Error in loadNamespace(name) : there is no package called ‘devtools’

[ForestCA]

Hello,

Could I get help with this - I'm getting this error message with Docker on my Mac:

Cloning into 'velocyto.R'... Removing intermediate container b9c8d82d66ce ---> 2cc4e53f0aa3 Step 11/12 : RUN echo '.libPaths(c("~/R/x86_64-redhat-linux-gnu-library/3.4", .libPaths()))' > .Rprofile && R -e 'devtools::install_local("~/velocyto.R/",dep=T,upgrade_dependencies=F)' ---> Running in d62d610d6c51

R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

devtools::install_local("~/velocyto.R/",dep=T,upgrade_dependencies=F) Error in loadNamespace(name) : there is no package called ‘devtools’ Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted The command '/bin/sh -c echo '.libPaths(c("~/R/x86_64-redhat-linux-gnu-library/3.4", .libPaths()))' > .Rprofile && R -e 'devtools::install_local("~/velocyto.R/",dep=T,upgrade_dependencies=F)'' returned a non-zero code: 1

[gitbuckley]

Same issue here with the Docker on mac.

[t-carroll]

Same issue here with the Docker image on Windows- anyone been able to resolve this?

[t-carroll]

Stared more closely at the console output during the various package installations and was able to find the problem in my case: R package xml2 fails to install. devtools needs Roxygen2 which depends on xml2, which is why devtools is not successfully installed. Presumably xml2 installation fails because libxml2 is missing. I found that manually editing the Dockerfile to include libxml2-dev as a package installed by apt-get solves this issue in my case (libxml2 is not sufficient). So my modified apt-get block looks like this:

> RUN apt-get update --yes && apt-get install --no-install-recommends --yes \
>   build-essential \
>   cmake \
>   git \
>   libbamtools-dev \
>   libboost-dev \
>   libboost-iostreams-dev \
>   libboost-log-dev \
>   libboost-system-dev \
>   libboost-test-dev \
>   libssl-dev \
>   libcurl4-openssl-dev \
>   libxml2-dev \
>   libz-dev \
>   curl \
>   libhdf5-cpp-100 \ 
>   libarmadillo7 \
>   libarmadillo-dev

@ForestCA @gitbuckley I am just picking up Docker so not sure if this will hold for Macs, but might be worth a shot if you're still having issues. Otherwise perhaps there's another missing dependency in your case that could be found in a similar way.