Issue in installing the package

[Ratheesh-kv]

Dear William,

Thanks very much for your wonderful package for various phylogenetic analysis. I have been trying to analyse my data using your R package pez, however, before that I am encountering the issue of installing the package. Therefore, it would be a great help if could please help me to solve this issue. Please see the message and session info below.

Sincerely
Ratheesh

installing the source package ‘pez’

trying URL 'https://cran.rstudio.com/src/contrib/pez_1.2-4.tar.gz'
Content type 'application/x-gzip' length 618094 bytes (603 KB)
downloaded 603 KB

• installing source package 'pez' ...
  ** package 'pez' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** data
  ** inst
  ** byte-compile and prepare package for lazy loading
  Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
  ** help
  *** installing help indices
  converting help for package 'pez'
  finding HTML links ... done
  ConDivSim html
  cc.manip html
  finding level-2 HTML links ... done

  comparative.comm html
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/comparative.comm.Rd:21: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  dist.xxx html
  drop_tip html
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/drop_tip.Rd:10: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/drop_tip.Rd:16: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/drop_tip.Rd:25: file link 'extract.clade' in package 'ape' does not exist and so has been treated as a topic
  eco.scape html
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/eco.scape.Rd:23: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/eco.scape.Rd:43: file link 'rnorm' in package 'stats' does not exist and so has been treated as a topic
  eco.xxx.regression html
  eco.xxx.regression.list html
  fibre.plot html
  fingerprint.regression html
  generic.metrics html
  laja html
  pez-internal html
  pez html
  pez.dispersion html
  pez.dissimilarity html
  pez.endemism html
  pez.evenness html
  pez.metrics html
  pez.shape html
  pglmm html
  phy.build html
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/phy.build.Rd:17: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/phy.build.Rd:28: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/phy.build.Rd:31: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/phy.build.Rd:49: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/phy.build.Rd:51: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  phy.signal html
  plot.comparative.comm html
  scape html
  sim.meta html
  sim.phy html
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/sim.phy.Rd:57: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/sim.phy.Rd:72: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  trait.asm html
  traitgram.cc html
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  *** arch - i386
  Error: package or namespace load failed for 'pez' in library.dynam(lib, package, package.lib):
  DLL 'maps' not found: maybe not installed for this architecture?
  Error: loading failed
  Execution halted
  *** arch - x64
  Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
  ERROR: loading failed for 'i386'

• removing 'C:/Users/Ratheeshkv/OneDrive - University of Lincoln/Documents/R/win-library/4.0/pez'
  Warning in install.packages :
  installation of package ‘pez’ had non-zero exit status

The downloaded source packages are in
‘C:\Users\Ratheeshkv\AppData\Local\Temp\RtmpYVtkjg\downloaded_packages’

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] caper_1.0.1 mvtnorm_1.1-3 MASS_7.3-53 phytools_0.7-70 maps_3.4.1
[6] ape_5.4-1

loaded via a namespace (and not attached):
[1] igraph_1.2.6 Rcpp_1.0.5 magrittr_2.0.3
[4] scatterplot3d_0.3-41 mnormt_2.0.2 lattice_0.20-41
[7] quadprog_1.5-8 fastmatch_1.1-3 tools_4.0.3
[10] parallel_4.0.3 grid_4.0.3 tmvnsim_1.0-2
[13] nlme_3.1-149 clusterGeneration_1.3.7 phangorn_2.5.5
[16] plotrix_3.8-2 coda_0.19-4 remotes_2.4.2
[19] gtools_3.9.4 numDeriv_2016.8-1.1 Matrix_1.5-3
[22] curl_5.0.0 compiler_4.0.3 combinat_0.0-8
[25] expm_0.999-6 pkgconfig_2.0.3

[willpearse]

Hello, Thanks for this - am I right in saying it was you who also emailed me about this privately? As I said there, this is likely fixed by updating your version of R, which is a few years out of date and so updating R should fix the issue. Let me know either way please. Thanks, Will

…

--- Measuring phylogenetic structure? Try install.packages('pez') Will Pearse (pearselab.com) <http://pearselab.com/> Senior Lecturer, Imperial College London

On Fri, 24 Mar 2023 at 23:27, Ratheesh-kv ***@***.***> wrote: Dear William, Thanks very much for your wonderful package for various phylogenetic analysis. I have been trying to analyse my data using your R package pez, however, before that I am encountering the issue of installing the package. Therefore, it would be a great help if could please help me to solve this issue. Please see the message and session info below. Sincerely Ratheesh installing the source package ‘pez’ trying URL 'https://cran.rstudio.com/src/contrib/pez_1.2-4.tar.gz' Content type 'application/x-gzip' length 618094 bytes (603 KB) downloaded 603 KB - installing *source* package 'pez' ... ** package 'pez' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning in .***@***.***, def, env) : undefined subclass "numericVector" of class "Mnumeric"; definition not updated ** help *** installing help indices converting help for package 'pez' finding HTML links ... done ConDivSim html cc.manip html finding level-2 HTML links ... done comparative.comm html Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/comparative.comm.Rd:21: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic dist.xxx html drop_tip html Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/drop_tip.Rd:10: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/drop_tip.Rd:16: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/drop_tip.Rd:25: file link 'extract.clade' in package 'ape' does not exist and so has been treated as a topic eco.scape html Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/eco.scape.Rd:23: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/eco.scape.Rd:43: file link 'rnorm' in package 'stats' does not exist and so has been treated as a topic eco.xxx.regression html eco.xxx.regression.list html fibre.plot html fingerprint.regression html generic.metrics html laja html pez-internal html pez html pez.dispersion html pez.dissimilarity html pez.endemism html pez.evenness html pez.metrics html pez.shape html pglmm html phy.build html Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/phy.build.Rd:17: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/phy.build.Rd:28: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/phy.build.Rd:31: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/phy.build.Rd:49: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/phy.build.Rd:51: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic phy.signal html plot.comparative.comm html scape html sim.meta html sim.phy html Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/sim.phy.Rd:57: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/Ratheeshkv/AppData/Local/Temp/RtmpQBLtOw/R.INSTALL3ff0341657fa/pez/man/sim.phy.Rd:72: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic trait.asm html traitgram.cc html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location *** arch - i386 Error: package or namespace load failed for 'pez' in library.dynam(lib, package, package.lib): DLL 'maps' not found: maybe not installed for this architecture? Error: loading failed Execution halted *** arch - x64 Warning in .***@***.***, def, env) : undefined subclass "numericVector" of class "Mnumeric"; definition not updated ERROR: loading failed for 'i386' - removing 'C:/Users/Ratheeshkv/OneDrive - University of Lincoln/Documents/R/win-library/4.0/pez' Warning in install.packages : installation of package ‘pez’ had non-zero exit status The downloaded source packages are in ‘C:\Users\Ratheeshkv\AppData\Local\Temp\RtmpYVtkjg\downloaded_packages’ *> sessionInfo()* R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] caper_1.0.1 mvtnorm_1.1-3 MASS_7.3-53 phytools_0.7-70 maps_3.4.1 [6] ape_5.4-1 loaded via a namespace (and not attached): [1] igraph_1.2.6 Rcpp_1.0.5 magrittr_2.0.3 [4] scatterplot3d_0.3-41 mnormt_2.0.2 lattice_0.20-41 [7] quadprog_1.5-8 fastmatch_1.1-3 tools_4.0.3 [10] parallel_4.0.3 grid_4.0.3 tmvnsim_1.0-2 [13] nlme_3.1-149 clusterGeneration_1.3.7 phangorn_2.5.5 [16] plotrix_3.8-2 coda_0.19-4 remotes_2.4.2 [19] gtools_3.9.4 numDeriv_2016.8-1.1 Matrix_1.5-3 [22] curl_5.0.0 compiler_4.0.3 combinat_0.0-8 [25] expm_0.999-6 pkgconfig_2.0.3 — Reply to this email directly, view it on GitHub <#74>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJNYUXS5LZDTAHSXZJUJHLW5YUXZANCNFSM6AAAAAAWHEKOY4> . 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