Problems installing in R version 3.4.1 (2017-06-30)

[oeco28]

Hi Liam, I am running into some issues installing from source locally (or via repository). Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) inferring 'repos = NULL' from 'pkgs'

• installing source package ‘phytools’ ... R data inst preparing package for lazy loading Error : objects ‘neworder_phylo’, ‘neworder_pruningwise’ are not exported by 'namespace:ape' ERROR: lazy loading failed for package ‘phytools’
• removing ‘/usr/local/lib/R/site-library/phytools’ Warning message: In install.packages("/media/venezuela1/packages/phytools-master.tar.gz", : installation of package ‘/media/venezuela1/packages/phytools-master.tar.gz’ had non-zero exit status

There seem to be some uncommented code in neworder_phylo or neworder_pruningwise that causes installation to fail. but I am not sure what could it be. Have you seen anything like this? I would appreciate any insight. Thanks!

Omar

[oeco28]

Sorry Liam, just to provide some additional information. If I try using devtools I obtain the same output:

devtools::install_github("liamrevell/phytools") Downloading GitHub repo liamrevell/phytools@master from URL https://api.github.com/repos/liamrevell/phytools/zipball/master Installing phytools '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ CMD INSTALL \ '/media/venezuela4/tmp/RtmpuxGLkD/devtools21af2c8f52c4/liamrevell-phytools-762158a' \ --library='/usr/local/lib/R/site-library' --install-tests

• installing source package ‘phytools’ ... R data inst preparing package for lazy loading Error : objects ‘neworder_phylo’, ‘neworder_pruningwise’ are not exported by 'namespace:ape' ERROR: lazy loading failed for package ‘phytools’
• removing ‘/usr/local/lib/R/site-library/phytools’ Installation failed: Command failed (1)

[liamrevell]

What is your ape package version?

[oeco28]

ape_4.1

[oeco28]

Ey Liam, I see what you meant. I found a thread (https://www.mail-archive.com/r-sig-phylo@r-project.org/msg04929.html). There are some issues with ape after updating R. The recommendation is to re-install ape and the problem disappear. I re-installed ape and then installed phytools successfully. thank you, Omar

[liamrevell]

Great. Thank you for reporting.

[oeco28]

no problem!