* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘ips’ ... ** this is package ‘ips’ version ‘0.0.12’ ** package ‘ips’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘ips’ finding HTML links ... done DNAbin2index html Rd warning: DNAbin2index.Rd:10: missing link ‘DNAbin’ EmptyCells html Rd warning: EmptyCells.Rd:44: missing link ‘DNAbin’ Rd warning: EmptyCells.Rd:25: missing link ‘DNAbin’ Rd warning: EmptyCells.Rd:41: missing link ‘DNAbin’ aliscore html beastLog html blastn html code.simple.gaps html Rd warning: code.simple.gaps.Rd:15: missing link ‘DNAbin’ Rd warning: code.simple.gaps.Rd:21: missing link ‘DNAbin’ collapseUnsupportedEdges html Rd warning: collapseUnsupportedEdges.Rd:10: missing link ‘phylo’ Rd warning: collapseUnsupportedEdges.Rd:19: missing link ‘phylo’ combMyTree html Rd warning: combMyTree.Rd:10: missing link ‘phylo’ Rd warning: combMyTree.Rd:23: missing link ‘phylo’ del.miss html Rd warning: del.miss.Rd:10: missing link ‘DNAbin’ deleteGaps html Rd warning: deleteGaps.Rd:10: missing link ‘DNAbin’ Rd warning: deleteGaps.Rd:18: missing link ‘DNAbin’ descendants html fixNodes html Rd warning: fixNodes.Rd:9: missing link ‘phylo’ Rd warning: fixNodes.Rd:17: missing link ‘phylo’ Rd warning: fixNodes.Rd:27: missing link ‘phylo’ Rd warning: fixNodes.Rd:36: missing link ‘read.nexus’ forceEqualTipHeights html Rd warning: forceEqualTipHeights.Rd:26: missing link ‘is.ultrametric’ Rd warning: forceEqualTipHeights.Rd:31: missing link ‘chronos’ gblocks html index2DNAbin html Rd warning: index2DNAbin.Rd:10: missing link ‘DNAbin’ ips-internal html ips-package html Rd warning: ips-package.Rd:18: missing link ‘ladderize’ Rd warning: ips-package.Rd:18: missing link ‘rotate’ ips.16S html Rd warning: ips.16S.Rd:10: missing link ‘DNAbin’ ips.28S html Rd warning: ips.28S.Rd:12: missing link ‘DNAbin’ ips.cox1 html Rd warning: ips.cox1.Rd:12: missing link ‘DNAbin’ ips.tree html mafft html Rd warning: mafft.Rd:53: missing link ‘phylo’ mafft.merge html Rd warning: mafft.merge.Rd:10: missing link ‘DNAbin’ Rd warning: mafft.merge.Rd:11: missing link ‘AAbin’ Rd warning: mafft.merge.Rd:20: missing link ‘phylo’ Rd warning: mafft.merge.Rd:34: missing link ‘DNAbin’ Rd warning: mafft.merge.Rd:34: missing link ‘AAbin’ mrbayes html Rd warning: mrbayes.Rd:22: missing link ‘DNAbin’ mrbayes.lset html mrbayes.mcmc html mrbayes.prset html multistate html Rd warning: multistate.Rd:63: missing link ‘ace’ neighboringPairs html Rd warning: neighboringPairs.Rd:10: missing link ‘mst’ ntip html Rd warning: ntip.Rd:10: missing link ‘phylo’ oi html partitionfinder html pathd8 html Rd warning: pathd8.Rd:10: missing link ‘phylo’ Rd warning: pathd8.Rd:22: missing link ‘phylo’ phylo2mafft html Rd warning: phylo2mafft.Rd:10: missing link ‘phylo’ phylo2mst html Rd warning: phylo2mst.Rd:10: missing link ‘phylo’ pis html Rd warning: pis.Rd:10: missing link ‘DNAbin’ prank html raxml html Rd warning: raxml.Rd:26: missing link ‘DNAbin’ Rd warning: raxml.Rd:57: missing link ‘phylo’ raxml.partitions html Rd warning: raxml.partitions.Rd:11: missing link ‘DNAbin’ Rd warning: raxml.partitions.Rd:23: missing link ‘cbind.DNAbin’ rbeauti html Rd warning: rbeauti.Rd:22: missing link ‘DNAbin’ rc html read html Rd warning: read.Rd:56: missing link ‘cbind.DNAbin’ read.beast html read.beast.table html sister html Rd warning: sister.Rd:10: missing link ‘phylo’ splitIntoClades html Rd warning: splitIntoClades.Rd:10: missing link ‘phylo’ terminalSisters html Rd warning: terminalSisters.Rd:10: missing link ‘phylo’ tipHeights html Rd warning: tipHeights.Rd:13: missing link ‘phylo’ Rd warning: tipHeights.Rd:23: missing link ‘branching.times’ traitRate html Rd warning: traitRate.Rd:14: missing link ‘phylo’ Rd warning: traitRate.Rd:16: missing link ‘DNAbin’ Rd warning: traitRate.Rd:44: missing link ‘read.tree’ trimEnds html unlistFirstLevel html write.fas html Rd warning: write.fas.Rd:26: missing link ‘DNAbin’ ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ips)