Can scFlow R package be installed in RStudio server? Does the requirement for libudunits2-dev block this?

[NathanSkene]

Presumably many people would try doing this the first time they try using it.

Mahdi reported: "A few packages need to be installed separately. Still struggling with “units”. It seems the only way is to first installing libudunits2-dev which needs a sudo access. Any clue? Or I will check with the RCS team."

If it cannot be done, the requirement should be clearly stated alongside installation instructions

[combiz]

I'll compile dependency related installation notes from everyone and add them to the instructions for package installation for a smoother package installation experience. That said, I think it's reasonable to expect users to have admin access (or be able to request an admin) for installation of dependencies.

[NathanSkene]

It’s certainly reasonable to expect admin access. Any non-R dependencies do need to be made very clear in documentation though. From: Combiz Khozoie <notifications@github.com> Reply-To: combiz/scflow <reply@reply.github.com> Date: Wednesday, 4 December 2019 at 16:16 To: combiz/scflow <scflow@noreply.github.com> Cc: "Skene, Nathan G" <n.skene@imperial.ac.uk>, Author <author@noreply.github.com> Subject: Re: [combiz/scflow] Can scFlow R package be installed in RStudio server? Does the requirement for libudunits2-dev block this? (#13) Caution - This email from notifications@github.com originated outside Imperial I'll compile dependency related installation notes from everyone and add them to the instructions for package installation for a smoother package installation experience. That said, I think it's reasonable to expect users to have admin access (or be able to request an admin) for installation of dependencies. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#13>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AH5ZPE4342BOLUHDW3DFLZLQW7JUPANCNFSM4JVLAKFQ>.

[MahdiMoradiMarjaneh]

Further to my original comment and to help @combiz with the installation notes, at least packages SingleCellExperiment, monocle, and monocle3 need to be installed separately. When installing monocle3, the following error appears:

configure: error: in `/tmp/RtmpjZbA29/R.INSTALL7afc2d99349d/units':
configure: error:
Configuration failed because libudunits2.so was not found. Try installing:
* deb: libudunits2-dev (Debian, Ubuntu, ...)
* rpm: udunits2-devel (Fedora, EPEL, ...)
* brew: udunits (OSX)
If udunits2 is already installed in a non-standard location, use:
--configure-args='--with-udunits2-lib=/usr/local/lib'
if the library was not found, and/or:
--configure-args='--with-udunits2-include=/usr/include/udunits2'
if the header was not found, replacing paths with appropriate values.
You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually.

See `config.log' for more details
ERROR: configuration failed for package ‘units’
*removing ‘/rdsgpfs/general/user/mmoradim/home/R/x86_64-redhat-linux-gnu-library/3.6/units’
Error: Failed to install 'monocle3' from GitHub:
(converted from warning) installation of package ‘units’ had non-zero exit status

[NathanSkene]

@MahdiMoradiMarjaneh can you get the documentation written up so that it explains how to install the R package from scratch? Easiest to do it first on a computer you've got full admin rights for.

[MahdiMoradiMarjaneh]

@MahdiMoradiMarjaneh can you get the documentation written up so that it explains how to install the R package from scratch? Easiest to do it first on a computer you've got full admin rights for.

Yep, I'm on it.