Error with Binder

[ivan-paleo]

I have create a Docker file for Binder with the command:
holepunch::write_dockerfile()

However, when running Binder, there are many errors. See the binder here and the GitHub repo there.
I copy the log below.

From my limited understanding, it seems there is an issue with the renv package (@kevinushey).

Any hint to solve the problem?

---

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerqyh9v61f'...
Updating files: 100% (724/724), done.
HEAD is now at b853852 Update README files and delete old files
Using DockerBuildPack builder
Step 1/11 : FROM rocker/binder:4.0.2
---> c12d2367b296e...
Step 2/11 : LABEL maintainer='Ivan Calandra'
---> Running in a7c34e2596d8
Removing intermediate container a7c34e2596d8
---> 962dac7cc903
Step 3/11 : USER root
---> Running in 440ca0a398e8
Removing intermediate container 440ca0a398e8
---> b8c1be48397a
Step 4/11 : COPY . ${HOME}
---> 6eed326d3051
Step 5/11 : RUN chown -R ${NB_USER} ${HOME}
---> Running in a2474602d73a
Removing intermediate container a2474602d73a
---> f0c81634f98a
Step 6/11 : USER ${NB_USER}
---> Running in 4f7204f139c1
Removing intermediate container 4f7204f139c1
---> bf17160a62ea
Step 7/11 : RUN wget https://github.com/tracer-monrepos/SSFAcomparisonPaper/raw/master/DESCRIPTION && R -e "options(repos = list(CRAN = 'http://mran.revolutionanalytics.com/snapshot/2021-01-26/')); devtools::install_deps()"
---> Running in 93c02b86bd99
--2022-09-12 15:32:12-- https://github.com/tracer-monrepos/SSFAcomparisonPaper/raw/master/DESCRIPTION
Resolving github.com (github.com)... 140.82.114.3
Connecting to github.com (github.com)|140.82.114.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://raw.githubusercontent.com/tracer-monrepos/SSFAcomparisonPaper/master/DESCRIPTION [following]
--2022-09-12 15:32:12-- https://raw.githubusercontent.com/tracer-monrepos/SSFAcomparisonPaper/master/DESCRIPTION
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 833 [text/plain]
Saving to: ‘DESCRIPTION.1’

 0K                                                       100% 27.4M=0s

2022-09-12 15:32:13 (27.4 MB/s) - ‘DESCRIPTION.1’ saved [833/833]

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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.

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.

Bootstrapping renv 0.14.0 --------------------------------------------------

• Downloading renv 0.14.0 ... OK
• Installing renv 0.14.0 ... Done!
  Error installing renv:
  ======================
  Error: ERROR: cannot cd to directory ‘/home/rstudio/renv/library/R-4.0/x86_64-pc-linux-gnu’
  Warning messages:
  1: In system2(r, args, stdout = TRUE, stderr = TRUE) :
  running command ''/usr/local/lib/R/bin/R' --vanilla CMD INSTALL -l '/home/rstudio/renv/library/R-4.0/x86_64-pc-linux-gnu' '/tmp/Rtmp4O2rQL/renv_0.14.0.tar.gz' 2>&1' had status 1
  2: Failed to find an renv installation: the project will not be loaded.
  Use renv::activate() to re-initialize the project.

options(repos = list(CRAN = 'http://mran.revolutionanalytics.com/snapshot/2021-01-26/')); devtools::install_deps()
rlang (0.4.8 -> 0.4.10 ) [CRAN]
R6 (2.4.1 -> 2.5.0 ) [CRAN]
fansi (0.4.1 -> 0.4.2 ) [CRAN]
jsonlite (1.7.1 -> 1.7.2 ) [CRAN]
gitcreds (NA -> 0.1.1 ) [CRAN]
cli (2.0.2 -> 2.2.0 ) [CRAN]
rstudioapi (0.11 -> 0.13 ) [CRAN]
rprojroot (1.3-2 -> 2.0.2 ) [CRAN]
digest (0.6.25 -> 0.6.27 ) [CRAN]
pillar (1.4.6 -> 1.4.7 ) [CRAN]
generics (0.0.2 -> 0.1.0 ) [CRAN]
cpp11 (0.2.2 -> 0.2.5 ) [CRAN]
vctrs (0.3.4 -> 0.3.6 ) [CRAN]
tibble (3.0.3 -> 3.0.5 ) [CRAN]
magrittr (1.5 -> 2.0.1 ) [CRAN]
dplyr (1.0.2 -> 1.0.3 ) [CRAN]
ps (1.4.0 -> 1.5.0 ) [CRAN]
xfun (0.18 -> 0.20 ) [CRAN]
tinytex (0.26 -> 0.29 ) [CRAN]
htmltools (0.5.0 -> 0.5.1.1 ) [CRAN]
processx (3.4.4 -> 3.4.5 ) [CRAN]
withr (2.3.0 -> 2.4.0 ) [CRAN]
rmarkdown (2.4 -> 2.6 ) [CRAN]
callr (3.5.0 -> 3.5.1 ) [CRAN]
hms (0.5.3 -> 1.0.0 ) [CRAN]
Rcpp (1.0.5 -> 1.0.6 ) [CRAN]
BH (1.72.0-3 -> 1.75.0-0 ) [CRAN]
backports (1.1.10 -> 1.2.1 ) [CRAN]
broom (0.7.1 -> 0.7.3 ) [CRAN]
DBI (1.1.0 -> 1.1.1 ) [CRAN]
colorspace (1.4-1 -> 2.0-0 ) [CRAN]
labeling (0.3 -> 0.4.2 ) [CRAN]
diffobj (NA -> 0.3.3 ) [CRAN]
pkgbuild (1.1.0 -> 1.2.0 ) [CRAN]
waldo (NA -> 0.2.3 ) [CRAN]
brio (NA -> 1.1.1 ) [CRAN]
testthat (2.3.2 -> 3.0.1 ) [CRAN]
isoband (0.2.2 -> 0.2.3 ) [CRAN]
RcppEigen (NA -> 0.3.3.9.1 ) [CRAN]
statmod (NA -> 1.4.35 ) [CRAN]
nloptr (NA -> 1.2.2.2 ) [CRAN]
minqa (NA -> 1.2.4 ) [CRAN]
numDeriv (NA -> 2016.8-1.1) [CRAN]
lme4 (NA -> 1.1-26 ) [CRAN]
gh (1.1.0 -> 1.2.0 ) [CRAN]
gert (1.0.0 -> 1.1.0 ) [CRAN]
lubridate (1.7.9 -> 1.7.9.2 ) [CRAN]
ggplot2 (3.3.2 -> 3.3.3 ) [CRAN]
dbplyr (1.4.4 -> 2.0.0 ) [CRAN]
Deriv (NA -> 4.1.2 ) [CRAN]
pbkrtest (NA -> 0.5-0.1 ) [CRAN]
usethis (1.6.3 -> 2.0.0 ) [CRAN]
renv (NA -> 0.12.5 ) [CRAN]
openxlsx (NA -> 4.2.3 ) [CRAN]
doBy (NA -> 4.6.8 ) [CRAN]
Skipping 2 packages not available: rrtools, holepunch
Installing 57 packages: rlang, R6, fansi, jsonlite, gitcreds, cli, rstudioapi, rprojroot, digest, pillar, generics, cpp11, vctrs, tibble, magrittr, dplyr, ps, xfun, tinytex, htmltools, processx, withr, rmarkdown, callr, hms, Rcpp, BH, backports, broom, DBI, colorspace, labeling, diffobj, pkgbuild, waldo, brio, testthat, isoband, RcppEigen, statmod, nloptr, minqa, numDeriv, lme4, gh, gert, lubridate, ggplot2, dbplyr, Deriv, pbkrtest, usethis, rrtools, renv, openxlsx, holepunch, doBy
Installing packages into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Error: (converted from warning) packages ‘rrtools’, ‘holepunch’ are not available (for R version 4.0.2)
Execution halted
Removing intermediate container 93c02b86bd99
The command '/bin/sh -c wget https://github.com/tracer-monrepos/SSFAcomparisonPaper/raw/master/DESCRIPTION && R -e "options(repos = list(CRAN = 'http://mran.revolutionanalytics.com/snapshot/2021-01-26/')); devtools::install_deps()"' returned a non-zero code: 1Built image, launching...
Failed to connect to event stream

[kevinushey]

From this error:

Error: ERROR: cannot cd to directory ‘/home/rstudio/renv/library/R-4.0/x86_64-pc-linux-gnu’
Warning messages:
1: In system2(r, args, stdout = TRUE, stderr = TRUE) :
running command ''/usr/local/lib/R/bin/R' --vanilla CMD INSTALL -l '/home/rstudio/renv/library/R-4.0/x86_64-pc-linux-gnu' '/tmp/Rtmp4O2rQL/renv_0.14.0.tar.gz' 2>&1' had status 1

it seems more like there's an issue with container permissions or something like that.

The later issue with installing rrtools / holepunch might be unrelated.

[ivan-paleo]

Thank you @kevinushey for looking into it. What can I do to solve the container permissions issue?