For about a month now, I have had a problem running update.packages() or install.packages() from source. About half the time, the code appears to hang at the compile step. This is an R problem, not an RStudio problem, as I have the same problem on both of my Windows 10 machines when I try to update or install a package from source in a native R instance. (It never occurs when I am running my Ubuntu machine.) But the RStudio Community has been very helpful in the past in dealing with R problems, so I am coming to you. I am running R 3.6.0 and RStudio Version 1.2.1335. Thanks in advance to anyone that can help me with this issue.
In native R, I am able to select my mirror and answer the question whether I want to install from source. The program appears to download the packages successfully, and then to unpack and check the MD5 sums successfully for one of the packages, but then the command hangs (never returns even after 30 min.) I suspect that the error occurs somewhere in the compile step. When this happens, I have to interrupt R and remove the package lock from my personal R package library. Sometimes I have also to delete the original package from my library, which suggests to me that the system is already trying to update the package (i.e., after completing the compilation). See the output from one session below.
Update: I checked Task Manager to see if I could figure out what is going wrong. When I first open R, Task Manager lists six R processes:
R for Windows front-end (4)
Console Window Host
R for Windows front-end
R for Windows terminal front-end
Rterm (64-bit)
Windows Command Processor
Windows Command Processor
When I then try to load the developer version of rlang from git-hub (devtools::install_github("r-lib/rlang", build_vignettes = TRUE), a batch of new processes come and go. But when R hangs at the end of the output listing below, two of the R processes are listed as suspended:
R for Windows terminal front-end *Suspended*
Windows Command Processor *Suspended*
Does anyone have any idea what is going on? Is this a Windows 10 problem?
R session output listing:
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
Natural language support but running in an English locale
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.
> update.packages()
--- Please select a CRAN mirror for use in this session ---
Warning: package 'cluster' in library 'C:/Program Files/R/R-3.6.0/library' will not be updated
Warning: package 'nlme' in library 'C:/Program Files/R/R-3.6.0/library' will not be updated
nlme :
Version 3.1-139 installed in c:/Larry/R/win-library/3.6
Version 3.1-140 available at https://cloud.r-project.org
Update? (Yes/no/cancel) Y
RcppArmadillo :
Version 0.9.400.2.0 installed in c:/Larry/R/win-library/3.6
Version 0.9.400.3.0 available at https://cloud.r-project.org
Update? (Yes/no/cancel) y
robustbase :
Version 0.93-4 installed in c:/Larry/R/win-library/3.6
Version 0.93-5 available at https://cloud.r-project.org
Update? (Yes/no/cancel) y
There are binary versions available but the source versions are later:
binary source needs_compilation
nlme 3.1-139 3.1-140 TRUE
RcppArmadillo 0.9.400.2.0 0.9.400.3.0 TRUE
robustbase 0.93-4 0.93-5 TRUE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) y
installing the source packages 'nlme', 'RcppArmadillo', 'robustbase'
trying URL 'https://cloud.r-project.org/src/contrib/nlme_3.1-140.tar.gz'
Content type 'application/x-gzip' length 793019 bytes (774 KB)
downloaded 774 KB
trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.9.400.3.0.tar.gz'
Content type 'application/x-gzip' length 1349340 bytes (1.3 MB)
downloaded 1.3 MB
trying URL 'https://cloud.r-project.org/src/contrib/robustbase_0.93-5.tar.gz'
Content type 'application/x-gzip' length 2957246 bytes (2.8 MB)
downloaded 2.8 MB
* installing *source* package 'nlme' ...
** package 'nlme' successfully unpacked and MD5 sums checked
[then the command hangs]