* using log directory 'C:/msys64/home/tomas/utf/ucrt64/inst_all/PhylogeneticEM.Rcheck' * using R Under development (unstable) (2020-06-23 r78739) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'PhylogeneticEM/DESCRIPTION' ... OK * this is package 'PhylogeneticEM' version '1.4.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Packages suggested but not available for checking: 'phytools', 'TreeSim' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'PhylogeneticEM' can be installed ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat_EM.R' Running 'testthat_core.R' Running 'testthat_independent.R' Running 'testthat_shifts.R' Running 'testthat_upward.R' Running 'testthat_utilities.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'monkeys.Rmd' using 'UTF-8'... OK 'tutorial.Rmd' using 'UTF-8'... OK NONE * checking re-building of vignette outputs ... WARNING Error(s) in re-building vignettes: --- re-building 'monkeys.Rmd' using rmarkdown Warning in engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1. Loading required package: ape Loading required package: Matrix starting worker pid=190244 on localhost:11888 at 23:54:53.429 starting worker pid=104576 on localhost:11888 at 23:54:53.508 Loading required package: PhylogeneticEM Loading required package: ape Loading required package: PhylogeneticEM Loading required package: ape Loading required package: Matrix Loading required package: Matrix loaded PhylogeneticEM and set parent environment loaded PhylogeneticEM and set parent environment Alpha 0.0131646571083129 Alpha 0.0517168558708096 | | | 0% | | | 0% | |====== | 9% | |====== | 9% | |============= | 18% | |============= | 18% | |=================== | 27% | |=================== | 27% | |========================= | 36% | |========================= | 36% | |================================ | 45% | |================================ | 45% | |====================================== | 55% | |====================================== | 55% | |============================================= | 64% | |============================================= | 64% | |=================================================== | 73% | |=================================================== | 73% | |========================================================= | 82% | |========================================================= | 82% | |================================================================ | 91% | |================================================================ | 91% | |======================================================================| 100% | |======================================================================| 100%Alpha 0.203167705710557 | | | 0%Alpha 0.798136621971044 | | | 0% | |====== | 9% | |============= | 18% | |====== | 9% | |=================== | 27% | |============= | 18% | |========================= | 36% | |=================== | 27% | |================================ | 45% | |========================= | 36% | |====================================== | 55% | |================================ | 45% | |============================================= | 64% | |====================================== | 55% | |=================================================== | 73% | |============================================= | 64% | |========================================================= | 82% | |=================================================== | 73% | |================================================================ | 91% | |========================================================= | 82% | |================================================================ | 91% | |======================================================================| 100% | |======================================================================| 100%There are some equivalent solutions to the set of shifts selected by the BGHlsq method. There are some equivalent solutions to the set of shifts selected by the BGHlsqraw method. There are some equivalent solutions to the set of shifts selected by the BGHmlraw method. starting worker pid=235476 on localhost:11888 at 23:55:28.137 starting worker pid=226696 on localhost:11888 at 23:55:28.216 Loading required package: PhylogeneticEM Loading required package: ape Loading required package: PhylogeneticEM Loading required package: ape Loading required package: Matrix Loading required package: Matrix loaded PhylogeneticEM and set parent environment loaded PhylogeneticEM and set parent environment Alpha 0.0131646571083129 Alpha 0.0517168558708096 | | | 0% | | | 0% | |====== | 9% | |====== | 9% | |============= | 18% | |============= | 18% | |=================== | 27% | |=================== | 27% | |========================= | 36% | |========================= | 36% | |================================ | 45% | |================================ | 45% | |====================================== | 55% | |====================================== | 55% | |============================================= | 64% | |============================================= | 64% | |=================================================== | 73% | |=================================================== | 73% | |========================================================= | 82% | |========================================================= | 82% | |================================================================ | 91% | |================================================================ | 91% | |======================================================================| 100%Alpha 0.203167705710557 | | | 0% | |======================================================================| 100%Alpha 0.798136621971044 | | | 0% | |====== | 9% | |====== | 9% | |============= | 18% | |============= | 18% | |=================== | 27% | |=================== | 27% | |========================= | 36% | |========================= | 36% | |================================ | 45% | |================================ | 45% | |====================================== | 55% | |====================================== | 55% | |============================================= | 64% | |============================================= | 64% | |=================================================== | 73% | |=================================================== | 73% | |========================================================= | 82% | |========================================================= | 82% | |================================================================ | 91% | |================================================================ | 91% | |======================================================================| 100% | |======================================================================| 100%There are some equivalent solutions to the set of shifts selected by the BGHlsq method. There are some equivalent solutions to the set of shifts selected by the BGHml method. There are some equivalent solutions to the set of shifts selected by the BGHlsqraw method. There are some equivalent solutions to the set of shifts selected by the BGHmlraw method. starting worker pid=157456 on localhost:11888 at 23:55:54.766 starting worker pid=196144 on localhost:11888 at 23:55:54.782 Loading required package: PhylogeneticEM Loading required package: PhylogeneticEM Loading required package: ape Loading required package: ape Loading required package: Matrix Loading required package: Matrix loaded PhylogeneticEM and set parent environment loaded PhylogeneticEM and set parent environment Alpha 0.0131646571083129 Alpha 0.798136621971044 | | | 0% | | | 0% | |====== | 9% | |====== | 9% | |============= | 18% | |============= | 18% | |=================== | 27% | |=================== | 27% | |========================= | 36% | |========================= | 36% | |================================ | 45% | |================================ | 45% | |====================================== | 55% | |====================================== | 55% | |============================================= | 64% | |============================================= | 64% | |=================================================== | 73% | |=================================================== | 73% | |========================================================= | 82% | |========================================================= | 82% | |================================================================ | 91% | |================================================================ | 91% | |======================================================================| 100% | |======================================================================| 100%There are some equivalent solutions to the set of shifts selected by the BGHlsq method. There are some equivalent solutions to the set of shifts selected by the BGHml method. There are some equivalent solutions to the set of shifts selected by the BGHlsqraw method. There are some equivalent solutions to the set of shifts selected by the BGHmlraw method. starting worker pid=217016 on localhost:11888 at 23:56:10.128 starting worker pid=225100 on localhost:11888 at 23:56:10.253 Loading required package: PhylogeneticEM Loading required package: ape Loading required package: PhylogeneticEM Loading required package: ape Loading required package: Matrix Loading required package: Matrix loaded PhylogeneticEM and set parent environment loaded PhylogeneticEM and set parent environment Alpha -0.640578156028118 Alpha -0.0131646571083129 | | | 0% | | | 0% | |====== | 9% | |====== | 9% | |============= | 18% | |============= | 18% | |=================== | 27% | |=================== | 27% | |========================= | 36% | |========================= | 36% | |================================ | 45% | |====================================== | 55% | |================================ | 45% | |============================================= | 64% | |====================================== | 55% | |=================================================== | 73% | |============================================= | 64% | |========================================================= | 82% | |=================================================== | 73% | |========================================================= | 82% | |================================================================ | 91% | |================================================================ | 91% | |======================================================================| 100%Alpha 0 | | | 0% | |====== | 9% | |======================================================================| 100% | |============= | 18%Alpha 0.0131646571083129 | | | 0% | |====== | 9% | |=================== | 27% | |============= | 18% | |========================= | 36% | |=================== | 27% | |================================ | 45% | |====================================== | 55% | |========================= | 36% | |============================================= | 64% | |================================ | 45% | |====================================== | 55% | |=================================================== | 73% | |============================================= | 64% | |========================================================= | 82% | |=================================================== | 73% | |================================================================ | 91% | |========================================================= | 82% | |================================================================ | 91% | |======================================================================| 100%Alpha 0.798136621971044 | | | 0% | |====== | 9% | |======================================================================| 100% | |============= | 18% | |=================== | 27% | |========================= | 36% | |================================ | 45% | |====================================== | 55% | |============================================= | 64% | |=================================================== | 73% | |========================================================= | 82% | |================================================================ | 91% | |======================================================================| 100%There are some equivalent solutions to the set of shifts selected by the BGHlsq method. There are some equivalent solutions to the set of shifts selected by the BGHml method. There are some equivalent solutions to the set of shifts selected by the BGHlsqraw method. There are some equivalent solutions to the set of shifts selected by the BGHmlraw method. --- finished re-building 'monkeys.Rmd' Warning messages: 1: In params_process.PhyloEM(res, K = 5) : There are several equivalent solutions for this shift position. 2: In params_process.PhyloEM(res, K = 5) : There are several equivalent solutions for this shift position. 3: In params_process.PhyloEM(x, method.selection = method.selection) : There are several equivalent solutions for this shift position. 4: In compute_ancestral_traits(x, params, method.selection, what, ...) : For K = 3, the log_likelihood of the transformed parameters on the er-scaled tree is different from the log_likelihood of the parameters on the original tree, with a tolerance of 0.000740095979741405. --- re-building 'tutorial.Rmd' using rmarkdown Warning in engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1. Loading required package: ape Loading required package: Matrix Quitting from lines 28-32 (tutorial.Rmd) Error: processing vignette 'tutorial.Rmd' failed with diagnostics: there is no package called 'TreeSim' --- failed re-building 'tutorial.Rmd' SUMMARY: processing the following file failed: 'tutorial.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See 'C:/msys64/home/tomas/utf/ucrt64/inst_all/PhylogeneticEM.Rcheck/00check.log' for details.