{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.iJPCVlZC/b1/r-cran-treescape_1.10.18+dfsg-2_amd64.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.iJPCVlZC/b2/r-cran-treescape_1.10.18+dfsg-2_amd64.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,3 +1,3 @@\n \n- fe5f079da243eec9969321b89f8cabcf 236420 debug optional r-cran-treescape-dbgsym_1.10.18+dfsg-2_amd64.deb\n- c0320fbdf857fdeac7ef3870b5bddf74 1117552 gnu-r optional r-cran-treescape_1.10.18+dfsg-2_amd64.deb\n+ 515ceaac360a2610447194aed31e82d5 236412 debug optional r-cran-treescape-dbgsym_1.10.18+dfsg-2_amd64.deb\n+ c66424b127097cddbc484c4f669a6c5d 1117688 gnu-r optional r-cran-treescape_1.10.18+dfsg-2_amd64.deb\n"}, {"source1": "r-cran-treescape_1.10.18+dfsg-2_amd64.deb", "source2": "r-cran-treescape_1.10.18+dfsg-2_amd64.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 1115248 2020-05-22 06:51:07.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 2116 2020-05-22 06:51:07.000000 control.tar.xz\n+-rw-r--r-- 0 0 0 1115380 2020-05-22 06:51:07.000000 data.tar.xz\n"}, {"source1": "control.tar.xz", "source2": "control.tar.xz", "unified_diff": null, "details": [{"source1": "control.tar", "source2": "control.tar", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "comments": ["Files differ"], "unified_diff": null}]}]}]}, {"source1": "data.tar.xz", "source2": "data.tar.xz", "unified_diff": null, "details": [{"source1": "data.tar", "source2": "data.tar", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -14,15 +14,15 @@\n -rw-r--r-- 0 root (0) root (0) 382 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/Meta/links.rds\n -rw-r--r-- 0 root (0) root (0) 808 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/Meta/nsInfo.rds\n -rw-r--r-- 0 root (0) root (0) 1456 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/Meta/package.rds\n -rw-r--r-- 0 root (0) root (0) 310 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/Meta/vignette.rds\n -rw-r--r-- 0 root (0) root (0) 1590 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/NAMESPACE\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/R/\n -rw-r--r-- 0 root (0) root (0) 1058 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/R/treescape\n--rw-r--r-- 0 root (0) root (0) 51502 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/R/treescape.rdb\n+-rw-r--r-- 0 root (0) root (0) 51505 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/R/treescape.rdb\n -rw-r--r-- 0 root (0) root (0) 542 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/R/treescape.rdx\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/data/\n -rw-r--r-- 0 root (0) root (0) 850392 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/data/Rdata.rdb\n -rw-r--r-- 0 root (0) root (0) 141 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/data/Rdata.rds\n -rw-r--r-- 0 root (0) root (0) 232 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/data/Rdata.rdx\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/\n -rw-r--r-- 0 root (0) root (0) 8869 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/DengueVignette.R\n@@ -31,17 +31,17 @@\n -rw-r--r-- 0 root (0) root (0) 8024 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/TransmissionTreesVignette.Rmd\n -rw-r--r-- 0 root (0) root (0) 2682 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/index.html\n -rw-r--r-- 0 root (0) root (0) 5345 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/treescape.R\n -rw-r--r-- 0 root (0) root (0) 16607 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/doc/treescape.Rmd\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/\n -rw-r--r-- 0 root (0) root (0) 468 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/AnIndex\n -rw-r--r-- 0 root (0) root (0) 257 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/aliases.rds\n--rw-r--r-- 0 root (0) root (0) 316 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/paths.rds\n--rw-r--r-- 0 root (0) root (0) 50773 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/treescape.rdb\n--rw-r--r-- 0 root (0) root (0) 624 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/treescape.rdx\n+-rw-r--r-- 0 root (0) root (0) 318 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/paths.rds\n+-rw-r--r-- 0 root (0) root (0) 50853 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/treescape.rdb\n+-rw-r--r-- 0 root (0) root (0) 628 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/help/treescape.rdx\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/html/\n -rw-r--r-- 0 root (0) root (0) 3597 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/html/00Index.html\n -rw-r--r-- 0 root (0) root (0) 1844 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/html/R.css\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/libs/\n -rw-r--r-- 0 root (0) root (0) 68528 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/libs/treescape.so\n drwxr-xr-x 0 root (0) root (0) 0 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/shiny/\n -rw-r--r-- 0 root (0) root (0) 36496 2020-05-22 06:51:07.000000 ./usr/lib/R/site-library/treescape/shiny/server.R\n"}, {"source1": "./usr/lib/R/site-library/treescape/R/treescape.rdb", "source2": "./usr/lib/R/site-library/treescape/R/treescape.rdb", "unified_diff": null, "details": [{"source1": "Rscript --vanilla - {}", "source2": "Rscript --vanilla - {}", "unified_diff": "@@ -261,15 +261,15 @@\n \"imports\" = \" phangorn = c(Descendants = \"Descendants\"), phangorn = c(KF.dist = \"KF.dist\"), \"\n \"imports\" = \" phangorn = c(RF.dist = \"RF.dist\"), phangorn = c(path.dist = \"path.dist\"), \"\n \"imports\" = \" phangorn = c(wRF.dist = \"wRF.dist\"), rgl = c(writeWebGL = \"writeWebGL\"), \"\n \"imports\" = \" shinyBS = c(bsTooltip = \"bsTooltip\"), stats = c(as.dist = \"as.dist\"), \"\n \"imports\" = \" stats = c(cutree = \"cutree\"), stats = c(dist = \"dist\"), stats = c(hclust = \"hclust\"), \"\n \"imports\" = \" utils = c(packageDescription = \"packageDescription\"))\"\n \"lazydata\" = \"\"\n- \"path\" = \"\"/build/1st/r-cran-treescape-1.10.18+dfsg/debian/r-cran-treescape/usr/lib/R/site-library/treescape\"\"\n+ \"path\" = \"\"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/debian/r-cran-treescape/usr/lib/R/site-library/treescape\"\"\n \"spec\" = \"c(name = \"treescape\", version = \"1.10.18\")\"\n }\n \n .__S3MethodsTable__. (environment) = \n {\n }\n \n"}]}, {"source1": "./usr/lib/R/site-library/treescape/R/treescape.rdx", "source2": "./usr/lib/R/site-library/treescape/R/treescape.rdx", "unified_diff": null, "details": [{"source1": "treescape.rdx-content", "source2": "treescape.rdx-content", "unified_diff": null, "details": [{"source1": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "source2": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "unified_diff": "@@ -1,82 +1,82 @@\n $variables\n $variables$.__NAMESPACE__.\n-[1] 5694 60\n+[1] 5697 60\n \n $variables$.__S3MethodsTable__.\n-[1] 5893 60\n+[1] 5896 60\n \n $variables$.packageName\n-[1] 5953 62\n+[1] 5956 62\n \n $variables$.render.server.info\n-[1] 6015 746\n+[1] 6018 746\n \n $variables$findGroves\n-[1] 6761 2312\n+[1] 6764 2312\n \n $variables$findMRCIs\n-[1] 9073 4199\n+[1] 9076 4199\n \n $variables$linearMrca\n-[1] 13272 2105\n+[1] 13275 2105\n \n $variables$medTree\n-[1] 15377 5405\n+[1] 15380 5405\n \n $variables$multiDist\n-[1] 20782 3462\n+[1] 20785 3462\n \n $variables$plotGroves\n-[1] 24244 3454\n+[1] 24247 3454\n \n $variables$plotGrovesD3\n-[1] 27698 1123\n+[1] 27701 1123\n \n $variables$plotTreeDiff\n-[1] 28821 2662\n+[1] 28824 2662\n \n $variables$refTreeDist\n-[1] 31483 2681\n+[1] 31486 2681\n \n $variables$tipDiff\n-[1] 34164 2382\n+[1] 34167 2382\n \n $variables$treeDist\n-[1] 36546 1245\n+[1] 36549 1245\n \n $variables$treeVec\n-[1] 37791 6965\n+[1] 37794 6965\n \n $variables$treescape\n-[1] 44756 3769\n+[1] 44759 3769\n \n $variables$treescapeServer\n-[1] 48525 329\n+[1] 48528 329\n \n $variables$updateDistancesWithCombinations\n-[1] 48854 438\n+[1] 48857 438\n \n $variables$wiwMedTree\n-[1] 49292 1384\n+[1] 49295 1384\n \n $variables$wiwTreeDist\n-[1] 50676 826\n+[1] 50679 826\n \n \n $references\n $references$`env::1`\n-[1] 309 5385\n+[1] 309 5388\n \n $references$`env::2`\n [1] 0 139\n \n $references$`env::3`\n [1] 139 170\n \n $references$`env::4`\n-[1] 5754 139\n+[1] 5757 139\n \n \n $compressed\n [1] TRUE\n \n"}]}]}, {"source1": "./usr/lib/R/site-library/treescape/help/paths.rds", "source2": "./usr/lib/R/site-library/treescape/help/paths.rds", "unified_diff": null, "details": [{"source1": "paths.rds-content", "source2": "paths.rds-content", "unified_diff": null, "details": [{"source1": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "source2": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "unified_diff": "@@ -1,23 +1,23 @@\n- [1] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueBEASTMCC.Rd\" \n- [2] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueSeqs.Rd\" \n- [3] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueTrees.Rd\" \n- [4] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/findGroves.Rd\" \n- [5] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/findMRCIs.Rd\" \n- [6] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/fluTrees.Rd\" \n- [7] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/linearMrca.Rd\" \n- [8] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/medTree.Rd\" \n- [9] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/multiDist.Rd\" \n-[10] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/plotGroves.Rd\" \n-[11] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/plotGrovesD3.Rd\" \n-[12] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/plotTreeDiff.Rd\" \n-[13] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/refTreeDist.Rd\" \n-[14] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/tipDiff.Rd\" \n-[15] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treeDist.Rd\" \n-[16] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treeVec.Rd\" \n-[17] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treescape.Rd\" \n-[18] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treescapeServer.Rd\"\n-[19] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/wiwMedTree.Rd\" \n-[20] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/wiwTreeDist.Rd\" \n-[21] \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/woodmiceTrees.Rd\" \n+ [1] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueBEASTMCC.Rd\" \n+ [2] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueSeqs.Rd\" \n+ [3] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueTrees.Rd\" \n+ [4] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/findGroves.Rd\" \n+ [5] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/findMRCIs.Rd\" \n+ [6] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/fluTrees.Rd\" \n+ [7] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/linearMrca.Rd\" \n+ [8] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/medTree.Rd\" \n+ [9] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/multiDist.Rd\" \n+[10] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotGroves.Rd\" \n+[11] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotGrovesD3.Rd\" \n+[12] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotTreeDiff.Rd\" \n+[13] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/refTreeDist.Rd\" \n+[14] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/tipDiff.Rd\" \n+[15] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treeDist.Rd\" \n+[16] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treeVec.Rd\" \n+[17] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treescape.Rd\" \n+[18] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treescapeServer.Rd\"\n+[19] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/wiwMedTree.Rd\" \n+[20] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/wiwTreeDist.Rd\" \n+[21] \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/woodmiceTrees.Rd\" \n attr(,\"first\")\n-[1] 46\n+[1] 48\n"}]}]}, {"source1": "./usr/lib/R/site-library/treescape/help/treescape.rdb", "source2": "./usr/lib/R/site-library/treescape/help/treescape.rdb", "unified_diff": null, "details": [{"source1": "Rscript --vanilla - {}", "source2": "Rscript --vanilla - {}", "unified_diff": "@@ -13,15 +13,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Drummond, A. J., and Rambaut, A. (2007) \\n\", Rd_tag = \"TEXT\"), \n structure(\"BEAST: Bayesian evolutionary analysis by sampling trees.\\n\", Rd_tag = \"TEXT\"), \n structure(list(structure(\"BMC Evolutionary Biology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n structure(\", 7(1), 214.\\n\", Rd_tag = \"TEXT\"), structure(\"\\n\", Rd_tag = \"TEXT\"), \n structure(\"Lanciotti, R. S., Gubler, D. J., and Trent, D. W. (1997)\\n\", Rd_tag = \"TEXT\"), \n structure(\"Molecular evolution and phylogeny of dengue-4 viruses.\\n\", Rd_tag = \"TEXT\"), \n structure(list(structure(\"Journal of General Virology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n- structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueBEASTMCC.Rd\", class = \"Rd\", meta = list(\n+ structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueBEASTMCC.Rd\", class = \"Rd\", meta = list(\n docType = \"data\"), prepared = 3L)\n \n DengueSeqs (list) = structure(list(structure(list(structure(\"Dengue fever sequences\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"DengueSeqs\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"DengueSeqs\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"datasets\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\keyword\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"17 dengue virus serotype 4 sequences from Lanciotti et al. (1997)\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n@@ -29,15 +29,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Michelle Kendall \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"michelle.louise.kendall@gmail.com\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\email\"), \n structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-214\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\source\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Lanciotti, R. S., Gubler, D. J., and Trent, D. W. (1997)\\n\", Rd_tag = \"TEXT\"), \n structure(\"Molecular evolution and phylogeny of dengue-4 viruses.\\n\", Rd_tag = \"TEXT\"), \n structure(list(structure(\"Journal of General Virology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n- structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueSeqs.Rd\", class = \"Rd\", meta = list(\n+ structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueSeqs.Rd\", class = \"Rd\", meta = list(\n docType = \"data\"), prepared = 3L)\n \n DengueTrees (list) = structure(list(structure(list(structure(\"BEAST analysis of Dengue fever\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"DengueTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"DengueTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"datasets\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\keyword\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"These trees were created using one of the \", Rd_tag = \"TEXT\"), \n@@ -57,15 +57,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Drummond, A. J., and Rambaut, A. (2007) \\n\", Rd_tag = \"TEXT\"), \n structure(\"BEAST: Bayesian evolutionary analysis by sampling trees.\\n\", Rd_tag = \"TEXT\"), \n structure(list(structure(\"BMC Evolutionary Biology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n structure(\", 7(1), 214.\\n\", Rd_tag = \"TEXT\"), structure(\"\\n\", Rd_tag = \"TEXT\"), \n structure(\"Lanciotti, R. S., Gubler, D. J., and Trent, D. W. (1997)\\n\", Rd_tag = \"TEXT\"), \n structure(\"Molecular evolution and phylogeny of dengue-4 viruses.\\n\", Rd_tag = \"TEXT\"), \n structure(list(structure(\"Journal of General Virology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n- structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/DengueTrees.Rd\", class = \"Rd\", meta = list(\n+ structure(\", 78(9), 2279-2286.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/DengueTrees.Rd\", class = \"Rd\", meta = list(\n docType = \"data\"), prepared = 3L)\n \n findGroves (list) = structure(list(structure(list(structure(\"Identify clusters of similar trees\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"findGroves\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"findGroves\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"This function uses hierarchical clustering on principal components output by \", Rd_tag = \"TEXT\"), \n structure(list(structure(list(structure(\"treescape\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\link\")), Rd_tag = \"\\\\code\"), \n@@ -125,15 +125,15 @@\n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## run findGroves: treescape+clustering\\n\", Rd_tag = \"RCODE\"), \n structure(\"res <- findGroves(woodmiceTrees, nf=5, nclust=6)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## plot results on first 2 axes\\n\", Rd_tag = \"RCODE\"), \n structure(\"PCs <- res$treescape$pco$li\\n\", Rd_tag = \"RCODE\"), \n structure(\"s.class(PCs, fac=res$groups, col=funky(6))\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## using plotGroves\\n\", Rd_tag = \"RCODE\"), \n structure(\"plotGroves(res)\\n\", Rd_tag = \"RCODE\"), structure(\"}\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/findGroves.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/findGroves.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n findMRCIs (list) = structure(list(structure(list(structure(\"Find MRCIs\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"findMRCIs\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"findMRCIs\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Function to find the most recent common infector (MRCI) matrix from \\\"who infected whom\\\" information.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"findMRCIs(wiw)\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\usage\"), \n@@ -154,15 +154,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Michelle Kendall \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"michelle.louise.kendall@gmail.com\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\email\"), \n structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## a simple who infected whom matrix:\\n\", Rd_tag = \"RCODE\"), \n structure(\"tree1 <- cbind(Infector=1:5,Infectee=2:6) \\n\", Rd_tag = \"RCODE\"), \n structure(\"findMRCIs(tree1)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/findMRCIs.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/findMRCIs.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n fluTrees (list) = structure(list(structure(list(structure(\"BEAST analysis of seasonal influenza (A/H3N2)\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"fluTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"fluTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"datasets\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\keyword\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"These trees were created using BEAST on hemagglutinin (HA) segments\\n\", Rd_tag = \"TEXT\"), \n@@ -170,15 +170,15 @@\n structure(\"http://beast.bio.ed.ac.uk/tutorials\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"A multiPhylo object containing 200 trees, each with 165 tips\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\format\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Only the first 200 trees (out of 10,000) were retained.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\details\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Thibaut Jombart \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"thibautjombart@gmail.com\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\email\"), \n structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"http://beast.bio.ed.ac.uk/tutorials\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\source\"), \n- structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"http://beast.bio.ed.ac.uk/tutorials\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/fluTrees.Rd\", class = \"Rd\", meta = list(\n+ structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"http://beast.bio.ed.ac.uk/tutorials\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/fluTrees.Rd\", class = \"Rd\", meta = list(\n docType = \"data\"), prepared = 3L)\n \n hideOutput (NULL) = NULL\n \n linearMrca (list) = structure(list(structure(list(structure(\"Linear MRCA function\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"linearMrca\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"linearMrca\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n@@ -197,15 +197,15 @@\n structure(list(structure(\"michelle.louise.kendall@gmail.com\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\email\"), \n structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## generate a random tree\\n\", Rd_tag = \"RCODE\"), \n structure(\"x <- rtree(6)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## create matrix of MRCAs: entry (i,j) is the node number of the MRCA of tips i and j\\n\", Rd_tag = \"RCODE\"), \n structure(\"linearMrca(x,6)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/linearMrca.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/linearMrca.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n medTree (list) = structure(list(structure(list(structure(\"Geometric median tree function\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"medTree\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"medTree\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Finds the geometric median of a set of trees according to the Kendall Colijn metric.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"medTree(x, groups = NULL, lambda = 0, weights = NULL,\\n\", Rd_tag = \"RCODE\"), \n@@ -290,15 +290,15 @@\n structure(\"names(res.with.grp)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## get the first median of each\\n\", Rd_tag = \"RCODE\"), \n structure(\"med.trees <- lapply(res.with.grp, function(e) ladderize(e$trees[[1]]))\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## plot trees\\n\", Rd_tag = \"RCODE\"), \n structure(\"par(mfrow=c(2,3))\\n\", Rd_tag = \"RCODE\"), structure(\"for(i in 1:length(med.trees)) plot(med.trees[[i]], main=paste(\\\"cluster\\\",i))\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## highlight the differences between a pair of median trees\\n\", Rd_tag = \"RCODE\"), \n structure(\"plotTreeDiff(med.trees[[1]],med.trees[[5]])\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/medTree.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/medTree.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n multiDist (list) = structure(list(structure(list(structure(\"Metric function for \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"multiPhylo\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\"), \n structure(\" input\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"multiDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"multiDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n@@ -350,15 +350,15 @@\n structure(\"multiDist(trees)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## pairwise distance matrix as a function of lambda:\\n\", Rd_tag = \"RCODE\"), \n structure(\"m <- multiDist(trees, return.lambda.function=TRUE)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## evaluate at lambda=0. Equivalent to multiDist(trees).\\n\", Rd_tag = \"RCODE\"), \n structure(\"m0 <- m(0)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## save memory by recomputing each tree vector for each pairwise tree comparison (for fixed lambda):\\n\", Rd_tag = \"RCODE\"), \n structure(\"m0.5 <- multiDist(trees,0.5,save.memory=TRUE)\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/multiDist.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/multiDist.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n plotGroves (list) = structure(list(structure(list(structure(\"Scatterplot of groups of trees\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"plotGroves\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"plotGroves\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"This function displays the scatterplot of the Multidimensional\\n\", Rd_tag = \"TEXT\"), \n structure(\"Scaling (MDS) output by treescape, superimposing group information\\n\", Rd_tag = \"TEXT\"), \n@@ -455,15 +455,15 @@\n structure(\"plotGroves(res, type=\\\"ellipse\\\", lab.show=TRUE,\\n\", Rd_tag = \"VERB\"), \n structure(\"lab.optim=FALSE, scree.size=.35)\\n\", Rd_tag = \"VERB\"), \n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"## example with no group information\\n\", Rd_tag = \"VERB\"), \n structure(\"plotGroves(res$treescape$pco)\\n\", Rd_tag = \"VERB\"), \n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"## adding labels\\n\", Rd_tag = \"VERB\"), \n structure(\"plotGroves(res$treescape$pco, lab.show=TRUE, lab.cex=2)\\n\", Rd_tag = \"VERB\"), \n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"}\\n\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\dontrun\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/plotGroves.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotGroves.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n plotGrovesD3 (list) = structure(list(structure(list(structure(\"Scatterplot of groups of trees using \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"scatterD3\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"plotGrovesD3\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"plotGrovesD3\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"This function displays the scatterplot of the Multidimensional\\n\", Rd_tag = \"TEXT\"), \n@@ -532,15 +532,15 @@\n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"## adding tree labels\\n\", Rd_tag = \"VERB\"), \n structure(\"plotGrovesD3(res, treeNames=1:201)\\n\", Rd_tag = \"VERB\"), \n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"## customizing: vary the colour and the symbol by group\\n\", Rd_tag = \"VERB\"), \n structure(\"plotGrovesD3(res, symbol_var=res$groups)\\n\", Rd_tag = \"VERB\"), \n structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"## example with no group information\\n\", Rd_tag = \"VERB\"), \n structure(\"plotGrovesD3(res$treescape$pco)\\n\", Rd_tag = \"VERB\"), \n structure(\"}\\n\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\dontrun\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/plotGrovesD3.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotGrovesD3.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n plotTreeDiff (list) = structure(list(structure(list(structure(\"Plot tree differences\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"plotTreeDiff\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"plotTreeDiff\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Highlight the topologicial differences between two trees, plotted side by side. \\n\", Rd_tag = \"TEXT\"), \n structure(\"This function is useful for comparing representative \\\"median\\\" trees - see \", Rd_tag = \"TEXT\"), \n@@ -651,15 +651,15 @@\n structure(\"plotTreeDiff(woodmiceTrees[[1]],woodmiceTrees[[2]], tipDiff=wmTipDiff,\\n\", Rd_tag = \"RCODE\"), \n structure(\" baseCol=\\\"grey2\\\", col1=\\\"cyan\\\", col2=\\\"navy\\\", \\n\", Rd_tag = \"RCODE\"), \n structure(\" edge.width=2, type=\\\"radial\\\", cex=0.5, font=2)\\n\", Rd_tag = \"RCODE\"), \n structure(\"## use colour palette from adegenet:\\n\", Rd_tag = \"RCODE\"), \n structure(\"plotTreeDiff(woodmiceTrees[[1]],woodmiceTrees[[2]], tipDiff=wmTipDiff,\\n\", Rd_tag = \"RCODE\"), \n structure(\" baseCol=\\\"black\\\", colourMethod=\\\"palette\\\", \\n\", Rd_tag = \"RCODE\"), \n structure(\" edge.width=2, type=\\\"cladogram\\\", cex=0.5, font=2) \\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/plotTreeDiff.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/plotTreeDiff.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n refTreeDist (list) = structure(list(structure(list(structure(\"Metric function for comparing a reference \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"phylo\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\"), \n structure(\" to \", Rd_tag = \"TEXT\"), structure(list(structure(\"multiPhylo\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\"), \n structure(\" input\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"refTreeDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n@@ -703,15 +703,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## generate a single reference tree with 6 tips\\n\", Rd_tag = \"RCODE\"), \n structure(\"refTree <- rtree(6)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## generate 10 random trees, each with 6 tips\\n\", Rd_tag = \"RCODE\"), \n structure(\"trees <- rmtree(10,6)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## find the distances from each of the 10 random trees to the single reference tree\\n\", Rd_tag = \"RCODE\"), \n structure(\"refTreeDist(refTree,trees)\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/refTreeDist.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/refTreeDist.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n safeDeparse (closure) = function (obj) \n {\n tryCatch({\n deparse(obj)\n }, error = function(e) {\n@@ -760,15 +760,15 @@\n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## simple example on trees with five tips:\\n\", Rd_tag = \"RCODE\"), \n structure(\"tr1 <- read.tree(text=\\\"((A:1,B:1):1,((C:1,D:1):1,E:1):1):1;\\\")\\n\", Rd_tag = \"RCODE\"), \n structure(\"tr2 <- read.tree(text=\\\"((A:1,B:1):1,(C:1,(D:1,E:1):1):1):1;\\\")\\n\", Rd_tag = \"RCODE\"), \n structure(\"tipDiff(tr1,tr2)\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(\"## example on larger woodmice trees\\n\", Rd_tag = \"RCODE\"), \n structure(\"data(woodmiceTrees)\\n\", Rd_tag = \"RCODE\"), \n structure(\"tipDiff(woodmiceTrees[[1]],woodmiceTrees[[2]])\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/tipDiff.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/tipDiff.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n treeDist (list) = structure(list(structure(list(structure(\"Metric function\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"treeDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"treeDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Comparison of two trees using the Kendall Colijn metric\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"treeDist(tree.a, tree.b, lambda = 0, return.lambda.function = FALSE,\\n\", Rd_tag = \"RCODE\"), \n@@ -817,15 +817,15 @@\n structure(\"dist.func <- treeDist(tree.a,tree.b,return.lambda.function=TRUE) # distance as a function of lambda\\n\", Rd_tag = \"RCODE\"), \n structure(\"dist.func(0) # evaluate at lambda=0. Equivalent to treeDist(tree.a,tree.b).\\n\", Rd_tag = \"RCODE\"), \n structure(\"## We can see how the distance changes when moving from focusing on topology to length:\\n\", Rd_tag = \"RCODE\"), \n structure(\"plot(sapply(seq(0,1,length.out=100), function(x) dist.func(x)), type=\\\"l\\\",ylab=\\\"\\\",xlab=\\\"\\\")\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"## The distance may also change if we emphasise the position of certain tips:\\n\", Rd_tag = \"RCODE\"), \n structure(\"plot(sapply(tree.a$tip.label, function(x) treeDist(tree.a,tree.b,emphasise.tips=x)),\\n\", Rd_tag = \"RCODE\"), \n structure(\" xlab=\\\"Tip number\\\",ylab=\\\"Distance when vector entries corresponding to tip are doubled\\\")\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treeDist.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treeDist.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n treeVec (list) = structure(list(structure(list(structure(\"Tree vector function\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"treeVec\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"treeVec\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Function which takes an object of class phylo and outputs the vector for the Kendall Colijn metric.\\n\", Rd_tag = \"TEXT\"), \n structure(\"The elements of the vector are numeric if \", Rd_tag = \"TEXT\"), \n@@ -866,15 +866,15 @@\n structure(\"## generate a random tree\\n\", Rd_tag = \"RCODE\"), \n structure(\"tree <- rtree(6)\\n\", Rd_tag = \"RCODE\"), structure(\"## topological vector of mrca distances from root:\\n\", Rd_tag = \"RCODE\"), \n structure(\"treeVec(tree)\\n\", Rd_tag = \"RCODE\"), structure(\"## vector of mrca distances from root when lambda=0.5:\\n\", Rd_tag = \"RCODE\"), \n structure(\"treeVec(tree,0.5)\\n\", Rd_tag = \"RCODE\"), structure(\"## vector of mrca distances as a function of lambda:\\n\", Rd_tag = \"RCODE\"), \n structure(\"vecAsFunction <- treeVec(tree,return.lambda.function=TRUE)\\n\", Rd_tag = \"RCODE\"), \n structure(\"## evaluate the vector at lambda=0.5:\\n\", Rd_tag = \"RCODE\"), \n structure(\"vecAsFunction(0.5)\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treeVec.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treeVec.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n treescape (list) = structure(list(structure(list(structure(\"Phylogenetic tree exploration\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"treescape\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"treescape\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Compares phylogenetic trees and maps them into a small number of dimensions for easy visualisation and identification of clusters.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"treescape(x, method = \\\"treeVec\\\", nf = NULL, return.tree.vectors = FALSE,\\n\", Rd_tag = \"RCODE\"), \n@@ -979,15 +979,15 @@\n structure(\"xlab(\\\"\\\") + ylab(\\\"\\\") + theme_bw(base_family=\\\"\\\") # remove axis labels and grey background\\n\", Rd_tag = \"RCODE\"), \n structure(\"}\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n structure(list(structure(\"\\n\", Rd_tag = \"VERB\"), structure(\"if(require(rgl)){\\n\", Rd_tag = \"VERB\"), \n structure(\"plot3d(woodmicedf[,1], woodmicedf[,2], woodmicedf[,3], type=\\\"s\\\", size=1.5,\\n\", Rd_tag = \"VERB\"), \n structure(\"col=\\\"navy\\\", alpha=0.5, xlab=\\\"\\\", ylab=\\\"\\\", zlab=\\\"\\\")\\n\", Rd_tag = \"VERB\"), \n structure(\"}\\n\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\dontrun\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treescape.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treescape.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n treescapeServer (list) = structure(list(structure(list(structure(\"Web-based tree explorer\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"treescapeServer\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"treescapeServer\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"This function opens up an application in a web browser for an interactive exploration of the diversity in a set of trees.\\n\", Rd_tag = \"TEXT\"), \n structure(\"For further details please see the \\\"help\\\" tab within the application.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n@@ -999,15 +999,15 @@\n structure(\"michelle.louise.kendall@gmail.com\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\email\"), \n structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\author\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"For convenience, \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"treescapeServer\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\code\"), \n structure(\" is also available as a separate web app which can be used from any browser (it is not necessary to have \", Rd_tag = \"TEXT\"), \n structure(list(), Rd_tag = \"\\\\R\"), structure(\" installed): \", Rd_tag = \"TEXT\"), \n structure(list(structure(list(structure(\"http://shiny.imperial-stats-experimental.co.uk/users/mlkendal/treescape/\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\url\")), Rd_tag = \"LIST\"), \n- structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\seealso\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/treescapeServer.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\seealso\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/treescapeServer.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n wiwMedTree (list) = structure(list(structure(list(structure(\"Median transmission tree\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"wiwMedTree\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"wiwMedTree\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Function to find the median of a list of transmission scenarios\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"wiwMedTree(matList, sampled = NULL, weights = NULL)\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\usage\"), \n@@ -1050,15 +1050,15 @@\n structure(\"tree3 <- cbind(Infector=c(2,2,3,4,5),Infectee=c(1,3,4,5,6)) \\n\", Rd_tag = \"RCODE\"), \n structure(\"# create list of the MRCI depth matrices:\\n\", Rd_tag = \"RCODE\"), \n structure(\"matList <- lapply(list(tree1,tree2,tree3), function(x) findMRCIs(x)$mrciDepths)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"# median tree, assuming all cases are sampled:\\n\", Rd_tag = \"RCODE\"), \n structure(\"wiwMedTree(matList)\\n\", Rd_tag = \"RCODE\"), \n structure(\"# median tree when cases 1, 2 and 4 are sampled:\\n\", Rd_tag = \"RCODE\"), \n structure(\"wiwMedTree(matList, sampled=c(1,2,4))\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/wiwMedTree.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/wiwMedTree.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n wiwTreeDist (list) = structure(list(structure(list(structure(\"Transmission tree distance\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"wiwTreeDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"wiwTreeDist\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Function to find the distance between transmission trees by comparing their MRCI depth matrices; to be precise, by finding the Euclidean distance between the tree vectors, restricted to their sampled node entries.\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\description\"), \n structure(list(structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"wiwTreeDist(matList, sampled = NULL)\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\usage\"), \n@@ -1081,15 +1081,15 @@\n structure(\"tree3 <- cbind(Infector=c(2,2,3,4,5),Infectee=c(1,3,4,5,6)) \\n\", Rd_tag = \"RCODE\"), \n structure(\"# create list of the MRCI depth matrices:\\n\", Rd_tag = \"RCODE\"), \n structure(\"matList <- lapply(list(tree1,tree2,tree3), function(x) findMRCIs(x)$mrciDepths)\\n\", Rd_tag = \"RCODE\"), \n structure(\"\\n\", Rd_tag = \"RCODE\"), structure(\"# transmission tree distance, assuming all cases are sampled:\\n\", Rd_tag = \"RCODE\"), \n structure(\"wiwTreeDist(matList)\\n\", Rd_tag = \"RCODE\"), \n structure(\"# transmission tree distance when cases 1, 2 and 4 are sampled:\\n\", Rd_tag = \"RCODE\"), \n structure(\"wiwTreeDist(matList, sampled=c(1,2,4))\\n\", Rd_tag = \"RCODE\"), \n- structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/wiwTreeDist.Rd\", class = \"Rd\", meta = list(\n+ structure(\"\\n\", Rd_tag = \"RCODE\")), Rd_tag = \"\\\\examples\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/wiwTreeDist.Rd\", class = \"Rd\", meta = list(\n docType = character(0)), prepared = 3L)\n \n woodmiceTrees (list) = structure(list(structure(list(structure(\"Bootstrap trees from woodmouse dataset\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\title\"), \n structure(list(structure(\"woodmiceTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\name\"), \n structure(list(structure(\"woodmiceTrees\", Rd_tag = \"VERB\")), Rd_tag = \"\\\\alias\"), \n structure(list(structure(\"datasets\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\keyword\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"These trees were created using the neighbour-joining and bootstrapping\\n\", Rd_tag = \"TEXT\"), \n@@ -1102,10 +1102,10 @@\n structure(\"woodmouse (Apodemus sylvaticus) which is a subset of the data analysed by\\n\", Rd_tag = \"TEXT\"), \n structure(\"Michaux et al. (2003). The full data set is available through GenBank\\n\", Rd_tag = \"TEXT\"), \n structure(\"(accession numbers AJ511877 to AJ511987)\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\source\"), \n structure(list(structure(\"\\n\", Rd_tag = \"TEXT\"), structure(\"Michaux, J. R., Magnanou, E., Paradis, E., Nieberding, C. and\\n\", Rd_tag = \"TEXT\"), \n structure(\"Libois, R. (2003) Mitochondrial phylogeography of the Woodmouse (Apodemus\\n\", Rd_tag = \"TEXT\"), \n structure(\"sylvaticus) in the Western Palearctic region. \", Rd_tag = \"TEXT\"), \n structure(list(structure(\"Molecular Ecology\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\emph\"), \n- structure(\", 12,\\n\", Rd_tag = \"TEXT\"), structure(\"685-697\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/1st/r-cran-treescape-1.10.18+dfsg/man/woodmiceTrees.Rd\", class = \"Rd\", meta = list(\n+ structure(\", 12,\\n\", Rd_tag = \"TEXT\"), structure(\"685-697\\n\", Rd_tag = \"TEXT\")), Rd_tag = \"\\\\references\")), Rdfile = \"/build/2/r-cran-treescape-1.10.18+dfsg/2nd/man/woodmiceTrees.Rd\", class = \"Rd\", meta = list(\n docType = \"data\"), prepared = 3L)\n \n"}]}, {"source1": "./usr/lib/R/site-library/treescape/help/treescape.rdx", "source2": "./usr/lib/R/site-library/treescape/help/treescape.rdx", "unified_diff": null, "details": [{"source1": "treescape.rdx-content", "source2": "treescape.rdx-content", "unified_diff": null, "details": [{"source1": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "source2": "Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}", "unified_diff": "@@ -1,133 +1,133 @@\n $variables\n $variables$DengueBEASTMCC\n-[1] 292 1207\n+[1] 294 1208\n \n $variables$DengueSeqs\n-[1] 1786 1015\n+[1] 1791 1018\n \n $variables$DengueTrees\n-[1] 3087 1619\n+[1] 3097 1622\n \n $variables$findGroves\n-[1] 4992 2583\n+[1] 5007 2586\n \n $variables$findMRCIs\n-[1] 7861 1528\n+[1] 7881 1531\n \n $variables$fluTrees\n-[1] 9673 1036\n+[1] 9698 1037\n \n $variables$linearMrca\n-[1] 10995 1197\n+[1] 11023 1200\n \n $variables$medTree\n-[1] 12475 3698\n+[1] 12508 3701\n \n $variables$multiDist\n-[1] 16458 2553\n+[1] 16496 2556\n \n $variables$plotGroves\n-[1] 19298 3447\n+[1] 19340 3449\n \n $variables$plotGrovesD3\n-[1] 23034 2822\n+[1] 23080 2823\n \n $variables$plotTreeDiff\n-[1] 26144 3963\n+[1] 26192 3965\n \n $variables$refTreeDist\n-[1] 30394 2192\n+[1] 30445 2194\n \n $variables$tipDiff\n-[1] 32870 1874\n+[1] 32924 1875\n \n $variables$treeDist\n-[1] 35027 2356\n+[1] 35084 2358\n \n $variables$treeVec\n-[1] 37666 2135\n+[1] 37726 2137\n \n $variables$treescape\n-[1] 40082 3623\n+[1] 40146 3624\n \n $variables$treescapeServer\n-[1] 43990 1153\n+[1] 44056 1156\n \n $variables$wiwMedTree\n-[1] 45430 1962\n+[1] 45501 1964\n \n $variables$wiwTreeDist\n-[1] 47678 1548\n+[1] 47754 1549\n \n $variables$woodmiceTrees\n-[1] 49514 1259\n+[1] 49592 1261\n \n \n $references\n $references$`env::1`\n-[1] 0 292\n+[1] 0 294\n \n $references$`env::10`\n-[1] 19011 287\n+[1] 19052 288\n \n $references$`env::11`\n-[1] 22745 289\n+[1] 22789 291\n \n $references$`env::12`\n-[1] 25856 288\n+[1] 25903 289\n \n $references$`env::13`\n-[1] 30107 287\n+[1] 30157 288\n \n $references$`env::14`\n-[1] 32586 284\n+[1] 32639 285\n \n $references$`env::15`\n-[1] 34744 283\n+[1] 34799 285\n \n $references$`env::16`\n-[1] 37383 283\n+[1] 37442 284\n \n $references$`env::17`\n-[1] 39801 281\n+[1] 39863 283\n \n $references$`env::18`\n-[1] 43705 285\n+[1] 43770 286\n \n $references$`env::19`\n-[1] 45143 287\n+[1] 45212 289\n \n $references$`env::2`\n-[1] 1499 287\n+[1] 1502 289\n \n $references$`env::20`\n-[1] 47392 286\n+[1] 47465 289\n \n $references$`env::21`\n-[1] 49226 288\n+[1] 49303 289\n \n $references$`env::3`\n-[1] 2801 286\n+[1] 2809 288\n \n $references$`env::4`\n-[1] 4706 286\n+[1] 4719 288\n \n $references$`env::5`\n-[1] 7575 286\n+[1] 7593 288\n \n $references$`env::6`\n-[1] 9389 284\n+[1] 9412 286\n \n $references$`env::7`\n-[1] 10709 286\n+[1] 10735 288\n \n $references$`env::8`\n-[1] 12192 283\n+[1] 12223 285\n \n $references$`env::9`\n-[1] 16173 285\n+[1] 16209 287\n \n \n $compressed\n [1] TRUE\n \n"}]}]}, {"source1": "./usr/lib/R/site-library/treescape/libs/treescape.so", "source2": "./usr/lib/R/site-library/treescape/libs/treescape.so", "comments": ["File has been modified after NT_GNU_BUILD_ID has been applied."], "unified_diff": null, "details": [{"source1": "readelf --wide --notes {}", "source2": "readelf --wide --notes {}", "unified_diff": "@@ -1,4 +1,4 @@\n \n Displaying notes found in: .note.gnu.build-id\n Owner Data size \tDescription\n- GNU 0x00000014\tNT_GNU_BUILD_ID (unique build ID bitstring)\t Build ID: 77267ce8dc33bfdadc634458e8e2dffa02ca3487\n+ GNU 0x00000014\tNT_GNU_BUILD_ID (unique build ID bitstring)\t Build ID: 2e58fb56a2733de8d462fc078df57fc924f23952\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": "@@ -191,49 +191,49 @@\n Rcpp::internal::enterRNGScope():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:93\n \tmov %r15,%rdi\n \tcall 5240 <__cxa_guard_abort@plt>\n \tmov %rbx,%rdi\n \tmov %rbp,%rax\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,%rax\n \tje 5989 , std::allocator > const&)@@Base+0x285>\n \tjg 58af , std::allocator > const&)@@Base+0x1ab>\n \tcmp $0x3,%rax\n \tje 59fd , std::allocator > const&)@@Base+0x2f9>\n \tcmp $0x1,%rax\n \tje 5a48 , std::allocator > const&)@@Base+0x344>\n \tcmp $0x2,%rax\n \tje 5a73 , std::allocator > const&)@@Base+0x36f>\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 \tcall 5150 <__cxa_begin_catch@plt>\n \tlea 0xb0(%rsp),%rbp\n \tlea 0x77fd(%rip),%rsi # d0c0 @@Base+0x50>\n \tmov %rbp,%rdi\n \tcall 6760 ::~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 \tmov %rbp,%rdi\n \tcall 5560 , std::allocator > const&)@plt>\n \tmov %rax,%rdi\n \tcall 5270 \n std::__cxx11::basic_string, std::allocator >::~basic_string():\n /usr/include/c++/12/bits/basic_string.h:795 (discriminator 35)\n \tmov %rbp,%rdi\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 \tmov %rax,%rbx\n std::__cxx11::basic_string, std::allocator >::~basic_string():\n /usr/include/c++/12/bits/basic_string.h:795 (discriminator 35)\n \tcall 5450 , std::allocator >::_M_dispose()@plt>\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 35)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 35)\n \tcall 5590 <__cxa_end_catch@plt>\n \tjmp 59ab , std::allocator > const&)@@Base+0x2a7>\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 \tmov %r15,%rdi\n \tcall 5240 <__cxa_guard_abort@plt>\n \tmov %rbx,%rdi\n \tcall 55f0 <_Unwind_Resume@plt>\n Rcpp::Rcpp_PreciousRelease(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/RcppCommon.h:121\n \tmov 0x98(%rsp),%rdi\n@@ -265,104 +265,104 @@\n \tcall 5250 <__cxa_guard_release@plt>\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:100\n \tcall *0xb082(%rip) \n \tmov %rbp,%rdi\n \tmov %r12,%rax\n \tjmp 5885 , std::allocator > const&)@@Base+0x181>\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 \tcall 5150 <__cxa_begin_catch@plt>\n exception_to_r_condition(std::exception const&):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:353 (discriminator 18)\n \tmov $0x1,%esi\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 %rax,%rdi\n exception_to_r_condition(std::exception const&):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:353 (discriminator 18)\n \tcall 50a0 (std::exception const&, bool)@plt>\n \tmov %rax,%rdi\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 \tcall 5270 \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 %rax,%rbx\n \tcall 5590 <__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 \tmov 0xacd6(%rip),%rdi \n \tmov %rbx,%rsi\n \tcall 5040 \n \tmov %rax,%rdi\n \tcall 5270 \n \tmov %rax,%rdi\n \tmov 0xa5d4(%rip),%rax \n \tmov (%rax),%rsi\n \tcall 5300 \n \tmov $0x2,%edi\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 \tcall 51a0 \n \tmov 0xa4d3(%rip),%rax \n \tmov (%rax),%rbp\n \tjmp 7189 \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 %rax,%rbx\n \tcall 5590 <__cxa_end_catch@plt>\n \tmov %rbx,%rdi\n \tcall 55f0 <_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 \tcall 5150 <__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 %rax,%rdi\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 %rax,%rbx\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 50c0 \n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:349\n \tmovzbl 0x28(%rbx),%esi\n \tmov %rbx,%rdi\n \tcall 5670 (Rcpp::exception const&, bool)@plt>\n \tmov %rax,%rdi\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 \tcall 5270 \n \tjmp 59a3 , std::allocator > const&)@@Base+0x29f>\n std::__cxx11::basic_string, std::allocator >::~basic_string():\n /usr/include/c++/12/bits/basic_string.h:795\n \tmov %rbp,%rdi\n \tmov %rax,%rbx\n \tcall 5450 , std::allocator >::_M_dispose()@plt>\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:22 (discriminator 32)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:22 (discriminator 32)\n \tcall 5590 <__cxa_end_catch@plt>\n \tmov %rbx,%rdi\n \tcall 55f0 <_Unwind_Resume@plt>\n Rcpp::internal::exitRNGScope():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:99\n \tmov %rbx,%rdi\n \tcall 5240 <__cxa_guard_abort@plt>\n treescape_updateDistancesWithCombinations():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/RNGScope.h:30\n \tcall 50d0 \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 \tcall 5150 <__cxa_begin_catch@plt>\n \tcall 5590 <__cxa_end_catch@plt>\n \tcall 5440 \n \txor %edi,%edi\n \tjmp 59d9 , std::allocator > const&)@@Base+0x2d5>\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 %rax,%rbx\n \tjmp 5a2e , std::allocator > const&)@@Base+0x32a>\n \tmov %rax,%rbx\n \tcall 5590 <__cxa_end_catch@plt>\n \tmov %rbx,%rdi\n \tcall 55f0 <_Unwind_Resume@plt>\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 \tcall 5150 <__cxa_begin_catch@plt>\n \tmov (%rax),%rbx\n \tcall 5590 <__cxa_end_catch@plt>\n Rcpp::internal::isLongjumpSentinel(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:139 (discriminator 16)\n \tlea 0x7672(%rip),%rsi # d0f9 @@Base+0x89>\n \tmov %rbx,%rdi\n@@ -410,26 +410,26 @@\n \tmov %rax,0xac27(%rip) \n \tcall 5120 \n \tmov %rbx,%rdi\n \tcall 55f0 <_Unwind_Resume@plt>\n _GLOBAL__sub_I_RcppExports.cpp.cold():\n \txchg %ax,%ax\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 %r13\n \tpush %r12\n \tpush %rbp\n /usr/include/c++/12/iostream:74\n \tlea 0xab54(%rip),%rbp \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 %rbx\n /usr/include/c++/12/iostream:74\n \tmov %rbp,%rdi\n \tlea 0xa819(%rip),%rbx \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 \tsub $0x28,%rsp\n \tmov 0xa3d6(%rip),%rax # ff08 >@GLIBCXX_3.4>\n \tmov 0xa3ef(%rip),%r12 # ff28 @@Base+0x360>\n \tmov 0xa3b8(%rip),%r13 # fef8 @@Base+0x3f0>\n \tadd $0x10,%rax\n \tmovq %rax,%xmm0\n \tlea 0x18(%r12),%rax\n@@ -554,47 +554,47 @@\n /usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:34\n \tadd $0x10,%rax\n \tmov %rax,0xa6d1(%rip) \n /usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:90\n \tcall 5330 <__cxa_atexit@plt>\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tmov 0xa275(%rip),%rdi \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 $0x28,%rsp\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tmov %rbx,%rdx\n \tlea 0xa68f(%rip),%rsi \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 \tpop %rbx\n \tpop %rbp\n \tpop %r12\n \tpop %r13\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tjmp 5330 <__cxa_atexit@plt>\n /usr/include/c++/12/bits/basic_ios.h:282\n \tmov %rax,%rbx\n \tjmp 56c0 <__cxa_finalize@plt+0x10>\n \tmov %rax,%rbx\n \tjmp 56e2 <__cxa_finalize@plt+0x32>\n \tnopl 0x0(%rax)\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 %r13\n \tpush %r12\n \tpush %rbp\n /usr/include/c++/12/iostream:74\n \tlea 0xac54(%rip),%rbp \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 %rbx\n __static_initialization_and_destruction_0():\n /usr/include/c++/12/iostream:74\n \tmov %rbp,%rdi\n \tlea 0xa5f9(%rip),%rbx \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 \tsub $0x28,%rsp\n \tmov 0xa1b6(%rip),%rax # ff08 >@GLIBCXX_3.4>\n \tmov 0xa1cf(%rip),%r12 # ff28 @@Base+0x360>\n \tmov 0xa198(%rip),%r13 # fef8 @@Base+0x3f0>\n \tadd $0x10,%rax\n \tmovq %rax,%xmm0\n \tlea 0x18(%r12),%rax\n@@ -760,22 +760,22 @@\n \tmov %rax,0xa7d1(%rip) \n __static_initialization_and_destruction_0():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:90\n \tcall 5330 <__cxa_atexit@plt>\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tmov 0xa055(%rip),%rdi \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 $0x28,%rsp\n __static_initialization_and_destruction_0():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tmov %rbx,%rdx\n \tlea 0xa78f(%rip),%rsi \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 \tpop %rbx\n \tpop %rbp\n \tpop %r12\n \tpop %r13\n __static_initialization_and_destruction_0():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/Named.h:64\n \tjmp 5330 <__cxa_atexit@plt>\n@@ -836,108 +836,108 @@\n frame_dummy():\n \tendbr64\n \tjmp 5f80 , std::allocator > const&)@@Base+0x87c>\n \tnopl 0x0(%rax)\n \n 0000000000006010 &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@@Base>:\n updateDistancesWithCombinations(Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int):\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:13\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:13\n \tpush %r15\n \tmov %rdi,%r15\n \tpush %r14\n \tmov %rsi,%r14\n \tpush %r13\n \tmov %r8,%r13\n \tpush %r12\n \tmov %rcx,%r12\n \tpush %rbp\n \tpush %rbx\n \tmov %rdx,%rbx\n \tsub $0x28,%rsp\n \tmov %r9d,0x14(%rsp)\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 \tmovq $0x0,0x18(%rsp)\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 \tmovsd %xmm0,0x8(%rsp)\n \tnopl 0x0(%rax)\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/Vector.h:276 (discriminator 1)\n \tmov (%rbx),%rdi\n \tcall 5410 \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 0x18(%rsp),%rcx\n \tcmp %rcx,%rax\n \tjle 60e8 &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@@Base+0xd8>\n \tlea 0x0(,%rcx,4),%rax\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 \txor %ebp,%ebp\n \tmov %rax,(%rsp)\n \tjmp 60c8 &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@@Base+0xb8>\n \txchg %ax,%ax\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 0x10(%rbx),%rax\n \tmov (%rsp),%rdx\n \tmov (%rax,%rdx,1),%esi\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 0x10(%r12),%rax\n \tmov (%rax,%rbp,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,%esi\n \tjle 608d &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@@Base+0x7d>\n \tmov %esi,%edi\n \tmov %eax,%esi\n \tmov %edi,%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 0x10(%r13),%r8\n \tlea -0x1(%rsi),%edi\n \tsub %esi,%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 \tpxor %xmm0,%xmm0\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/traits.h:46 (discriminator 2)\n \tmovslq %edi,%rdi\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 0x10(%r15),%rsi\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 \tcvtsi2sdl 0x14(%rsp),%xmm0\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 \tmovsd 0x8(%rsp),%xmm1\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 (%r8,%rdi,4),%eax\n \tadd $0x1,%rbp\n \tsub $0x1,%eax\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/traits.h:46 (discriminator 2)\n \tcltq\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 \tmovsd %xmm1,(%rsi,%rax,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 \tmov 0x10(%r14),%rsi\n \tmovsd %xmm0,(%rsi,%rax,8)\n /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/Vector.h:276 (discriminator 1)\n \tmov (%r12),%rdi\n \tcall 5410 \n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/CPP_update_combinations.cpp:16 (discriminator 1)\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/CPP_update_combinations.cpp:16 (discriminator 1)\n \tcmp %rbp,%rax\n \tjg 6070 &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@@Base+0x60>\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 \taddq $0x1,0x18(%rsp)\n \tjmp 6048 &, Rcpp::Vector<14, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, Rcpp::Vector<13, Rcpp::PreserveStorage>&, double, int)@@Base+0x38>\n \tnopl 0x0(%rax)\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 $0x28,%rsp\n \tpop %rbx\n \tpop %rbp\n \tpop %r12\n \tpop %r13\n \tpop %r14\n \tpop %r15\n \tret\n \tnopw 0x0(%rax,%rax,1)\n \n 0000000000006100 :\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 \tcs nopw 0x0(%rax,%rax,1)\n \tnopl 0x0(%rax,%rax,1)\n \n 0000000000006110 ::xsputn(char const*, long)@@Base>:\n Rcpp::Rstreambuf::xsputn(char const*, long):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:56\n@@ -2288,15 +2288,15 @@\n Rcpp::Vector<13, Rcpp::PreserveStorage> Rcpp::internal::as >(SEXPREC*, Rcpp::traits::r_type_generic_tag) [clone .isra.0]:\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:159\n \tdata16 cs nopw 0x0(%rax,%rax,1)\n \tnopl (%rax)\n \n 0000000000006fe0 :\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 %r15\n \tpush %r14\n \tmov %rdi,%r14\n \tpush %r13\n \tmov %rsi,%r13\n \tpush %r12\n \tmov %rdx,%r12\n@@ -2307,19 +2307,19 @@\n \tsub $0xe8,%rsp\n \tmov 0x120(%rsp),%rax\n \tmov %r9,(%rsp)\n \tmov %rax,0x8(%rsp)\n \tmov %fs:0x28,%rax\n \tmov %rax,0xd8(%rsp)\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 0x9655(%rip),%eax \n \ttest %al,%al\n \tjne 7046 \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 \tlea 0x964a(%rip),%r15 \n \tmov %r15,%rdi\n \tcall 5620 <__cxa_guard_acquire@plt>\n \ttest %eax,%eax\n \tjne 7370 \n Rcpp::internal::enterRNGScope():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:93 (discriminator 2)\n@@ -2362,29 +2362,29 @@\n int Rcpp::internal::as(SEXPREC*, Rcpp::traits::r_type_primitive_tag):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/as.h:44\n \tmov %eax,%ebx\n double Rcpp::internal::as(SEXPREC*, Rcpp::traits::r_type_primitive_tag):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/as.h:44\n \tcall 51e0 (SEXPREC*)@plt>\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:20\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:20\n \tmov %ebx,%r9d\n \tmov %rbp,%r8\n \tmov %r12,%rcx\n \tmov %r13,%rdx\n \tmov %r14,%rsi\n \tmov %r15,%rdi\n \tcall 54b0 &, 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 0x8dd7(%rip),%rax \n Rcpp::PreserveStorage >::~PreserveStorage():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/storage/PreserveStorage.h:34\n \tmov 0x98(%rsp),%r12\n treescape_updateDistancesWithCombinations():\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:21\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:21\n \tmov (%rax),%rbp\n Rcpp::Rcpp_precious_remove(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:159\n \tmovzbl 0x98e5(%rip),%eax \n \ttest %al,%al\n \tje 72f0 \n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:160\n@@ -2438,15 +2438,15 @@\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:99\n \tmovzbl 0x9879(%rip),%eax \n \ttest %al,%al\n \tje 71b8 \n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:100\n \tcall *0x9877(%rip) \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 0xd8(%rsp),%rax\n \tsub %fs:0x28,%rax\n \tjne 7390 \n \tadd $0xe8,%rsp\n \tmov %rbp,%rax\n \tpop %rbx\n \tpop %rbp\n@@ -2550,51 +2550,51 @@\n \tcall 5350 \n \tmov %r15,%rdi\n \tmov %rax,0x96ac(%rip) \n \tcall 5250 <__cxa_guard_release@plt>\n \tjmp 7055 \n \txchg %ax,%ax\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 \tlea 0x63b0(%rip),%rdi # d727 @@Base+0x6b7>\n \tcall 5260 \n \tmov %r15,%rdi\n \tmov %rax,0x9302(%rip) \n \tcall 5250 <__cxa_guard_release@plt>\n \tjmp 7046 \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 53e0 <__stack_chk_fail@plt>\n \tjmp 5829 , std::allocator > const&)@@Base+0x125>\n \tjmp 5836 , std::allocator > const&)@@Base+0x132>\n \tjmp 5843 , std::allocator > const&)@@Base+0x13f>\n \tjmp 5850 , std::allocator > const&)@@Base+0x14c>\n \tjmp 585d , std::allocator > const&)@@Base+0x159>\n \tjmp 586a , std::allocator > const&)@@Base+0x166>\n Rcpp::internal::enterRNGScope():\n /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:93\n \tmov %rax,%rbx\n \tmov %rdx,%rbp\n \tjmp 5877 , std::allocator > const&)@@Base+0x173>\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 %rax,%rbx\n \tjmp 58f0 , std::allocator > const&)@@Base+0x1ec>\n Rcpp::Rcpp_PreciousRelease(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/RcppCommon.h:121\n \tmov %rax,%rbp\n \tmov %rdx,%rbx\n \tjmp 5900 , std::allocator > const&)@@Base+0x1fc>\n \tmov %rax,%rbp\n \tmov %rdx,%rbx\n \tjmp 592b , std::allocator > const&)@@Base+0x227>\n \tmov %rax,%rbp\n \tmov %rdx,%rbx\n \tjmp 5917 , std::allocator > const&)@@Base+0x213>\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 %rax,%rdi\n \tmov %rdx,%rax\n \tjmp 5885 , std::allocator > const&)@@Base+0x181>\n Rcpp::Rcpp_PreciousRelease(SEXPREC*):\n /usr/lib/R/site-library/Rcpp/include/RcppCommon.h:121\n \tmov %rax,%rbp\n \tmov %rdx,%rbx\n@@ -2609,17 +2609,17 @@\n \tjmp 5938 , std::allocator > const&)@@Base+0x234>\n treescape_updateDistancesWithCombinations():\n \tcs nopw 0x0(%rax,%rax,1)\n \tnopl (%rax)\n \n 0000000000007420 ::do_widen(char) const@@Base>:\n std::ctype::do_widen(char) const:\n-/build/1st/r-cran-treescape-1.10.18+dfsg/src/RcppExports.cpp:1092\n+/build/2/r-cran-treescape-1.10.18+dfsg/2nd/src/RcppExports.cpp:1092\n \tmov %esi,%eax\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 \tret\n \tcs nopw 0x0(%rax,%rax,1)\n \tnopl (%rax)\n \n 0000000000007430 :\n Rcpp::exception::what() const:\n /usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:53\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 32363763 65386463 33336266 64616463 267ce8dc33bfdadc\n- 0x00000010 36333434 35386538 65326466 66613032 634458e8e2dffa02\n- 0x00000020 63613334 38372e64 65627567 00000000 ca3487.debug....\n- 0x00000030 88ff5bf2 ..[.\n+ 0x00000000 35386662 35366132 37333364 65386434 58fb56a2733de8d4\n+ 0x00000010 36326663 30373864 66353766 63393234 62fc078df57fc924\n+ 0x00000020 66323339 35322e64 65627567 00000000 f23952.debug....\n+ 0x00000030 45c2fb81 E...\n \n"}]}]}]}]}, {"source1": "r-cran-treescape-dbgsym_1.10.18+dfsg-2_amd64.deb", "source2": "r-cran-treescape-dbgsym_1.10.18+dfsg-2_amd64.deb", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,3 +1,3 @@\n -rw-r--r-- 0 0 0 4 2020-05-22 06:51:07.000000 debian-binary\n--rw-r--r-- 0 0 0 544 2020-05-22 06:51:07.000000 control.tar.xz\n--rw-r--r-- 0 0 0 235684 2020-05-22 06:51:07.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 548 2020-05-22 06:51:07.000000 control.tar.xz\n+-rw-r--r-- 0 0 0 235672 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: amd64\n Maintainer: Debian R Packages Maintainers \n Installed-Size: 254\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: 77267ce8dc33bfdadc634458e8e2dffa02ca3487\n+Build-Ids: 2e58fb56a2733de8d462fc078df57fc924f23952\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/77/267ce8dc33bfdadc634458e8e2dffa02ca3487.debug\n+usr/lib/debug/.build-id/2e/58fb56a2733de8d462fc078df57fc924f23952.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", 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94\t(udata)\t21\t(line_strp)\t(offset: 0x6c9): time_t.h\n+ 95\t(udata)\t18\t(line_strp)\t(offset: 0x6d2): stdint-intn.h\n+ 96\t(udata)\t21\t(line_strp)\t(offset: 0x6e0): __sigset_t.h\n+ 97\t(udata)\t21\t(line_strp)\t(offset: 0x6ed): struct_timespec.h\n+ 98\t(udata)\t20\t(line_strp)\t(offset: 0x6ff): stdarg.h\n+ 99\t(udata)\t0\t(line_strp)\t(offset: 0x708): \n+ 100\t(udata)\t21\t(line_strp)\t(offset: 0x713): wint_t.h\n+ 101\t(udata)\t21\t(line_strp)\t(offset: 0x71c): __mbstate_t.h\n+ 102\t(udata)\t21\t(line_strp)\t(offset: 0x71e): mbstate_t.h\n+ 103\t(udata)\t21\t(line_strp)\t(offset: 0x72a): __FILE.h\n+ 104\t(udata)\t21\t(line_strp)\t(offset: 0x733): struct_FILE.h\n+ 105\t(udata)\t21\t(line_strp)\t(offset: 0x72c): FILE.h\n+ 106\t(udata)\t19\t(line_strp)\t(offset: 0x80a): wchar.h\n+ 107\t(udata)\t18\t(line_strp)\t(offset: 0x741): wchar2.h\n+ 108\t(udata)\t21\t(line_strp)\t(offset: 0x74a): struct_tm.h\n+ 109\t(udata)\t18\t(line_strp)\t(offset: 0x756): stdint-uintn.h\n+ 110\t(udata)\t19\t(line_strp)\t(offset: 0x765): stdint.h\n+ 111\t(udata)\t19\t(line_strp)\t(offset: 0x76e): locale.h\n+ 112\t(udata)\t18\t(line_strp)\t(offset: 0x777): stdlib-float.h\n+ 113\t(udata)\t18\t(line_strp)\t(offset: 0x786): stdlib-bsearch.h\n+ 114\t(udata)\t18\t(line_strp)\t(offset: 0x6b6): stdlib.h\n+ 115\t(udata)\t21\t(line_strp)\t(offset: 0x797): __fpos_t.h\n+ 116\t(udata)\t19\t(line_strp)\t(offset: 0x7a2): stdio.h\n+ 117\t(udata)\t18\t(line_strp)\t(offset: 0x7aa): stdio2.h\n+ 118\t(udata)\t18\t(line_strp)\t(offset: 0x7a2): stdio.h\n+ 119\t(udata)\t22\t(line_strp)\t(offset: 0xc1a): Boolean.h\n+ 120\t(udata)\t22\t(line_strp)\t(offset: 0x7b3): Complex.h\n+ 121\t(udata)\t19\t(line_strp)\t(offset: 0x5e7): string.h\n+ 122\t(udata)\t22\t(line_strp)\t(offset: 0x7bd): Rdynload.h\n+ 123\t(udata)\t23\t(line_strp)\t(offset: 0x7c8): Rinternals.h\n+ 124\t(udata)\t18\t(line_strp)\t(offset: 0x7d5): setjmp.h\n+ 125\t(udata)\t21\t(line_strp)\t(offset: 0x7de): struct___jmp_buf_tag.h\n+ 126\t(udata)\t16\t(line_strp)\t(offset: 0x7f5): atomic_word.h\n+ 127\t(udata)\t18\t(line_strp)\t(offset: 0x803): wctype-wchar.h\n+ 128\t(udata)\t19\t(line_strp)\t(offset: 0x812): wctype.h\n+ 129\t(udata)\t19\t(line_strp)\t(offset: 0x81b): time.h\n+ 130\t(udata)\t24\t(line_strp)\t(offset: 0x822): execution_defs.h\n+ 131\t(udata)\t25\t(line_strp)\t(offset: 0x840): macros.h\n+ 132\t(udata)\t8\t(line_strp)\t(offset: 0x849): const_string_proxy.h\n+ 133\t(udata)\t8\t(line_strp)\t(offset: 0x86f): const_generic_proxy.h\n+ 134\t(udata)\t11\t(line_strp)\t(offset: 0xc24): caster.h\n+ 135\t(udata)\t13\t(line_strp)\t(offset: 0x892): integral_constant.h\n+ 136\t(udata)\t13\t(line_strp)\t(offset: 0x8a6): expands_to_logical.h\n+ 137\t(udata)\t13\t(line_strp)\t(offset: 0x8bb): storage_type.h\n+ 138\t(udata)\t13\t(line_strp)\t(offset: 0xc2d): r_type_traits.h\n+ 139\t(udata)\t13\t(line_strp)\t(offset: 0xc3d): wrap_type_traits.h\n+ 140\t(udata)\t8\t(line_strp)\t(offset: 0x87d): proxy.h\n+ 141\t(udata)\t13\t(line_strp)\t(offset: 0xc50): enable_if.h\n+ 142\t(udata)\t26\t(line_strp)\t(offset: 0x8ca): r_binary_op.h\n+ 143\t(udata)\t27\t(line_strp)\t(offset: 0x8d8): median.h\n+ 144\t(udata)\t27\t(line_strp)\t(offset: 0x8e1): cbind.h\n+ 145\t(udata)\t28\t(line_strp)\t(offset: 0x8e9): trimws.h\n+ 146\t(udata)\t8\t(line_strp)\t(offset: 0x8f2): VectorBase.h\n+ 147\t(udata)\t29\t(line_strp)\t(offset: 0x8ff): Range.h\n+ 148\t(udata)\t2\t(line_strp)\t(offset: 0x907): Dimension.h\n+ 149\t(udata)\t8\t(line_strp)\t(offset: 0x913): no_init.h\n+ 150\t(udata)\t15\t(line_strp)\t(offset: 0x91d): SlotProxy.h\n+ 151\t(udata)\t15\t(line_strp)\t(offset: 0x93a): RObjectMethods.h\n+ 152\t(udata)\t2\t(line_strp)\t(offset: 0x94b): RObject.h\n+ 153\t(udata)\t15\t(line_strp)\t(offset: 0x955): NamesProxy.h\n+ 154\t(udata)\t2\t(line_strp)\t(offset: 0x962): String.h\n+ 155\t(udata)\t15\t(line_strp)\t(offset: 0x96b): GenericProxy.h\n+ 156\t(udata)\t2\t(line_strp)\t(offset: 0xc5c): Interrupt.h\n+ 157\t(udata)\t2\t(line_strp)\t(offset: 0x97a): Na_Proxy.h\n+ 158\t(udata)\t8\t(line_strp)\t(offset: 0x985): instantiation.h\n+ 159\t(udata)\t30\t(line_strp)\t(offset: 0x995): dpq.h\n+ 160\t(udata)\t2\t(line_strp)\t(offset: 0x99b): algorithm.h\n+ 161\t(udata)\t19\t(line_strp)\t(offset: 0x7d5): setjmp.h\n+ 162\t(udata)\t18\t(line_strp)\t(offset: 0x9a7): setjmp2.h\n+ 163\t(udata)\t2\t(line_strp)\t(offset: 0x9b1): Module.h\n+ 164\t(udata)\t22\t(line_strp)\t(offset: 0x9ba): Print.h\n+ 165\t(udata)\t6\t(line_strp)\t(offset: 0x9c2): new\n+ 166\t(udata)\t19\t(line_strp)\t(offset: 0xc68): execinfo.h\n+ 167\t(udata)\t23\t(line_strp)\t(offset: 0x9d3): R.h\n+ 168\t(udata)\t22\t(line_strp)\t(offset: 0xc73): GraphicsDevice.h\n+ 169\t(udata)\t6\t(line_strp)\t(offset: 0x9c6): system_error\n \n Line Number Statements:\n [0x0000100d] Set column to 7\n [0x0000100f] Extended opcode 2: set Address to 0x7420\n [0x0000101a] Advance Line by 1091 to 1092\n [0x0000101d] Copy\n [0x0000101e] Set column to 9\n"}, {"source1": "readelf --wide --debug-dump=info {}", "source2": "readelf --wide --debug-dump=info {}", "unified_diff": "@@ -4,15 +4,15 @@\n Length: 0x6de2 (32-bit)\n Version: 5\n Unit Type: DW_UT_partial (3)\n Abbrev Offset: 0\n Pointer Size: 8\n <0>: Abbrev Number: 71 (DW_TAG_partial_unit)\n DW_AT_stmt_list : (sec_offset) 0\n- <11> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/1st/r-cran-treescape-1.10.18+dfsg/src\n+ <11> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/2/r-cran-treescape-1.10.18+dfsg/2nd/src\n <1><15>: Abbrev Number: 10 (DW_TAG_namespace)\n <16> DW_AT_name : (string) std\n <1a> DW_AT_sibling : (ref2) <0x439c>\n <2><1c>: Abbrev Number: 34 (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@@ -19128,15 +19128,15 @@\n Unit Type: DW_UT_compile (1)\n Abbrev Offset: 0x7a2\n Pointer Size: 8\n <0><6df2>: Abbrev Number: 162 (DW_TAG_compile_unit)\n <6df4> DW_AT_producer : (strp) (offset: 0x19c01): GNU C++17 12.2.0 -mtune=generic -march=x86-64 -g -O2 -std=gnu++17 -fpic -fstack-protector-strong -fasynchronous-unwind-tables\n <6df8> DW_AT_language : (data1) 33\t(C++14)\n <6df9> DW_AT_name : (line_strp) (offset: 0): CPP_update_combinations.cpp\n- <6dfd> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/1st/r-cran-treescape-1.10.18+dfsg/src\n+ <6dfd> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/2/r-cran-treescape-1.10.18+dfsg/2nd/src\n <6e01> DW_AT_ranges : (sec_offset) 0x304\n <6e05> DW_AT_low_pc : (addr) 0\n <6e0d> DW_AT_stmt_list : (sec_offset) 0\n <1><6e11>: Abbrev Number: 201 (DW_TAG_imported_unit)\n <6e13> DW_AT_import : (ref_addr) <0xc>\t[Abbrev Number: 71 (DW_TAG_partial_unit)]\n <1><6e17>: Abbrev Number: 196 (DW_TAG_namespace)\n <6e19> DW_AT_name : (string) std\n@@ -48918,16 +48918,16 @@\n Version: 5\n Unit Type: DW_UT_compile (1)\n Abbrev Offset: 0x1696\n Pointer Size: 8\n <0><126a8>: Abbrev Number: 277 (DW_TAG_compile_unit)\n <126aa> DW_AT_producer : (strp) (offset: 0x19c01): GNU C++17 12.2.0 -mtune=generic -march=x86-64 -g -O2 -std=gnu++17 -fpic -fstack-protector-strong -fasynchronous-unwind-tables\n <126ae> DW_AT_language : (data1) 33\t(C++14)\n- <126af> DW_AT_name : (line_strp) (offset: 0x9d5): RcppExports.cpp\n- <126b3> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/1st/r-cran-treescape-1.10.18+dfsg/src\n+ <126af> DW_AT_name : (line_strp) (offset: 0x9d7): RcppExports.cpp\n+ <126b3> DW_AT_comp_dir : (line_strp) (offset: 0x1c): /build/2/r-cran-treescape-1.10.18+dfsg/2nd/src\n <126b7> DW_AT_ranges : (sec_offset) 0x439c\n <126bb> DW_AT_low_pc : (addr) 0\n <126c3> DW_AT_stmt_list : (sec_offset) 0xc16\n <1><126c7>: Abbrev Number: 334 (DW_TAG_imported_unit)\n <126c9> DW_AT_import : (ref_addr) <0xc>\t[Abbrev Number: 71 (DW_TAG_partial_unit)]\n <1><126cd>: Abbrev Number: 328 (DW_TAG_namespace)\n <126cf> DW_AT_name : (string) std\n"}, {"source1": "strings --all --bytes=8 {}", "source2": "strings --all --bytes=8 {}", "unified_diff": "@@ -1,8 +1,8 @@\n-GCC: (Debian 12.2.0-14) 12.2.0\n+9RGCC: (Debian 12.2.0-14) 12.2.0\n b[o?i&SO\n tPb} 'SC9T\n >V/F[TLk\n /Hx!&+O#\n 0KVR3Moe\n J!~_U T0\n rz 4vB\"R\n@@ -11,36 +11,45 @@\n &v.B]=OSbG~\n \"<;bvQq'8\n %|j/-?mH\n 7!mY@}\n+oEDk>nq`\n+W[|'Oj7'\n+iDdm?GohYU\n+^IWVJ_yek}\n+9p@aB^\tG\n+}e!{\t;m$\n+^<-sK$sy8@\n+$fjCN.~waz\n+fB=iF-gA\n+KS;=D-y`Q\n .VPo748D\n gE)rfDXY0c\n h%60Mg<&h{\n k-DT{Z>u\n TUm'4T[184\n-DROOSIDX\n-2?X,I=m>\n-\"wP>CE,:\n-@.JdY(1P=\n-m\"*UL^$(\n-&X=qX=\tX=\tX=\n+Hu-Ae>R8+k\n+U]3-um#~\n+^{z(,(d_9\n+Dq:8'[K\"v\n+${NrH 4\t\n+*m-j/NYm\n+l>xUSY:0>x\n+~K`bovK`]\n+AZfM5A*BdAM\n+U +7Pu1AY/}AV\n+%,=\ty\\X*\n+m\"*UL^&(\n+:i/SE\t5iP\n+1F)ewl2(\n $n$ozYF/&\n eyl\\EhyI\n X!37K4M1\n VU$4IW+U\n $!,f$&\t3\n b4Cv)bF2C\n [++o]s,s\n"}, {"source1": "readelf --wide --decompress --string-dump=.debug_line_str {}", "source2": "readelf --wide --decompress --string-dump=.debug_line_str {}", "unified_diff": "@@ -1,187 +1,187 @@\n \n String dump of section 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setjmp.h\n- [ 7dc] struct___jmp_buf_tag.h\n- [ 7f3] atomic_word.h\n- [ 801] wctype-wchar.h\n- [ 810] wctype.h\n- [ 819] time.h\n- [ 820] execution_defs.h\n- [ 831] tinyformat.h\n- [ 83e] macros.h\n- [ 847] const_string_proxy.h\n- [ 85c] Proxy_Iterator.h\n- [ 86d] const_generic_proxy.h\n- [ 883] RcppCommon.h\n- [ 890] integral_constant.h\n- [ 8a4] expands_to_logical.h\n- [ 8b9] storage_type.h\n- [ 8c8] r_binary_op.h\n- [ 8d6] median.h\n- [ 8df] cbind.h\n- [ 8e7] trimws.h\n- [ 8f0] VectorBase.h\n- [ 8fd] Range.h\n- [ 905] Dimension.h\n- [ 911] no_init.h\n- [ 91b] SlotProxy.h\n- [ 927] AttributeProxy.h\n- [ 938] RObjectMethods.h\n- [ 949] RObject.h\n- [ 953] NamesProxy.h\n- [ 960] String.h\n- [ 969] GenericProxy.h\n- [ 978] Na_Proxy.h\n- [ 983] instantiation.h\n- [ 993] dpq.h\n- [ 999] algorithm.h\n- [ 9a5] setjmp2.h\n- [ 9af] Module.h\n- [ 9b8] Print.h\n- [ 9c0] new\n- [ 9c4] system_error\n- [ 9d1] R.h\n- [ 9d5] RcppExports.cpp\n- [ 9e5] 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wrap_type_traits.h\n- [ c4e] enable_if.h\n- [ c5a] Interrupt.h\n- [ c66] execinfo.h\n- [ c71] 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/x86_64-linux-gnu/c++/12/bits\n+ [ 162] /usr/include/c++/12/debug\n+ [ 17c] /usr/include/c++/12/ext\n+ [ 194] /usr/include/x86_64-linux-gnu/bits\n+ [ 1b7] /usr/include\n+ [ 1c4] /usr/lib/gcc/x86_64-linux-gnu/12/include\n+ [ 1ed] /usr/include/x86_64-linux-gnu/bits/types\n+ [ 216] /usr/share/R/include/R_ext\n+ [ 231] /usr/share/R/include\n+ [ 246] /usr/include/c++/12/pstl\n+ [ 25f] /usr/lib/R/site-library/Rcpp/include/Rcpp/utils/tinyformat\n+ [ 29a] /usr/lib/R/site-library/Rcpp/include/Rcpp/macros\n+ [ 2cb] 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5ab] postypes.h\n+ [ 5b6] cstdint\n+ [ 5be] clocale\n+ [ 5c6] string_view\n+ [ 5d2] cstdlib\n+ [ 5da] cstdio\n+ [ 5e1] basic_string.h\n+ [ 5f0] stringfwd.h\n+ [ 5fc] cstddef\n+ [ 604] cstdarg\n+ [ 60c] cstring\n+ [ 614] locale_classes.h\n+ [ 625] exception_ptr.h\n+ [ 635] ios_base.h\n+ [ 640] cwctype\n+ [ 648] streambuf.tcc\n+ [ 656] ctime\n+ [ 65c] functional\n+ [ 667] stl_vector.h\n+ [ 674] vector.tcc\n+ [ 67f] csetjmp\n+ [ 687] basic_ios.tcc\n+ [ 695] predefined_ops.h\n+ [ 6a6] math.h\n+ [ 6ad] stddef.h\n+ [ 6b6] stdlib.h\n+ [ 6bf] clock_t.h\n+ [ 6c9] time_t.h\n+ [ 6d2] stdint-intn.h\n+ [ 6e0] __sigset_t.h\n+ [ 6ed] struct_timespec.h\n+ [ 6ff] stdarg.h\n+ [ 708] \n+ [ 713] wint_t.h\n+ [ 71c] __mbstate_t.h\n+ [ 72a] __FILE.h\n+ [ 733] struct_FILE.h\n+ [ 741] wchar2.h\n+ [ 74a] struct_tm.h\n+ [ 756] stdint-uintn.h\n+ [ 765] stdint.h\n+ [ 76e] locale.h\n+ [ 777] stdlib-float.h\n+ [ 786] stdlib-bsearch.h\n+ [ 797] __fpos_t.h\n+ [ 7a2] stdio.h\n+ [ 7aa] stdio2.h\n+ [ 7b3] Complex.h\n+ [ 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wrap_type_traits.h\n+ [ c50] enable_if.h\n+ [ c5c] Interrupt.h\n+ [ c68] execinfo.h\n+ [ c73] GraphicsDevice.h\n \n"}]}]}]}]}]}