- The project is out-of-sync -- use `renv::status()` for details.
Detecting R version...
R version: 4.4.2


Attaching package: ‘renv’

The following objects are masked from ‘package:stats’:

    embed, update

The following objects are masked from ‘package:utils’:

    history, upgrade

The following objects are masked from ‘package:base’:

    autoload, load, remove, use

Initializing renv...
- The project is out-of-sync -- use `renv::status()` for details.
Setting up BiocManager with appropriate version for R 4.4...
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.20 (BiocManager 1.30.27), R 4.4.2 (2024-10-31)
Installing package(s) 'BiocVersion'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/BiocVersion_3.20.0.tar.gz'
Content type 'application/gzip' length 983 bytes
==================================================
downloaded 983 bytes

Error in eval(quote({ : object 'repos' not found
Calls: source ... local -> eval.parent -> eval -> eval -> eval -> eval
Execution halted

The downloaded source packages are in
	‘/tmp/Rtmp1o7ryx/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘BiocVersion’ had non-zero exit status

Installing CRAN packages...
  - magrittr
# Downloading packages -------------------------------------------------------
- Downloading magrittr from CRAN ...            OK [file is up to date]
Successfully downloaded 1 package in 0.87 seconds.

The following package(s) will be installed:
- magrittr [2.0.4]
These packages will be installed into "/oak/stanford/groups/akundaje/airanman/.local/share/R/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".

# Installing packages --------------------------------------------------------
- Installing magrittr ...                       OK [built from source and cached in 11s]
Successfully installed 1 package in 12 seconds.
  - dplyr
The following package(s) will be installed:
- dplyr [1.1.4]
These packages will be installed into "/oak/stanford/groups/akundaje/airanman/.local/share/R/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".

# Installing packages --------------------------------------------------------
- Installing dplyr ...                          OK [linked from cache]
Successfully installed 1 package in 36 milliseconds.
  - stringr
# Downloading packages -------------------------------------------------------
- Downloading stringr from CRAN ...             OK [191.2 Kb in 1.8s]
Successfully downloaded 1 package in 2.3 seconds.

The following package(s) will be installed:
- stringr [1.6.0]
These packages will be installed into "/oak/stanford/groups/akundaje/airanman/.local/share/R/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".

# Installing packages --------------------------------------------------------
- Installing stringr ...                        OK [built from source and cached in 32s]
Successfully installed 1 package in 32 seconds.
  - ggplot2
# Downloading packages -------------------------------------------------------
- Downloading ggplot2 from CRAN ...             OK [file is up to date]
- Downloading S7 from CRAN ...                  OK [file is up to date]
- Downloading scales from CRAN ...              OK [file is up to date]
Successfully downloaded 3 packages in 2.2 seconds.

The following package(s) will be installed:
- ggplot2 [4.0.1]
- S7      [0.2.1]
- scales  [1.4.0]
These packages will be installed into "/oak/stanford/groups/akundaje/airanman/.local/share/R/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".

# Installing packages --------------------------------------------------------
- Installing S7 ...                             OK [built from source and cached in 40s]
- Installing scales ...                         OK [built from source and cached in 51s]
- Installing ggplot2 ...                        OK [built from source and cached in 1.3m]
Successfully installed 3 packages in 2.8 minutes.
  - ggrepel
The following package(s) will be installed:
- ggrepel [0.9.6]
These packages will be installed into "/oak/stanford/groups/akundaje/airanman/.local/share/R/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".

# Installing packages --------------------------------------------------------
- Installing ggrepel ...                        OK [linked from cache]
Successfully installed 1 package in 36 milliseconds.
  - ggrastr
The following package(s) will be installed:
- ggrastr [1.0.2]
These packages will be installed into "/oak/stanford/groups/akundaje/airanman/.local/share/R/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".

# Installing packages --------------------------------------------------------
- Installing ggrastr ...                        OK [linked from cache]
Successfully installed 1 package in 37 milliseconds.
  - ggdendro
# Downloading packages -------------------------------------------------------
- Downloading ggdendro from CRAN ...            OK [163.9 Kb in 0.42s]
Successfully downloaded 1 package in 0.88 seconds.

The following package(s) will be installed:
- ggdendro [0.2.0]
These packages will be installed into "/oak/stanford/groups/akundaje/airanman/.local/share/R/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".

# Installing packages --------------------------------------------------------
- Installing ggdendro ...                       OK [built from source and cached in 14s]
Successfully installed 1 package in 14 seconds.
  - ggthemes
# Downloading packages -------------------------------------------------------
- Downloading ggthemes from CRAN ...            OK [633.7 Kb in 0.43s]
Successfully downloaded 1 package in 1 second.

The following package(s) will be installed:
- ggthemes [5.2.0]
These packages will be installed into "/oak/stanford/groups/akundaje/airanman/.local/share/R/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".

# Installing packages --------------------------------------------------------
- Installing ggthemes ...                       FAILED
Error: Error installing package 'ggthemes':
====================================

* installing *source* package ‘ggthemes’ ...
** package ‘ggthemes’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
Error : excel_new_pal.Rd:13: 'ggthemes_data' is not an exported object from 'namespace:ggthemes'
ERROR: installing Rd objects failed for package ‘ggthemes’
* removing ‘/oak/stanford/groups/akundaje/airanman/projects/lab/rare-disease-manuscript/datasets/fetal_brain_trevino_2021/brainchromatin/renv/staging/1/ggthemes’
install of package 'ggthemes' failed [error code 1]
Traceback (most recent calls last):
12: renv::install(pkg)
11: renv_install_impl(records)
10: renv_install_staged(records)
 9: renv_install_default(records)
 8: handler(package, renv_install_package(record))
 7: renv_install_package(record)
 6: withCallingHandlers(renv_install_package_impl(record), error = function(e) writef("FAILED"))
 5: renv_install_package_impl(record)
 4: r_cmd_install(package, path)
 3: r_exec_error(package, output, "install", status)
 2: abort(all)
 1: stop(fallback)
Execution halted