rstudio / rstudio/packrat

Failed packrat::init() leaves broken .Rprofile

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Dominant language
R
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Forks
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Description

When running packrat::init() on an existing project, it is not uncommon to discover that a package used in the project is not installed locally.

> packrat::init()
Initializing packrat project in directory:
- "~/my_project"
Error: Unable to retrieve package records for the following packages:
- 'Biobase'
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
  Package 'Biobase' not available in repository or locally

At this stage, the most natural thing to do is to install the missing package, but the installation will fail because source("packrat/init.R") is now included in the project's .Rprofile even though the packrat/ directory doesn't exist. Furthermore, if there are multiple missing packages, install.packages() doesn't stop on error but tries to download the full package list and then those packages' installations individually fail.

> BiocManager::install("Biobase")
Bioconductor version 3.7 (BiocManager 1.30.1), R 3.5.0 (2018-04-23)
Installing package(s) 'Biobase'
also installing the dependency ‘BiocGenerics’

trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/BiocGenerics_0.26.0.tar.gz'
Content type 'application/x-gzip' length 45638 bytes (44 KB)
==================================================
downloaded 44 KB

trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/Biobase_2.40.0.tar.gz'
Content type 'application/x-gzip' length 1657220 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'packrat/init.R': No such file or directory
Execution halted
Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'packrat/init.R': No such file or directory
Execution halted
... even more output ...

It may be better to condition the sourcing on the existence of packrat/

if (dir.exists("packrat")) source("packrat/init.R")

or to possibly defer updating .Rprofile until init() succeeds, or to restore the old .Rprofile if init() fails.

Edit: I'd be happy to submit a PR for any of the above options if desired.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start at packrat::init() and inspect how it updates the project's .Rprofile and creates packrat/init.R. Reproduce the missing-package failure; done means a failed init does not leave .Rprofile sourcing a nonexistent packrat/init.R, and subsequent package installation no longer triggers that error.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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