 <virtual thunk to Rcpp::Rostream<false>::~Rostream()@@Base+0x71>\n \tadd $0xbd8f,%eax\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 \tpush %ebp\n \tpush %edi\n \tpush %esi\n \tpush %ebx\n \tsub $0x3c,%esp\n \tmov 0x5c(%esp),%edi\n \tmov 0x58(%esp),%esi\n \tmov %eax,0xc(%esp)\n \tmov 0x64(%esp),%eax\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 \tmovl $0x0,0x14(%esp)\n \tmov %edi,%ebp\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 \tmov %eax,0x18(%esp)\n \tmov 0x68(%esp),%eax\n \tmov %eax,0x1c(%esp)\n \tlea 0x0(%esi,%eiz,1),%esi\n \txchg %ax,%ax\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/Vector.h:276 (discriminator 1)\n \tsub $0xc,%esp\n \tpush (%esi)\n \tmov 0x1c(%esp),%ebx\n \tcall 4410 <Rf_xlength@plt>\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:15 (discriminator 1)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:15 (discriminator 1)\n \tmov 0x24(%esp),%edi\n \tadd $0x10,%esp\n \tcmp %eax,%edi\n \tjge 5348 <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)@@Base+0xe8>\n \tlea 0x0(,%edi,4),%eax\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:16\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:16\n \txor %edi,%edi\n \tmov %eax,0x10(%esp)\n \tjmp 5321 <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)@@Base+0xc1>\n \tlea 0x0(%esi,%eiz,1),%esi\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 \tmov 0x8(%esi),%eax\n \tmov 0x10(%esp),%edx\n \tmov (%eax,%edx,1),%ecx\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 \tmov 0x8(%ebp),%eax\n \tmov (%eax,%edi,4),%eax\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 %eax,%ecx\n \tjle 52ea <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)@@Base+0x8a>\n \tmov %ecx,%ebx\n \tmov %eax,%ecx\n \tmov %ebx,%eax\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:25 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:25 (discriminator 2)\n \tmov 0x60(%esp),%edx\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:27 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:27 (discriminator 2)\n \tfldl 0x18(%esp)\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:25 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:25 (discriminator 2)\n \tsub %ecx,%eax\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:16 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:16 (discriminator 2)\n \tadd $0x1,%edi\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:25 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:25 (discriminator 2)\n \tmov 0x8(%edx),%ebx\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:27 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:27 (discriminator 2)\n \tmov 0x50(%esp),%edx\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:25 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:25 (discriminator 2)\n \tadd -0x4(%ebx,%ecx,4),%eax\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:27 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:27 (discriminator 2)\n \tmov 0x8(%edx),%ecx\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:25 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:25 (discriminator 2)\n \tsub $0x1,%eax\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:28 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:28 (discriminator 2)\n \tmov 0x54(%esp),%ebx\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:27 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:27 (discriminator 2)\n \tfstpl (%ecx,%eax,8)\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:28 (discriminator 2)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:28 (discriminator 2)\n \tfildl 0x6c(%esp)\n \tmov 0x8(%ebx),%ecx\n \tfstpl 0x28(%esp)\n \tfldl 0x28(%esp)\n \tfstpl (%ecx,%eax,8)\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/Vector.h:276 (discriminator 1)\n \tsub $0xc,%esp\n \tpush 0x0(%ebp)\n \tmov 0x1c(%esp),%ebx\n \tcall 4410 <Rf_xlength@plt>\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 \tadd $0x10,%esp\n \tcmp %eax,%edi\n \tjl 52d0 <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)@@Base+0x70>\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 \taddl $0x1,0x14(%esp)\n \tjmp 52a0 <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)@@Base+0x40>\n \tlea 0x0(%esi,%eiz,1),%esi\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 \tadd $0x3c,%esp\n \tpop %ebx\n \tpop %esi\n \tpop %edi\n \tpop %ebp\n \tret\n \n 00005350 <Rcpp::internal::NamedPlaceHolder::~NamedPlaceHolder()@@Base>:\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 \txchg %ax,%ax\n \txchg %ax,%ax\n \txchg %ax,%ax\n \txchg %ax,%ax\n \txchg %ax,%ax\n \txchg %ax,%ax\n@@ -3029,15 +3029,15 @@\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/Vector.h:74\n \tlea 0x0(%esi,%eiz,1),%esi\n \tlea 0x0(%esi,%eiz,1),%esi\n \tnop\n \n 00006410 <treescape_updateDistancesWithCombinations@@Base>:\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 \tpush %ebp\n \tmov %esp,%ebp\n \tpush %edi\n \tcall c43c <double Rcpp::internal::primitive_as<double>(SEXPREC*)@@Base+0x19c>\n \tadd $0xabdb,%edi\n \tpush %esi\n \tpush %ebx\n@@ -3054,19 +3054,19 @@\n \tmov 0x1c(%ebp),%eax\n \tmov %eax,-0x8c(%ebp)\n \tmov 0x20(%ebp),%eax\n \tmov %eax,-0x90(%ebp)\n \tmov %gs:0x14,%eax\n \tmov %eax,-0x1c(%ebp)\n \txor %eax,%eax\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 \tmovzbl 0x38c(%edi),%eax\n \ttest %al,%al\n \tjne 6492 <treescape_updateDistancesWithCombinations@@Base+0x82>\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 \tsub $0xc,%esp\n \tlea 0x38c(%edi),%eax\n \tmov %edi,%ebx\n \tmov %eax,-0x94(%ebp)\n \tpush %eax\n \tcall 4630 <__cxa_guard_acquire@plt>\n \tadd $0x10,%esp\n@@ -3119,29 +3119,29 @@\n double Rcpp::internal::as<double>(SEXPREC*, Rcpp::traits::r_type_primitive_tag):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/as.h:44\n \tpush -0x8c(%ebp)\n \tcall 41e0 <double Rcpp::internal::primitive_as<double>(SEXPREC*)@plt>\n \tadd $0x10,%esp\n \tfstpl -0x78(%ebp)\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 \tpush -0x7c(%ebp)\n \tpush -0x74(%ebp)\n \tpush -0x78(%ebp)\n \tpush -0x88(%ebp)\n \tpush -0x84(%ebp)\n \tpush -0x80(%ebp)\n \tpush %esi\n \tpush -0x94(%ebp)\n \tcall 44c0 <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)@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 \tmov -0x90(%edi),%eax\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 \tadd $0x20,%esp\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 \tmov (%eax),%eax\n \tmov %eax,-0x80(%ebp)\n Rcpp::PreserveStorage<Rcpp::Vector<13, Rcpp::PreserveStorage> >::~PreserveStorage():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/storage/PreserveStorage.h:34\n \tmov -0x3c(%ebp),%eax\n \tmov %eax,-0x7c(%ebp)\n Rcpp::Rcpp_precious_remove(SEXPREC*):\n@@ -3214,15 +3214,15 @@\n \tmovzbl 0x59c(%edi),%eax\n \tadd $0x10,%esp\n \ttest %al,%al\n \tje 6640 <treescape_updateDistancesWithCombinations@@Base+0x230>\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:100\n \tcall *0x5a4(%edi)\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 \tmov -0x1c(%ebp),%eax\n \tsub %gs:0x14,%eax\n \tjne 6891 <treescape_updateDistancesWithCombinations@@Base+0x481>\n \tmov -0x80(%ebp),%eax\n \tlea -0xc(%ebp),%esp\n \tpop %ebx\n \tpop %esi\n@@ -3378,55 +3378,55 @@\n \tmov %eax,0x5b4(%edi)\n \tpush -0x94(%ebp)\n \tcall 4260 <__cxa_guard_release@plt>\n \tadd $0x10,%esp\n \tjmp 64a1 <treescape_updateDistancesWithCombinations@@Base+0x91>\n \tlea 0x0(%esi),%esi\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 \tsub $0xc,%esp\n \tlea -0x38f5(%edi),%eax\n \tpush %eax\n \tcall 4270 <Rf_install@plt>\n \tpop %ecx\n \tmov %eax,0x394(%edi)\n \tpush -0x94(%ebp)\n \tcall 4260 <__cxa_guard_release@plt>\n \tadd $0x10,%esp\n \tjmp 6492 <treescape_updateDistancesWithCombinations@@Base+0x82>\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 \tcall c440 <double Rcpp::internal::primitive_as<double>(SEXPREC*)@@Base+0x1a0>\n \tjmp 48e9 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x1e1>\n \tjmp 48f9 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x1f1>\n \tjmp 4909 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x201>\n \tjmp 4919 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x211>\n \tjmp 4929 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x221>\n \tjmp 4939 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x231>\n Rcpp::internal::enterRNGScope():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:93\n \tmov %edx,-0x7c(%ebp)\n \tmov %eax,%esi\n \tjmp 4949 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x241>\n treescape_updateDistancesWithCombinations():\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 \tmov %eax,%esi\n \tjmp 49cf <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x2c7>\n Rcpp::Rcpp_PreciousRelease(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/RcppCommon.h:121\n \tmov %eax,%ebx\n \tmov %edx,%esi\n \tjmp 49e7 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x2df>\n \tmov %eax,%ebx\n \tmov %edx,%esi\n \tjmp 4a1f <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x317>\n \tmov %eax,%ebx\n \tmov %edx,%esi\n \tjmp 4a03 <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x2fb>\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 \tmov %eax,%esi\n \tmov %edx,%eax\n \tjmp 495f <Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@@Base+0x257>\n Rcpp::Rcpp_PreciousRelease(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/RcppCommon.h:121\n \tmov %eax,%ebx\n \tmov %edx,%esi\n@@ -3444,15 +3444,15 @@\n \txchg %ax,%ax\n \txchg %ax,%ax\n \txchg %ax,%ax\n \txchg %ax,%ax\n \n 00006910 <std::ctype<char>::do_widen(char) const@@Base>:\n std::ctype<char>::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 \tmovzbl 0x8(%esp),%eax\n \tret\n \txchg %ax,%ax\n \txchg %ax,%ax\n \txchg %ax,%ax\n \txchg %ax,%ax\n \txchg %ax,%ax\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 32623062 65336561 30663538 31653735 2b0be3ea0f581e75\n- 0x00000010 38616330 63346366 38323864 66303666 8ac0c4cf828df06f\n- 0x00000020 33663130 65622e64 65627567 00000000 3f10eb.debug....\n- 0x00000030 d4977b4b ..{K\n+ 0x00000000 34383666 35663666 64353763 30346132 486f5f6fd57c04a2\n+ 0x00000010 33313733 61633935 31376633 66326239 3173ac9517f3f2b9\n+ 0x00000020 38343938 32632e64 65627567 00000000 84982c.debug....\n+ 0x00000030 d503dd15 ....\n \n"}]}]}]}]}, {"source1": "r-cran-treescape-dbgsym_1.10.18+dfsg-2_i386.deb", "source2": "r-cran-treescape-dbgsym_1.10.18+dfsg-2_i386.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 0 548 2020-05-22 06:51:07.000000 control.tar.xz\n--rw-r--r-- 0 0 0 224060 2020-05-22 06:51:07.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 224064 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: i386\n Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>\n Installed-Size: 240\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: cb2b0be3ea0f581e758ac0c4cf828df06f3f10eb\n+Build-Ids: a7486f5f6fd57c04a23173ac9517f3f2b984982c\n"}, {"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "comments": ["Files differ"], "unified_diff": null}, {"source1": "line order", "source2": "line order", "unified_diff": "@@ -1 +1 @@\n-usr/lib/debug/.build-id/cb/2b0be3ea0f581e758ac0c4cf828df06f3f10eb.debug\n+usr/lib/debug/.build-id/a7/486f5f6fd57c04a23173ac9517f3f2b984982c.debug\n"}]}]}]}, {"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": "@@ -1,10 +1,10 @@\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/debug/\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/debug/.build-id/\n-drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/debug/.build-id/cb/\n--rw-r--r-- 0 root (0) root (0) 235232 2020-05-22 06:51:07.000000 ./usr/lib/debug/.build-id/cb/2b0be3ea0f581e758ac0c4cf828df06f3f10eb.debug\n+drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/debug/.build-id/a7/\n+-rw-r--r-- 0 root (0) root (0) 235236 2020-05-22 06:51:07.000000 ./usr/lib/debug/.build-id/a7/486f5f6fd57c04a23173ac9517f3f2b984982c.debug\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/share/\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/share/doc/\n lrwxrwxrwx 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/share/doc/r-cran-treescape-dbgsym -> r-cran-treescape\n"}, {"source1": "./usr/lib/debug/.build-id/cb/2b0be3ea0f581e758ac0c4cf828df06f3f10eb.debug", "source2": "./usr/lib/debug/.build-id/a7/486f5f6fd57c04a23173ac9517f3f2b984982c.debug", "comments": ["File has been modified after NT_GNU_BUILD_ID has been applied.", "Files 5% similar despite different names"], "unified_diff": null, "details": [{"source1": "readelf --wide --file-header {}", "source2": "readelf --wide --file-header {}", "unified_diff": "@@ -6,15 +6,15 @@\n OS/ABI: UNIX - System V\n ABI Version: 0\n Type: DYN (Shared object file)\n Machine: Intel 80386\n Version: 0x1\n Entry point address: 0x0\n Start of program headers: 52 (bytes into file)\n- Start of section headers: 233712 (bytes into file)\n+ Start of section headers: 233716 (bytes into file)\n Flags: 0x0\n Size of this header: 52 (bytes)\n Size of program headers: 32 (bytes)\n Number of program headers: 9\n Size of section headers: 40 (bytes)\n Number of section headers: 38\n Section header string table index: 37\n"}, {"source1": "readelf --wide --sections {}", "source2": "readelf --wide --sections {}", "unified_diff": "@@ -1,8 +1,8 @@\n-There are 38 section headers, starting at offset 0x390f0:\n+There are 38 section headers, starting at offset 0x390f4:\n \n Section Headers:\n [Nr] Name Type Addr Off Size ES Flg Lk Inf Al\n [ 0] NULL 00000000 000000 000000 00 0 0 0\n [ 1] .note.gnu.build-id NOTE 00000154 000154 000024 00 A 0 0 4\n [ 2] .gnu.hash NOBITS 00000178 000178 0002c8 04 A 3 0 4\n [ 3] .dynsym NOBITS 00000440 000178 000cc0 10 A 4 1 4\n@@ -28,20 +28,20 @@\n [23] .got.plt NOBITS 00010ff4 000c8c 0001ac 04 WA 0 0 4\n [24] .data NOBITS 000111a0 000c8c 000018 00 WA 0 0 4\n [25] .bss NOBITS 000111c0 000c8c 0003ec 00 WA 0 0 32\n [26] .comment PROGBITS 00000000 000178 00001f 01 MS 0 0 1\n [27] .debug_aranges PROGBITS 00000000 000198 000173 00 C 0 0 4\n [28] .debug_info PROGBITS 00000000 00030c 02235c 00 C 0 0 4\n [29] .debug_abbrev PROGBITS 00000000 022668 000f10 00 C 0 0 4\n- [30] .debug_line PROGBITS 00000000 023578 003738 00 C 0 0 4\n- [31] .debug_str PROGBITS 00000000 026cb0 006c5b 01 MSC 0 0 4\n- [32] .debug_line_str PROGBITS 00000000 02d90c 00045e 01 MSC 0 0 4\n- [33] .debug_loclists PROGBITS 00000000 02dd6c 005cd7 00 C 0 0 4\n- [34] .debug_rnglists PROGBITS 00000000 033a44 001b26 00 C 0 0 4\n- [35] .symtab SYMTAB 00000000 03556c 0012b0 10 36 96 4\n- [36] .strtab STRTAB 00000000 03681c 002753 00 0 0 1\n- [37] .shstrtab STRTAB 00000000 038f6f 00017e 00 0 0 1\n+ [30] .debug_line PROGBITS 00000000 023578 00373b 00 C 0 0 4\n+ [31] .debug_str PROGBITS 00000000 026cb4 006c5b 01 MSC 0 0 4\n+ [32] .debug_line_str PROGBITS 00000000 02d910 000460 01 MSC 0 0 4\n+ [33] .debug_loclists PROGBITS 00000000 02dd70 005cd7 00 C 0 0 4\n+ [34] .debug_rnglists PROGBITS 00000000 033a48 001b26 00 C 0 0 4\n+ [35] .symtab SYMTAB 00000000 035570 0012b0 10 36 96 4\n+ [36] .strtab STRTAB 00000000 036820 002753 00 0 0 1\n+ [37] .shstrtab STRTAB 00000000 038f73 00017e 00 0 0 1\n Key to Flags:\n W (write), A (alloc), X (execute), M (merge), S (strings), I (info),\n L (link order), O (extra OS processing required), G (group), T (TLS),\n C (compressed), x (unknown), o (OS specific), E (exclude),\n D (mbind), p (processor specific)\n"}, {"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: cb2b0be3ea0f581e758ac0c4cf828df06f3f10eb\n+ GNU 0x00000014\tNT_GNU_BUILD_ID (unique build ID bitstring)\t Build ID: a7486f5f6fd57c04a23173ac9517f3f2b984982c\n"}, {"source1": "readelf --wide --debug-dump=rawline {}", "source2": "readelf --wide --debug-dump=rawline {}", "unified_diff": "@@ -25,171 +25,171 @@\n Opcode 9 has 1 arg\n Opcode 10 has 0 args\n Opcode 11 has 0 args\n Opcode 12 has 1 arg\n \n The 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Type: DW_UT_partial (3)\n Abbrev Offset: 0\n Pointer Size: 4\n <0><c>: Abbrev Number: 73 (DW_TAG_partial_unit)\n <d> 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: 11 (DW_TAG_namespace)\n <16> DW_AT_name : (string) std\n <1a> DW_AT_sibling : (ref2) <0x3611>\n <2><1c>: Abbrev Number: 37 (DW_TAG_imported_declaration)\n <1d> DW_AT_decl_file : (data1) 12\n <1e> DW_AT_decl_line : (data2) 1065\n <20> DW_AT_decl_column : (data1) 11\n@@ -16450,15 +16450,15 @@\n Unit Type: DW_UT_compile (1)\n Abbrev Offset: 0x746\n Pointer Size: 4\n <0><5e85>: Abbrev Number: 152 (DW_TAG_compile_unit)\n <5e87> DW_AT_producer : (strp) (offset: 0xf3a1): GNU C++14 12.2.0 -mtune=generic -march=i686 -g -O2 -std=gnu++14 -fpic -fstack-protector-strong -ffloat-store -fasynchronous-unwind-tables\n <5e8b> DW_AT_language : (data1) 33\t(C++14)\n <5e8c> DW_AT_name : (line_strp) (offset: 0): CPP_update_combinations.cpp\n- <5e90> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/1st/r-cran-treescape-1.10.18+dfsg/src\n+ <5e90> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/2/r-cran-treescape-1.10.18+dfsg/2nd/src\n <5e94> DW_AT_ranges : (sec_offset) 0x1a1\n <5e98> DW_AT_low_pc : (addr) 0\n <5e9c> DW_AT_stmt_list : (sec_offset) 0\n <1><5ea0>: Abbrev Number: 190 (DW_TAG_imported_unit)\n <5ea2> DW_AT_import : (ref_addr) <0xc>\t[Abbrev Number: 73 (DW_TAG_partial_unit)]\n <1><5ea6>: Abbrev Number: 186 (DW_TAG_namespace)\n <5ea8> DW_AT_name : (string) std\n@@ -45917,16 +45917,16 @@\n Version: 5\n Unit Type: DW_UT_compile (1)\n Abbrev Offset: 0x1573\n Pointer Size: 4\n <0><11229>: Abbrev Number: 270 (DW_TAG_compile_unit)\n <1122b> DW_AT_producer : (strp) (offset: 0xf3a1): GNU C++14 12.2.0 -mtune=generic -march=i686 -g -O2 -std=gnu++14 -fpic -fstack-protector-strong -ffloat-store 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wrap_end.h\n- [ b04] r_vector.h\n- [ b0f] typeinfo\n- [ b18] Shelter.h\n- [ b22] stl_uninitialized.h\n- [ b36] stl_algo.h\n- [ b41] r_cast.h\n- [ b4a] as.h\n- [ b4f] Exporter.h\n- [ b5a] RNGScope.h\n- [ b65] InputParameter.h\n- [ b76] sstream.tcc\n- [ b82] ostream.tcc\n- [ b8e] iosfwd\n- [ b95] ptr_traits.h\n- [ ba2] exception.h\n- [ bae] functexcept.h\n- [ bbc] ostream_insert.h\n- [ bcd] cpp_type_traits.h\n- [ bdf] Boolean.h\n- [ be9] caster.h\n- [ bf2] r_type_traits.h\n- [ c02] wrap_type_traits.h\n- [ c15] enable_if.h\n- [ c21] Interrupt.h\n- [ c2d] execinfo.h\n- [ c38] GraphicsDevice.h\n+ [ 1c] /build/2/r-cran-treescape-1.10.18+dfsg/2nd/src\n+ [ 4b] /usr/lib/R/site-library/Rcpp/include/Rcpp\n+ [ 75] /usr/lib/R/site-library/Rcpp/include/Rcpp/iostream\n+ [ a8] /usr/include/c++/12\n+ [ bc] /usr/include/c++/12/bits\n+ [ d5] /usr/lib/R/site-library/Rcpp/include/Rcpp/vector\n+ [ 106] /usr/lib/R/site-library/Rcpp/include/Rcpp/storage\n+ [ 138] /usr/include/i386-linux-gnu/c++/12/bits\n+ [ 160] /usr/include/c++/12/debug\n+ [ 17a] /usr/include/c++/12/ext\n+ [ 192] /usr/include/i386-linux-gnu/bits\n+ [ 1b3] /usr/include\n+ [ 1c0] /usr/lib/gcc/i686-linux-gnu/12/include\n+ [ 1e7] /usr/include/i386-linux-gnu/bits/types\n+ [ 20e] /usr/share/R/include/R_ext\n+ [ 229] /usr/share/R/include\n+ [ 23e] /usr/lib/R/site-library/Rcpp/include/Rcpp/utils/tinyformat\n+ [ 279] /usr/lib/R/site-library/Rcpp/include/Rcpp/macros\n+ [ 2aa] /usr/lib/R/site-library/Rcpp/include/Rcpp/internal\n+ [ 2dd] /usr/lib/R/site-library/Rcpp/include\n+ [ 302] /usr/lib/R/site-library/Rcpp/include/Rcpp/traits\n+ [ 333] /usr/lib/R/site-library/Rcpp/include/Rcpp/sugar/operators\n+ [ 36d] /usr/lib/R/site-library/Rcpp/include/Rcpp/sugar/functions\n+ [ 3a7] /usr/lib/R/site-library/Rcpp/include/Rcpp/sugar/functions/strings\n+ [ 3e9] /usr/lib/R/site-library/Rcpp/include/Rcpp/sugar\n+ [ 419] /usr/lib/R/site-library/Rcpp/include/Rcpp/proxy\n+ [ 449] /usr/lib/R/site-library/Rcpp/include/Rcpp/api/meat\n+ [ 47c] /usr/lib/R/site-library/Rcpp/include/Rcpp/stats/dpq\n+ [ 4b0] Named.h\n+ [ 4b8] Rstreambuf.h\n+ [ 4c5] streambuf\n+ [ 4cf] basic_ios.h\n+ [ 4db] char_traits.h\n+ [ 4e9] Vector.h\n+ [ 4f2] PreserveStorage.h\n+ [ 504] cmath\n+ [ 50a] type_traits\n+ [ 516] c++config.h\n+ [ 522] new_allocator.h\n+ [ 532] stl_iterator_base_types.h\n+ [ 54c] stl_pair.h\n+ [ 557] uses_allocator.h\n+ [ 568] tuple\n+ [ 56e] debug.h\n+ [ 576] stl_iterator.h\n+ [ 585] cwchar\n+ [ 58c] postypes.h\n+ [ 597] cstdint\n+ [ 59f] clocale\n+ [ 5a7] cstdlib\n+ [ 5af] cstdio\n+ [ 5b6] alloc_traits.h\n+ [ 5c5] basic_string.h\n+ [ 5d4] initializer_list\n+ [ 5e5] stringfwd.h\n+ [ 5f1] cstddef\n+ [ 5f9] cstdarg\n+ [ 601] cstring\n+ [ 609] locale_classes.h\n+ [ 61a] exception_ptr.h\n+ [ 62a] ios_base.h\n+ [ 635] cwctype\n+ [ 63d] streambuf.tcc\n+ [ 64b] ctime\n+ [ 651] functional\n+ [ 65c] stl_vector.h\n+ [ 669] vector.tcc\n+ [ 674] csetjmp\n+ [ 67c] basic_ios.tcc\n+ [ 68a] predefined_ops.h\n+ [ 69b] math.h\n+ [ 6a2] stddef.h\n+ [ 6ab] stdlib.h\n+ [ 6b4] clock_t.h\n+ [ 6be] time_t.h\n+ [ 6c7] stdint-intn.h\n+ [ 6d5] __sigset_t.h\n+ [ 6e2] stdarg.h\n+ [ 6eb] wint_t.h\n+ [ 6f4] __mbstate_t.h\n+ [ 702] __FILE.h\n+ [ 70b] struct_FILE.h\n+ [ 719] wchar2.h\n+ [ 722] struct_tm.h\n+ [ 72e] stdint-uintn.h\n+ [ 73d] stdint.h\n+ [ 746] locale.h\n+ [ 74f] stdlib-float.h\n+ [ 75e] stdlib-bsearch.h\n+ [ 76f] __fpos_t.h\n+ [ 77a] stdio.h\n+ [ 782] stdio2.h\n+ [ 78b] Complex.h\n+ [ 795] Rdynload.h\n+ [ 7a0] Rinternals.h\n+ [ 7ad] setjmp.h\n+ [ 7b6] struct___jmp_buf_tag.h\n+ [ 7cd] atomic_word.h\n+ [ 7db] wctype-wchar.h\n+ [ 7ea] wctype.h\n+ [ 7f3] time.h\n+ [ 7fa] tinyformat.h\n+ [ 807] macros.h\n+ [ 810] const_string_proxy.h\n+ [ 825] Proxy_Iterator.h\n+ [ 836] const_generic_proxy.h\n+ [ 84c] RcppCommon.h\n+ [ 859] integral_constant.h\n+ [ 86d] expands_to_logical.h\n+ [ 882] storage_type.h\n+ [ 891] r_binary_op.h\n+ [ 89f] median.h\n+ [ 8a8] cbind.h\n+ [ 8b0] trimws.h\n+ [ 8b9] VectorBase.h\n+ [ 8c6] Range.h\n+ [ 8ce] Dimension.h\n+ [ 8da] no_init.h\n+ [ 8e4] SlotProxy.h\n+ [ 8f0] AttributeProxy.h\n+ [ 901] RObjectMethods.h\n+ [ 912] RObject.h\n+ [ 91c] NamesProxy.h\n+ [ 929] String.h\n+ [ 932] GenericProxy.h\n+ [ 941] Na_Proxy.h\n+ [ 94c] instantiation.h\n+ [ 95c] dpq.h\n+ [ 962] algorithm.h\n+ [ 96e] setjmp2.h\n+ [ 978] Module.h\n+ [ 981] Print.h\n+ [ 989] new\n+ [ 98d] system_error\n+ [ 99a] R.h\n+ [ 99e] RcppExports.cpp\n+ [ 9ae] /usr/lib/R/site-library/Rcpp/include/Rcpp/protection\n+ [ 9e3] /usr/lib/R/site-library/Rcpp/include/Rcpp/generated\n+ [ a17] locale_facets.h\n+ [ a27] exceptions.h\n+ [ a34] Rcpp_eval.h\n+ [ a40] unwindProtect.h\n+ [ a50] basic_string.tcc\n+ [ a61] stl_iterator_base_funcs.h\n+ [ a7b] stl_construct.h\n+ [ a8b] routines.h\n+ [ a96] sstream\n+ [ a9e] Shield.h\n+ [ aa7] exceptions_impl.h\n+ [ ab9] stl_algobase.h\n+ [ ac8] wrap.h\n+ [ acf] named_object.h\n+ [ ade] Vector__create.h\n+ [ aef] converter.h\n+ [ afb] wrap_end.h\n+ [ b06] r_vector.h\n+ [ b11] typeinfo\n+ [ b1a] Shelter.h\n+ [ b24] stl_uninitialized.h\n+ [ b38] stl_algo.h\n+ [ b43] r_cast.h\n+ [ b4c] as.h\n+ [ b51] Exporter.h\n+ [ b5c] RNGScope.h\n+ [ b67] InputParameter.h\n+ [ b78] sstream.tcc\n+ [ b84] ostream.tcc\n+ [ b90] iosfwd\n+ [ b97] ptr_traits.h\n+ [ ba4] exception.h\n+ [ bb0] functexcept.h\n+ [ bbe] ostream_insert.h\n+ [ bcf] cpp_type_traits.h\n+ [ be1] Boolean.h\n+ [ beb] caster.h\n+ [ bf4] r_type_traits.h\n+ [ c04] wrap_type_traits.h\n+ [ c17] enable_if.h\n+ [ c23] Interrupt.h\n+ [ c2f] execinfo.h\n+ [ c3a] GraphicsDevice.h\n \n"}]}]}]}]}]}