issue at project startup: "Error in readRDS(file) : error reading from connection"

I'm getting an error at project startup. It says: "Error in readRDS(file) : error reading from connection".

Besides the sessionInfo() listed below, there are some other notables. I have a strong firewall. As such, I can only access package repositories on my organization's servers.

Also, one of the repositories is preceded by "file://". I noticed this could be related to closed issue #389.

Please let me know if I can provide anything else to assist with troubleshooting.

Thank you!

Restarting R session...

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

Error in readRDS(file) : error reading from connection
* Project '~/fbar-ovdp' loaded. [renv 0.13.0]
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default
BLAS: /opt/R/R-3.5.3/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-3.5.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.3 tools_3.5.3    renv_0.13.0

Can you try editing the project .Rprofile, and adding the following line before the source("renv/activate.R") call?

trace(readRDS, quote(print(ls.str())))
options(error = quote(print(sys.calls())))

Hopefully this will then print some extra output when the error occurs and give us a hint as to what's going wrong.

Here is the output.

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

Error in readRDS(file) : error reading from connection
* Project '~/fbar-ovdp' loaded. [renv 0.13.0]
Tracing function "readRDS" in package "base"
[1] "readRDS"
Tracing readRDS(pfile) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/datasets/Meta/package.rds"
refhook :  NULL
Tracing readRDS(nsInfoFilePath) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/datasets/Meta/nsInfo.rds"
refhook :  NULL
Tracing readRDS(pkgInfoFP) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/datasets/Meta/package.rds"
refhook :  NULL
Tracing readRDS(ffile) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/datasets/Meta/features.rds"
refhook :  NULL
Tracing readRDS(pfile) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/grDevices/Meta/package.rds"
refhook :  NULL
Tracing readRDS(pfile) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/graphics/Meta/package.rds"
refhook :  NULL
Tracing readRDS(pfile) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/stats/Meta/package.rds"
refhook :  NULL
Tracing readRDS(nsInfoFilePath) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/compiler/Meta/nsInfo.rds"
refhook :  NULL
Tracing readRDS(pkgInfoFP) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/compiler/Meta/package.rds"
refhook :  NULL
Tracing readRDS(ffile) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/compiler/Meta/features.rds"
refhook :  NULL
Tracing readRDS(pfile) on entry 
file :  chr "/home/user/fbar-ovdp/renv/library/R-3.5/x86_64-pc-linux-gnu/knitr/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/home/user/fbar-ovdp/renv/library/R-3.5/x86_64-pc-linux-gnu/knitr/Meta/package.rds"
refhook :  NULL
[Workspace loaded from ~/fbar-ovdp/.RData]

Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/base/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/boot/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/class/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/cluster/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/codetools/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/compiler/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/datasets/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/foreign/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/graphics/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/grDevices/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/grid/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/KernSmooth/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/lattice/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/MASS/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/Matrix/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/methods/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/mgcv/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/nlme/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/nnet/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/parallel/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/rpart/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/spatial/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/splines/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/stats/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/stats4/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/survival/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/tcltk/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/tools/Meta/package.rds"
refhook :  NULL
Tracing readRDS(file) on entry 
file :  chr "/tmp/Rtmp90kITV/renv-system-library/utils/Meta/package.rds"
refhook :  NULL
Tracing readRDS(dest) on entry 
file :  chr "//projects/Analysts/R/src/contrib/PACKAGES.rds"
refhook :  NULL
Tracing readRDS(dest) on entry 
file :  chr "//projects/Analysts/R/src/contrib/PACKAGES.rds"
refhook :  NULL
Tracing readRDS(rds) on entry 
file :  chr "/tmp/Rtmp90kITV/rstudio-available-packages-d6f02fe52fd6/packages.rds"
refhook :  NULL

Thanks! Strange -- based on the logs, it looks like the error might have happened even before renv was loaded. Could the error be coming from something else (e.g. sourcing of the user profile at ~/.Rprofile)?

Do you see the error if you deactivate renv in that project?

I couldn't even close the project after deactivating renv in the project. I had to rename the .rstudio folder. But when I restarted the project I had no errors.

Here is my user profile at ~/.Rprofile:

# Assign a user library to R
myPaths <- c("/projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5")

.libPaths(myPaths)

# set a CRAN mirror
local({r <- getOption("repos")
r["local"] <- "file://projects/Analysts/R/" #This is the local repo
r["system"] <- "xx.xxx.xx.xxx/R/"       #This is the system repo
options(repos=r)})

Here are my user environment settings at ~/.Renviron:

# below is now set in nano .bash_profile
# CLASSPATH = /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.265.b01-1.el7_9.x86_64/lib

GDAL_DATA=/usr/share/epsg_csv

HOSTNAME = xxxxxxxxxxxxxxxx.xxx.xxxxxxxxxx.xxx.xxx

IQDIR16 = /opt/app/SybaseIQ/IQ-16_1

#JAVA_HOME = /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.265.b01-1.el7_9.x86_64

# the java path can be changed depending on the java home
LD_LIBRARY_PATH = /opt/glpk-4.65/lib:/usr/local/lib:/opt/app/SybaseIQ/IQ-16_1/lib64:/lib:/usr/local/lib64
#:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.265.b01-1.el7_9.x86_64/lib

# is the java home path supposed to be in here?
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/app/SybaseIQ/IQ-16_1/bin64
#:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.265.b01-1.el7_9.x86_64/bin

ODBCINI = /opt/app/SybaseODBC/odbc.ini

R_DOC_DIR = /opt/R/R-3.5.3/lib64/R/doc

RENV_CONFIG_AUTO_SNAPSHOT = TRUE

RENV_CONFIG_BITBUCKET_HOST = NULL

RENV_CONFIG_GITHUB_HOST = NULL

RENV_CONFIG_GITLAB_HOST = NULL

RENV_CONFIG_INSTALL_VERBOSE = TRUE

RENV_CONFIG_MRAN_ENABLED = FALSE

RENV_CONFIG_RSPM_ENABLED = FALSE

R_HOME = /opt/R/R-3.5.3/lib64/R

R_INCLUDE_DIR = /opt/R/R-3.5.3/lib64/R/include

R_LIBS =

R_LIBS_USER = /projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5

R_LIBS_SITE = 

# R_MAKEVARS_USER = ~/.R/Makevars

R_SHARE_DIR = /opt/R/R-3.5.3/lib64/R/share

SAP_JRE8 = /opt/app/SybaseIQ/shared/SAPJRE-8_1_046_64BIT

SAP_JRE8_64 = /opt/app/SybaseIQ/shared/SAPJRE-8_1_046_64BIT

SYBASE = /opt/app/SybaseIQ

SYBROOT = /opt/app/SybaseIQ

Please let me know if making some changes might help.

One other thing worth checking: with renv active, do you see the same error in a plain R session launched in that project, outside of RStudio?

I thought this would be trivial. I have no idea how to open a project outside of RStudio. Then after opening the project, I'm guessing I would run renv::init(). Then restart R and reopen the project.

I thought this would be trivial. I have no idea how to open a project outside of RStudio. Then after opening the project, I'm guessing I would run renv::init(). Then restart R and reopen the project.

You should just need to open a terminal session, set the working directory to the associated project, and then run R to start R in that renv project. If the project has already been initialized, then renv will automatically be activated when the new R session is launched.

Thank you for the explanation on how to run the project from the terminal. It looks like the error message is still there.

Here's what I see after running renv::init():

> renv::init()
* Initializing project ...
* Discovering package dependencies ... Done!
Error in readRDS(file) : error reading from connection
* Copying packages into the cache ... [114/114] Done!
The following package(s) have unsatisfied dependencies:

        'strex    ' requires 'stringi (>= 1.3.1)', but version '1.1.7' will be snapshotted
        'rmarkdown' requires 'tinytex (>= 0.11) ', but version '0.4  ' will be snapshotted

Consider updating the required dependencies as appropriate.

The following package(s) will be updated in the lockfile:

# CRAN ===============================
- BH             [* -> 1.75.0-0]
- DBI            [* -> 1.1.1]
- Formula        [* -> 1.2-2]
- Hmisc          [* -> 4.1-1]
- MASS           [* -> 7.3-53.1]
- Matrix         [* -> 1.2-18]
- R6             [* -> 2.5.0]
- RColorBrewer   [* -> 1.1-2]
- Rcpp           [* -> 1.0.6]
- XML            [* -> 3.98-1.10]
- acepack        [* -> 1.4.1]
- assertthat     [* -> 0.2.1]
- backports      [* -> 1.1.2]
- base64enc      [* -> 0.1-3]
- blob           [* -> 1.2.1]
- brio           [* -> 1.1.1]
- broom          [* -> 0.7.4]
- callr          [* -> 3.5.1]
- cellranger     [* -> 1.1.0]
- checkmate      [* -> 2.0.0]
- cli            [* -> 2.3.0]
- clipr          [* -> 0.7.1]
- cluster        [* -> 2.0.7-1]
- colorspace     [* -> 1.3-2]
- cpp11          [* -> 0.2.6]
- crayon         [* -> 1.4.1]
- curl           [* -> 4.3]
- data.table     [* -> 1.14.0]
- dbplyr         [* -> 2.0.0]
- desc           [* -> 1.1.1]
- diffobj        [* -> 0.3.3]
- digest         [* -> 0.6.27]
- dplyr          [* -> 1.0.4]
- easyr          [* -> 0.5-2]
- ellipsis       [* -> 0.3.1]
- evaluate       [* -> 0.14]
- fansi          [* -> 0.4.2]
- farver         [* -> 2.0.3]
- forcats        [* -> 0.5.1]
- foreign        [* -> 0.8-71]
- fs             [* -> 1.5.0]
- generics       [* -> 0.0.2]
- ggplot2        [* -> 3.3.3]
- glue           [* -> 1.4.2]
- gridExtra      [* -> 2.3]
- gtable         [* -> 0.2.0]
- haven          [* -> 2.3.1]
- highr          [* -> 0.6]
- hms            [* -> 1.0.0]
- htmlTable      [* -> 1.11.2]
- htmltools      [* -> 0.5.1]
- htmlwidgets    [* -> 1.5.3]
- httr           [* -> 1.4.2]
- isoband        [* -> 0.2.2]
- jsonlite       [* -> 1.7.2]
- knitr          [* -> 1.30]
- labeling       [* -> 0.4.2]
- lattice        [* -> 0.20-41]
- latticeExtra   [* -> 0.6-28]
- lifecycle      [* -> 1.0.0]
- lubridate      [* -> 1.7.10]
- magrittr       [* -> 2.0.1]
- markdown       [* -> 0.8]
- matrixStats    [* -> 0.53.1]
- mgcv           [* -> 1.8-27]
- mime           [* -> 0.9]
- modelr         [* -> 0.1.8]
- munsell        [* -> 0.5.0]
- nlme           [* -> 3.1-137]
- nnet           [* -> 7.3-12]
- openssl        [* -> 1.0.1]
- ore            [* -> 1.6.3]
- pillar         [* -> 1.5.0]
- pkgbuild       [* -> 1.2.0]
- pkgconfig      [* -> 2.0.1]
- pkgload        [* -> 1.1.0]
- praise         [* -> 1.0.0]
- prettyunits    [* -> 1.1.1]
- processx       [* -> 3.4.5]
- progress       [* -> 1.2.2]
- ps             [* -> 1.6.0]
- purrr          [* -> 0.3.4]
- readr          [* -> 1.4.0]
- readxl         [* -> 1.3.1]
- rematch        [* -> 1.0.1]
- rematch2       [* -> 2.1.0]
- renv           [* -> 0.13.0]
- reprex         [* -> 1.0.0]
- rlang          [* -> 0.4.10]
- rmarkdown      [* -> 2.6]
- rpart          [* -> 4.1-13]
- rprojroot      [* -> 2.0.2]
- rstudioapi     [* -> 0.13]
- rvest          [* -> 0.3.6]
- scales         [* -> 1.1.1]
- selectr        [* -> 0.4-1]
- strex          [* -> 1.1.0]
- stringi        [* -> 1.1.7]
- stringr        [* -> 1.4.0]
- survival       [* -> 2.43-3]
- testthat       [* -> 3.0.1]
- tibble         [* -> 3.1.0]
- tidyr          [* -> 1.1.3]
- tidyselect     [* -> 1.1.0]
- tidyverse      [* -> 1.3.0]
- tinytex        [* -> 0.4]
- utf8           [* -> 1.1.4]
- vctrs          [* -> 0.3.6]
- viridis        [* -> 0.5.1]
- viridisLite    [* -> 0.3.0]
- waldo          [* -> 0.2.3]
- withr          [* -> 2.4.1]
- xfun           [* -> 0.20]
- xml2           [* -> 1.3.2]
- yaml           [* -> 2.2.0]

* Lockfile written to '~/fbar-ovdp/renv.lock'.
* Project '~/fbar-ovdp' loaded. [renv 0.13.0]
* renv activated -- please restart the R session.

And here's what I see in the restarted R session:

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

Error in readRDS(file) : error reading from connection
* Project '~/fbar-ovdp' loaded. [renv 0.13.0]
[Previously saved workspace restored]

Please let me know if there's anything else I can provide.

This may be related. If not, please let me know. I can delete and/or open a new issue.

I ran renv::diagnostics(), because renv was not recognizing an installed package: pdftools. I know the package is installed in the following library path /opt/R/R-3.5.3/lib64/R/library. Along with /projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5, this is path [2] in the diagnostics. I also list these libraries in my user environmental variables for RENV_CONFIG_EXTERNAL_LIBRARIES. For whatever reason, only paths [1] and [3] are referenced in the list of packages in the diagnostics. Also, I see the following in the diagnostic: external.libraries : chr(0). And I should mention that the version of pdftools installed in the library is not included in one of my two repositories.

Here is the full output from renv::diagnostics:

> renv::diagnostics()
Diagnostics Report [renv 0.13.0]
================================

# Session Info =======================
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default
BLAS: /opt/R/R-3.5.3/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-3.5.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] strex_1.1.0       formattable_0.2.1 lubridate_1.7.10  easyr_0.5-2      
 [5] forcats_0.5.1     stringr_1.4.0     dplyr_1.0.4       purrr_0.3.4      
 [9] readr_1.4.0       tidyr_1.1.3       tibble_3.1.0      ggplot2_3.3.3    
[13] tidyverse_1.3.0  

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.0  xfun_0.20         haven_2.3.1       colorspace_1.3-2 
 [5] vctrs_0.3.6       generics_0.0.2    htmltools_0.5.1   yaml_2.2.0       
 [9] utf8_1.1.4        rlang_0.4.10      pillar_1.5.0      withr_2.4.1      
[13] glue_1.4.2        DBI_1.1.1         dbplyr_2.0.0      modelr_0.1.8     
[17] readxl_1.3.1      lifecycle_1.0.0   munsell_0.5.0     gtable_0.2.0     
[21] cellranger_1.1.0  rvest_0.3.6       htmlwidgets_1.5.3 evaluate_0.14    
[25] knitr_1.30        ps_1.6.0          fansi_0.4.2       broom_0.7.4      
[29] Rcpp_1.0.6        renv_0.13.0       scales_1.1.1      backports_1.1.2  
[33] jsonlite_1.7.2    fs_1.5.0          hms_1.0.0         digest_0.6.27    
[37] stringi_1.1.7     processx_3.4.5    grid_3.5.3        cli_2.3.0        
[41] tools_3.5.3       magrittr_2.0.1    crayon_1.4.1      pkgconfig_2.0.1  
[45] ellipsis_0.3.1    xml2_1.3.2        reprex_1.0.0      assertthat_0.2.1 
[49] rmarkdown_2.6     httr_1.4.2        rstudioapi_0.13   R6_2.5.0         
[53] compiler_3.5.3   

# Project ============================
Project path: "~/fbar-ovdp"

# Status =============================
The following package(s) are installed but not recorded in the lockfile:
              _
  formattable   [0.2.1]

Use `renv::snapshot()` to add these packages to your lockfile.

The following package(s) are out of sync:

   Package   Lockfile Version   Library Version
   tinytex                0.4              0.30

Use `renv::snapshot()` to save the state of your library to the lockfile.
Use `renv::restore()` to restore your library from the lockfile.

The following package(s) are used in the project, but are not installed:

    pdftools

Consider installing these packages, and then using `renv::snapshot()`
to record these packages in the lockfile.

# Packages ===========================
               Library Source  Lockfile Source Path Dependency
BH            1.75.0-0   CRAN  1.75.0-0   CRAN  [1]   indirect
DBI              1.1.1   CRAN     1.1.1   CRAN  [1]   indirect
Formula          1.2-2   CRAN     1.2-2   CRAN  [1]   indirect
Hmisc            4.1-1   CRAN     4.1-1   CRAN  [1]   indirect
KernSmooth     2.23-15   CRAN      <NA>   <NA>  [3]       <NA>
MASS          7.3-53.1   CRAN  7.3-53.1   CRAN  [1]   indirect
Matrix          1.2-18   CRAN    1.2-18   CRAN  [1]   indirect
R6               2.5.0   CRAN     2.5.0   CRAN  [1]   indirect
RColorBrewer     1.1-2   CRAN     1.1-2   CRAN  [1]   indirect
Rcpp             1.0.6   CRAN     1.0.6   CRAN  [1]   indirect
XML          3.98-1.10   CRAN 3.98-1.10   CRAN  [1]   indirect
acepack          1.4.1   CRAN     1.4.1   CRAN  [1]   indirect
assertthat       0.2.1   CRAN     0.2.1   CRAN  [1]   indirect
backports        1.1.2   CRAN     1.1.2   CRAN  [1]   indirect
base64enc        0.1-3   CRAN     0.1-3   CRAN  [1]   indirect
blob             1.2.1   CRAN     1.2.1   CRAN  [1]   indirect
boot            1.3-20   CRAN      <NA>   <NA>  [3]       <NA>
brio             1.1.1   CRAN     1.1.1   CRAN  [1]   indirect
broom            0.7.4   CRAN     0.7.4   CRAN  [1]   indirect
callr            3.5.1   CRAN     3.5.1   CRAN  [1]   indirect
cellranger       1.1.0   CRAN     1.1.0   CRAN  [1]   indirect
checkmate        2.0.0   CRAN     2.0.0   CRAN  [1]   indirect
class           7.3-15   CRAN      <NA>   <NA>  [3]       <NA>
cli              2.3.0   CRAN     2.3.0   CRAN  [1]   indirect
clipr            0.7.1   CRAN     0.7.1   CRAN  [1]   indirect
cluster        2.0.7-1   CRAN   2.0.7-1   CRAN  [1]   indirect
codetools       0.2-16   CRAN      <NA>   <NA>  [3]       <NA>
colorspace       1.3-2   CRAN     1.3-2   CRAN  [1]   indirect
cpp11            0.2.6   CRAN     0.2.6   CRAN  [1]   indirect
crayon           1.4.1   CRAN     1.4.1   CRAN  [1]   indirect
curl               4.3   CRAN       4.3   CRAN  [1]   indirect
data.table      1.14.0   CRAN    1.14.0   CRAN  [1]   indirect
dbplyr           2.0.0   CRAN     2.0.0   CRAN  [1]   indirect
desc             1.1.1   CRAN     1.1.1   CRAN  [1]   indirect
diffobj          0.3.3   CRAN     0.3.3   CRAN  [1]   indirect
digest          0.6.27   CRAN    0.6.27   CRAN  [1]   indirect
dplyr            1.0.4   CRAN     1.0.4   CRAN  [1]   indirect
easyr            0.5-2   CRAN     0.5-2   CRAN  [1]     direct
ellipsis         0.3.1   CRAN     0.3.1   CRAN  [1]   indirect
evaluate          0.14   CRAN      0.14   CRAN  [1]   indirect
fansi            0.4.2   CRAN     0.4.2   CRAN  [1]   indirect
farver           2.0.3   CRAN     2.0.3   CRAN  [1]   indirect
forcats          0.5.1   CRAN     0.5.1   CRAN  [1]   indirect
foreign         0.8-71   CRAN    0.8-71   CRAN  [1]   indirect
formattable      0.2.1   CRAN      <NA>   <NA>  [1]     direct
fs               1.5.0   CRAN     1.5.0   CRAN  [1]   indirect
generics         0.0.2   CRAN     0.0.2   CRAN  [1]   indirect
ggplot2          3.3.3   CRAN     3.3.3   CRAN  [1]   indirect
glue             1.4.2   CRAN     1.4.2   CRAN  [1]   indirect
grDevices         <NA>   <NA>      <NA>   <NA>  [3]   indirect
graphics          <NA>   <NA>      <NA>   <NA>  [3]   indirect
grid              <NA>   <NA>      <NA>   <NA>  [3]   indirect
gridExtra          2.3   CRAN       2.3   CRAN  [1]   indirect
gtable           0.2.0   CRAN     0.2.0   CRAN  [1]   indirect
haven            2.3.1   CRAN     2.3.1   CRAN  [1]   indirect
highr              0.6   CRAN       0.6   CRAN  [1]   indirect
hms              1.0.0   CRAN     1.0.0   CRAN  [1]   indirect
htmlTable       1.11.2   CRAN    1.11.2   CRAN  [1]   indirect
htmltools        0.5.1   CRAN     0.5.1   CRAN  [1]   indirect
htmlwidgets      1.5.3   CRAN     1.5.3   CRAN  [1]   indirect
httr             1.4.2   CRAN     1.4.2   CRAN  [1]   indirect
isoband          0.2.2   CRAN     0.2.2   CRAN  [1]   indirect
jsonlite         1.7.2   CRAN     1.7.2   CRAN  [1]   indirect
knitr             1.30   CRAN      1.30   CRAN  [1]   indirect
labeling         0.4.2   CRAN     0.4.2   CRAN  [1]   indirect
lattice        0.20-41   CRAN   0.20-41   CRAN  [1]   indirect
latticeExtra    0.6-28   CRAN    0.6-28   CRAN  [1]   indirect
lifecycle        1.0.0   CRAN     1.0.0   CRAN  [1]   indirect
lubridate       1.7.10   CRAN    1.7.10   CRAN  [1]     direct
magrittr         2.0.1   CRAN     2.0.1   CRAN  [1]   indirect
markdown           0.8   CRAN       0.8   CRAN  [1]   indirect
matrixStats     0.53.1   CRAN    0.53.1   CRAN  [1]   indirect
methods           <NA>   <NA>      <NA>   <NA>  [3]   indirect
mgcv            1.8-27   CRAN    1.8-27   CRAN  [1]   indirect
mime               0.9   CRAN       0.9   CRAN  [1]   indirect
modelr           0.1.8   CRAN     0.1.8   CRAN  [1]   indirect
munsell          0.5.0   CRAN     0.5.0   CRAN  [1]   indirect
nlme           3.1-137   CRAN   3.1-137   CRAN  [1]   indirect
nnet            7.3-12   CRAN    7.3-12   CRAN  [1]   indirect
openssl          1.0.1   CRAN     1.0.1   CRAN  [1]   indirect
ore              1.6.3   CRAN     1.6.3   CRAN  [1]   indirect
pdftools          <NA>   <NA>      <NA>   <NA> <NA>     direct
pillar           1.5.0   CRAN     1.5.0   CRAN  [1]   indirect
pkgbuild         1.2.0   CRAN     1.2.0   CRAN  [1]   indirect
pkgconfig        2.0.1   CRAN     2.0.1   CRAN  [1]   indirect
pkgload          1.1.0   CRAN     1.1.0   CRAN  [1]   indirect
praise           1.0.0   CRAN     1.0.0   CRAN  [1]   indirect
prettyunits      1.1.1   CRAN     1.1.1   CRAN  [1]   indirect
processx         3.4.5   CRAN     3.4.5   CRAN  [1]   indirect
progress         1.2.2   CRAN     1.2.2   CRAN  [1]   indirect
ps               1.6.0   CRAN     1.6.0   CRAN  [1]   indirect
purrr            0.3.4   CRAN     0.3.4   CRAN  [1]   indirect
readr            1.4.0   CRAN     1.4.0   CRAN  [1]   indirect
readxl           1.3.1   CRAN     1.3.1   CRAN  [1]   indirect
rematch          1.0.1   CRAN     1.0.1   CRAN  [1]   indirect
rematch2         2.1.0   CRAN     2.1.0   CRAN  [1]   indirect
renv            0.13.0   CRAN    0.13.0   CRAN  [1]     direct
reprex           1.0.0   CRAN     1.0.0   CRAN  [1]   indirect
rlang           0.4.10   CRAN    0.4.10   CRAN  [1]   indirect
rmarkdown          2.6   CRAN       2.6   CRAN  [1]     direct
rpart           4.1-13   CRAN    4.1-13   CRAN  [1]   indirect
rprojroot        2.0.2   CRAN     2.0.2   CRAN  [1]   indirect
rstudioapi        0.13   CRAN      0.13   CRAN  [1]   indirect
rvest            0.3.6   CRAN     0.3.6   CRAN  [1]   indirect
scales           1.1.1   CRAN     1.1.1   CRAN  [1]   indirect
selectr          0.4-1   CRAN     0.4-1   CRAN  [1]   indirect
spatial         7.3-11   CRAN      <NA>   <NA>  [3]       <NA>
splines           <NA>   <NA>      <NA>   <NA>  [3]   indirect
stats             <NA>   <NA>      <NA>   <NA>  [3]   indirect
strex            1.1.0   CRAN     1.1.0   CRAN  [1]     direct
stringi          1.1.7   CRAN     1.1.7   CRAN  [1]   indirect
stringr          1.4.0   CRAN     1.4.0   CRAN  [1]   indirect
survival        2.43-3   CRAN    2.43-3   CRAN  [1]   indirect
testthat         3.0.1   CRAN     3.0.1   CRAN  [1]   indirect
tibble           3.1.0   CRAN     3.1.0   CRAN  [1]   indirect
tidyr            1.1.3   CRAN     1.1.3   CRAN  [1]   indirect
tidyselect       1.1.0   CRAN     1.1.0   CRAN  [1]   indirect
tidyverse        1.3.0   CRAN     1.3.0   CRAN  [1]     direct
tinytex           0.30   CRAN       0.4   CRAN  [1]   indirect
tools             <NA>   <NA>      <NA>   <NA>  [3]   indirect
utf8             1.1.4   CRAN     1.1.4   CRAN  [1]   indirect
utils             <NA>   <NA>      <NA>   <NA>  [3]   indirect
vctrs            0.3.6   CRAN     0.3.6   CRAN  [1]   indirect
viridis          0.5.1   CRAN     0.5.1   CRAN  [1]   indirect
viridisLite      0.3.0   CRAN     0.3.0   CRAN  [1]   indirect
waldo            0.2.3   CRAN     0.2.3   CRAN  [1]   indirect
withr            2.4.1   CRAN     2.4.1   CRAN  [1]   indirect
xfun              0.20   CRAN      0.20   CRAN  [1]   indirect
xml2             1.3.2   CRAN     1.3.2   CRAN  [1]   indirect
yaml             2.2.0   CRAN     2.2.0   CRAN  [1]   indirect

[1]: /home/user/fbar-ovdp/renv/library/R-3.5/x86_64-pc-linux-gnu                          
[2]: /projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5:/opt/R/R-3.5.3/lib64/R/library
[3]: /tmp/RtmpVlGPAg/renv-system-library                                                   

# User Profile =======================
[no R packages referenced in user profile

# Settings ===========================
List of 7
 $ external.libraries       : chr(0) 
 $ ignored.packages         : chr(0) 
 $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
 $ r.version                : chr(0) 
 $ snapshot.type            : chr "implicit"
 $ use.cache                : logi TRUE
 $ vcs.ignore.library       : logi TRUE

# Options ============================
List of 6
 $ defaultPackages     : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
 $ download.file.method: NULL
 $ download.file.extra : NULL
 $ repos               : Named chr [1:2] "file://projects/Analysts/R" "xx.xxx.xx.xxx/R"
  ..- attr(*, "names")= chr [1:2] "WORK" "SYSTEM"
 $ renv.consent        : logi TRUE
 $ renv.verbose        : logi TRUE

# Environment Variables ==============
HOME                           = /home/user
LANG                           = en_US.UTF-8
R_LIBS                         = <NA>
R_LIBS_SITE                    = 
R_LIBS_USER                    = /home/user/fbar-ovdp/renv/library/R-3.5/x86_64-pc-linux-gnu:/projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5:/opt/R/R-3.5.3/lib64/R/library:/tmp/RtmpVlGPAg/renv-system-library
RENV_CONFIG_EXTERNAL_LIBRARIES = /projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5:/opt/R/R-3.5.3/lib64/R/library
RENV_DEFAULT_R_ENVIRON         = <NA>
RENV_DEFAULT_R_ENVIRON_USER    = <NA>
RENV_DEFAULT_R_LIBS            = <NA>
RENV_DEFAULT_R_LIBS_SITE       = 
RENV_DEFAULT_R_LIBS_USER       = /projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5
RENV_DEFAULT_R_PROFILE         = <NA>
RENV_DEFAULT_R_PROFILE_USER    = <NA>
RENV_PROJECT                   = /home/user/fbar-ovdp

# PATH ===============================
- /usr/local/sbin
- /usr/local/bin
- /usr/sbin
- /usr/bin
- /opt/app/SybaseIQ/IQ-16_1/bin64

# Cache ==============================
There are a total of 133 package(s) installed in the renv cache.
Cache path: "~/.local/share/renv/cache/v5/R-3.5/x86_64-pc-linux-gnu"

renv was not recognizing an installed package: pdftools. I know the package is installed in the following library path /opt/R/R-3.5.3/lib64/R/library.

This may be due to the renv sandbox -- see ?renv::config for more details. You can set:

RENV_CONFIG_SANDBOX_ENABLED = FALSE

in an appropriate .Renviron file to disable this.

Also, I see the following in the diagnostic: external.libraries : chr(0).

This is expected, although a bit confusing -- renv has the notion of project-local settings, and user-level configuration. It is possible to configure this both in a project-specific way (renv::settings$external.libraries()) and in a user-specific way (renv::config$external.libraries()).

/projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5:/opt/R/R-3.5.3/lib64/R/library

This output makes it clear that renv is not correctly parsing your library paths: it's treating them as a single library path, rather than a vector of library paths. I can take a look at that. Do you have better luck if you use , as a delimiter?

As suggested, I set: RENV_CONFIG_SANDBOX_ENABLED = FALSE in the user .Renviron.

I see your point about the project-local settings and user-level configuration. I already had a user-level configuration for external.libraries in the .Renviron.

Using , as a delimiter seems to work, insofar as two libraries in the config are being recognized.

I no longer receive Error in readRDS(file) : error reading from connection at project startup. After starting up the project, I ran renv::diagnostics() and received the error just under # Status =============================. I ran renv::diagnostics() again, and the error didn't show up.

I closed and reopened the project and saw the same behavior (error followed by no error after renv::diagnostics). I closed the project, reopened the project, and then ran R in the Terminal. I saw the same behavior.

Here are the results from running renv::diagnostics() the first time:

> renv::diagnostics()
Diagnostics Report [renv 0.13.0]
================================

# Session Info =======================
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default
BLAS: /opt/R/R-3.5.3/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-3.5.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.3 tools_3.5.3    packrat_0.5.0  renv_0.13.0   

# Project ============================
Project path: "~/fbar-ovdp"

# Status =============================
Error in readRDS(file) : error reading from connection
* The project is already synchronized with the lockfile.

# Packages ===========================
                         Library  Source Lockfile Source Path Dependency
AER                        1.2-5    CRAN     <NA>   <NA>  [2]       <NA>
AGD                         0.35    CRAN     <NA>   <NA>  [2]       <NA>
AICcmodavg                 2.1-1    CRAN     <NA>   <NA>  [2]       <NA>
AUC                        0.3.0    CRAN     <NA>   <NA>  [2]       <NA>
AlgDesign                1.1-7.3    CRAN     <NA>   <NA>  [2]       <NA>
Amelia                     1.7.4    CRAN     <NA>   <NA>  [2]       <NA>
AsioHeaders             1.16.1-1    CRAN     <NA>   <NA>  [2]       <NA>
BB                     2014.10-1    CRAN     <NA>   <NA>  [2]       <NA>
BBmisc                      1.11    CRAN     <NA>   <NA>  [2]       <NA>
BH                      1.75.0-0    CRAN 1.75.0-0   CRAN  [1]   indirect
BSDA                       1.2.0    CRAN     <NA>   <NA>  [2]       <NA>
BTM                        0.3.1    CRAN     <NA>   <NA>  [2]       <NA>
BayesFactor             0.9.12-2    CRAN     <NA>   <NA>  [2]       <NA>
BayesX                     0.2-9    CRAN     <NA>   <NA>  [2]       <NA>
BiasedUrn                   1.07    CRAN     <NA>   <NA>  [2]       <NA>
BradleyTerry2              1.0-8    CRAN     <NA>   <NA>  [2]       <NA>
Brobdingnag                1.2-5    CRAN     <NA>   <NA>  [2]       <NA>
CALIBERrfimpute            0.1-6    CRAN     <NA>   <NA>  [2]       <NA>
CVST                       0.2-1    CRAN     <NA>   <NA>  [2]       <NA>
Cairo                      1.5-9    CRAN     <NA>   <NA>  [2]       <NA>
CircStats                  0.2-4    CRAN     <NA>   <NA>  [2]       <NA>
Ckmeans.1d.dp              4.2.1    CRAN     <NA>   <NA>  [2]       <NA>
CompQuadForm               1.4.3    CRAN     <NA>   <NA>  [2]       <NA>
CoxBoost                     1.4    CRAN     <NA>   <NA>  [2]       <NA>
Cubist                     0.2.1    CRAN     <NA>   <NA>  [2]       <NA>
DBI                        1.1.1    CRAN    1.1.1   CRAN  [1]   indirect
DBItest                    1.5-2    CRAN     <NA>   <NA>  [2]       <NA>
DEoptimR                   1.0-8    CRAN     <NA>   <NA>  [2]       <NA>
DMwR                       0.4.1    CRAN     <NA>   <NA>  [2]       <NA>
DRR                        0.0.3    CRAN     <NA>   <NA>  [2]       <NA>
DT                          0.17    CRAN     <NA>   <NA>  [1]       <NA>
DendSer                    1.0.1    CRAN     <NA>   <NA>  [2]       <NA>
DescTools                0.99.24    CRAN     <NA>   <NA>  [2]       <NA>
DiagrammeR               1.0.6.1    CRAN     <NA>   <NA>  [2]       <NA>
DiagrammeRsvg                0.1    CRAN     <NA>   <NA>  [2]       <NA>
DiceDesign                 1.8-1    CRAN     <NA>   <NA>  [2]       <NA>
DiceKriging                1.5.6    CRAN     <NA>   <NA>  [2]       <NA>
DistributionUtils          0.5-1    CRAN     <NA>   <NA>  [2]       <NA>
ECharts2Shiny             0.2.13    CRAN     <NA>   <NA>  [2]       <NA>
Ecdat                      0.3-1    CRAN     <NA>   <NA>  [2]       <NA>
Ecfun                      0.1-7    CRAN     <NA>   <NA>  [2]       <NA>
Epi                         2.26    CRAN     <NA>   <NA>  [2]       <NA>
FMStable                   0.1-2    CRAN     <NA>   <NA>  [2]       <NA>
FNN                          1.1    CRAN     <NA>   <NA>  [2]       <NA>
Formula                    1.2-2    CRAN    1.2-2   CRAN  [2]   indirect
GA                         3.0.2    CRAN     <NA>   <NA>  [2]       <NA>
GAMBoost                   1.2-3    CRAN     <NA>   <NA>  [2]       <NA>
GERGM                     0.11.2    CRAN     <NA>   <NA>  [2]       <NA>
GGally                     1.3.2    CRAN     <NA>   <NA>  [2]       <NA>
GISTools                   0.7-4    CRAN     <NA>   <NA>  [2]       <NA>
GPArotation            2014.11-1    CRAN     <NA>   <NA>  [2]       <NA>
GPfit                      1.0-8    CRAN     <NA>   <NA>  [2]       <NA>
GenABEL                    1.8-0    CRAN     <NA>   <NA>  [2]       <NA>
GenABEL.data               1.0.0    CRAN     <NA>   <NA>  [2]       <NA>
GeneralizedHyperbolic      0.8-1    CRAN     <NA>   <NA>  [2]       <NA>
GetEdgarData               0.1.0 unknown     <NA>   <NA>  [2]       <NA>
GetoptLong                 0.1.6    CRAN     <NA>   <NA>  [2]       <NA>
GlobalOptions             0.0.13    CRAN     <NA>   <NA>  [2]       <NA>
HSAUR                      1.3-9    CRAN     <NA>   <NA>  [2]       <NA>
HSAUR2                    1.1-17    CRAN     <NA>   <NA>  [2]       <NA>
HSAUR3                     1.0-8    CRAN     <NA>   <NA>  [2]       <NA>
Hmisc                      4.1-1    CRAN    4.1-1   CRAN  [2]   indirect
IRdisplay                  0.4.4    CRAN     <NA>   <NA>  [2]       <NA>
ISLR                         1.2    CRAN     <NA>   <NA>  [2]       <NA>
ISOcodes              2017.09.27    CRAN     <NA>   <NA>  [2]       <NA>
ISwR                       2.0-7    CRAN     <NA>   <NA>  [2]       <NA>
Iso                       0.0-17    CRAN     <NA>   <NA>  [2]       <NA>
JavaGD                     0.6-1    CRAN     <NA>   <NA>  [2]       <NA>
JuliaCall                 0.12.2    CRAN     <NA>   <NA>  [2]       <NA>
KMsurv                     0.1-5    CRAN     <NA>   <NA>  [2]       <NA>
KernSmooth               2.23-15    CRAN     <NA>   <NA>  [2]       <NA>
LDAvis                     0.3.2    CRAN     <NA>   <NA>  [2]       <NA>
LDAvisData                   0.1 unknown     <NA>   <NA>  [2]       <NA>
LaF                        0.8.0    CRAN     <NA>   <NA>  [2]       <NA>
Lahman                     6.0-0    CRAN     <NA>   <NA>  [2]       <NA>
LearnBayes                2.15.1    CRAN     <NA>   <NA>  [2]       <NA>
MASS                    7.3-53.1    CRAN 7.3-53.1   CRAN  [1]   indirect
MBESS                      4.4.3    CRAN     <NA>   <NA>  [2]       <NA>
MCMCglmm                    2.25    CRAN     <NA>   <NA>  [2]       <NA>
MCMCpack                   1.4-2    CRAN     <NA>   <NA>  [2]       <NA>
MEMSS                      0.9-2    CRAN     <NA>   <NA>  [2]       <NA>
MLmetrics                  1.1.1    CRAN     <NA>   <NA>  [2]       <NA>
MPV                         1.38    CRAN     <NA>   <NA>  [2]       <NA>
MatchIt                    4.1.0    CRAN     <NA>   <NA>  [2]       <NA>
Matching                   4.9-2    CRAN     <NA>   <NA>  [2]       <NA>
Matrix                    1.2-18    CRAN   1.2-18   CRAN  [1]   indirect
MatrixModels               0.4-1    CRAN     <NA>   <NA>  [2]       <NA>
ModelMetrics               1.1.0    CRAN     <NA>   <NA>  [2]       <NA>
MuMIn                     1.40.4    CRAN     <NA>   <NA>  [2]       <NA>
NISTunits                  1.0.1    CRAN     <NA>   <NA>  [2]       <NA>
NLP                       0.1-11    CRAN     <NA>   <NA>  [2]       <NA>
NetSwan                      0.1    CRAN     <NA>   <NA>  [2]       <NA>
OAIHarvester               0.3-0    CRAN     <NA>   <NA>  [2]       <NA>
OceanView                  1.0.4    CRAN     <NA>   <NA>  [2]       <NA>
OpenMPController           0.2-5    CRAN     <NA>   <NA>  [2]       <NA>
OpenMx                     2.9.6    CRAN     <NA>   <NA>  [2]       <NA>
PBSmapping                2.70.4    CRAN     <NA>   <NA>  [2]       <NA>
PKI                      0.1-5.1    CRAN     <NA>   <NA>  [2]       <NA>
PKPDmodels                 0.3.2    CRAN     <NA>   <NA>  [2]       <NA>
PRROC                      1.3.1    CRAN     <NA>   <NA>  [2]       <NA>
ParamHelpers                1.13    CRAN     <NA>   <NA>  [2]       <NA>
PerformanceAnalytics       1.5.2    CRAN     <NA>   <NA>  [2]       <NA>
ProjectTemplate              0.8    CRAN     <NA>   <NA>  [2]       <NA>
R.cache                   0.13.0    CRAN     <NA>   <NA>  [2]       <NA>
R.devices                 2.15.1    CRAN     <NA>   <NA>  [2]       <NA>
R.matlab                   3.6.1    CRAN     <NA>   <NA>  [2]       <NA>
R.methodsS3                1.8.1    CRAN     <NA>   <NA>  [1]       <NA>
R.oo                      1.24.0    CRAN     <NA>   <NA>  [1]       <NA>
R.rsp                     0.42.0    CRAN     <NA>   <NA>  [2]       <NA>
R.utils                   2.10.1    CRAN     <NA>   <NA>  [1]       <NA>
R2Cuba                     1.1-0    CRAN     <NA>   <NA>  [2]       <NA>
R2HTML                     2.3.2    CRAN     <NA>   <NA>  [2]       <NA>
R2OpenBUGS               3.2-3.2    CRAN     <NA>   <NA>  [2]       <NA>
R2SWF                      0.9-5    CRAN     <NA>   <NA>  [1]       <NA>
R2WinBUGS                 2.1-21    CRAN     <NA>   <NA>  [2]       <NA>
R6                         2.5.0    CRAN    2.5.0   CRAN  [1]   indirect
RANN                       2.5.1    CRAN     <NA>   <NA>  [2]       <NA>
RApiSerialize              0.1.0    CRAN     <NA>   <NA>  [1]       <NA>
RAppArmor                  3.2.2    CRAN     <NA>   <NA>  [1]       <NA>
RColorBrewer               1.1-2    CRAN    1.1-2   CRAN  [2]   indirect
RCurl                  1.95-4.10    CRAN     <NA>   <NA>  [2]       <NA>
RGraphics                 2.0-14    CRAN     <NA>   <NA>  [2]       <NA>
RGtk2                    2.20.34    CRAN     <NA>   <NA>  [2]       <NA>
RGtk2Extras                0.6.1    CRAN     <NA>   <NA>  [2]       <NA>
RH2                        0.2.4    CRAN     <NA>   <NA>  [2]       <NA>
RInside                   0.2.16    CRAN     <NA>   <NA>  [1]       <NA>
RItools                   0.1-15    CRAN     <NA>   <NA>  [2]       <NA>
RJDBC                      0.2-8    CRAN     <NA>   <NA>  [2]       <NA>
RJSONIO                    1.3-0    CRAN     <NA>   <NA>  [2]       <NA>
RMariaDB                   1.0.5    CRAN     <NA>   <NA>  [2]       <NA>
RMySQL                   0.10.14    CRAN     <NA>   <NA>  [2]       <NA>
RNeo4j                     1.6.4    CRAN     <NA>   <NA>  [2]       <NA>
RNetLogo                   1.0-4    CRAN     <NA>   <NA>  [2]       <NA>
ROCR                       1.0-7    CRAN     <NA>   <NA>  [2]       <NA>
RODBC                     1.3-16    CRAN     <NA>   <NA>  [2]       <NA>
RPostgreSQL                0.6-2    CRAN     <NA>   <NA>  [2]       <NA>
RPostgres                  1.2.0    CRAN     <NA>   <NA>  [2]       <NA>
RProtoBuf                 0.4.11    CRAN     <NA>   <NA>  [2]       <NA>
RSAGA                      1.3.0    CRAN     <NA>   <NA>  [1]       <NA>
RSQLite                    2.1.0    CRAN     <NA>   <NA>  [2]       <NA>
RSVGTipsDevice             1.0-7    CRAN     <NA>   <NA>  [2]       <NA>
RSclient                   0.7-3    CRAN     <NA>   <NA>  [2]       <NA>
RSelenium                  1.7.1    CRAN     <NA>   <NA>  [2]       <NA>
RSiena                     1.2-3    CRAN     <NA>   <NA>  [2]       <NA>
RSpectra                  0.12-0    CRAN     <NA>   <NA>  [2]       <NA>
RUnit                     0.4.31    CRAN     <NA>   <NA>  [2]       <NA>
RWeka                     0.4-37    CRAN     <NA>   <NA>  [2]       <NA>
RWekajars                3.9.2-1    CRAN     <NA>   <NA>  [2]       <NA>
RWiener                    1.3-1    CRAN     <NA>   <NA>  [2]       <NA>
RandomFields              3.1.50    CRAN     <NA>   <NA>  [2]       <NA>
RandomFieldsUtils         0.3.25    CRAN     <NA>   <NA>  [2]       <NA>
Rcgmin                 2013-2.21    CRAN     <NA>   <NA>  [2]       <NA>
Rcmdr                      2.4-3    CRAN     <NA>   <NA>  [2]       <NA>
RcmdrMisc                 1.0-10    CRAN     <NA>   <NA>  [2]       <NA>
Rcpp                       1.0.6    CRAN    1.0.6   CRAN  [1]   indirect
Rcpp11                 3.1.2.0.1    CRAN     <NA>   <NA>  [1]       <NA>
RcppArmadillo         0.10.2.1.0    CRAN     <NA>   <NA>  [1]       <NA>
RcppCCTZ                   0.2.3    CRAN     <NA>   <NA>  [2]       <NA>
RcppEigen              0.3.3.9.1    CRAN     <NA>   <NA>  [1]       <NA>
RcppParallel               5.0.2    CRAN     <NA>   <NA>  [1]       <NA>
RcppProgress                 0.4    CRAN     <NA>   <NA>  [2]       <NA>
RcppRoll                   0.2.2    CRAN     <NA>   <NA>  [2]       <NA>
Rcsdp                     0.1.55    CRAN     <NA>   <NA>  [2]       <NA>
RefManageR               0.14.20    CRAN     <NA>   <NA>  [2]       <NA>
Rglpk                      0.6-3    CRAN     <NA>   <NA>  [2]       <NA>
RgoogleMaps                1.4.1    CRAN     <NA>   <NA>  [2]       <NA>
 [ reached 'max' / getOption("max.print") -- omitted 998 rows ]

[1]: /projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5
[2]: /opt/R/R-3.5.3/lib64/R/library                         

# User Profile =======================
                 Source Package Require Version   Dev
1 /home/8b3sb/.Rprofile    renv                 FALSE

# Settings ===========================
List of 7
 $ external.libraries       : chr(0) 
 $ ignored.packages         : chr "dbx"
 $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
 $ r.version                : chr(0) 
 $ snapshot.type            : chr "implicit"
 $ use.cache                : logi TRUE
 $ vcs.ignore.library       : logi TRUE

# Options ============================
List of 5
 $ defaultPackages     : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
 $ download.file.method: NULL
 $ download.file.extra : NULL
 $ repos               : Named chr [1:2] "file://projects/Analysts/R/" "xx.xxx.xx.xxx/R/"
  ..- attr(*, "names")= chr [1:2] "WORK" "SYSTEM"
 $ renv.verbose        : logi TRUE

# Environment Variables ==============
HOME                           = /home/user
LANG                           = en_US.UTF-8
R_LIBS                         = <NA>
R_LIBS_SITE                    = 
R_LIBS_USER                    = /projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5
RENV_CONFIG_EXTERNAL_LIBRARIES = /projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5,/opt/R/R-3.5.3/lib64/R/library
RENV_CONFIG_SANDBOX_ENABLED    = FALSE

# PATH ===============================
- /usr/local/sbin
- /usr/local/bin
- /usr/sbin
- /usr/bin
- /opt/app/SybaseIQ/IQ-16_1/bin64

# Cache ==============================
There are a total of 133 package(s) installed in the renv cache.
Cache path: "~/.local/share/renv/cache/v5/R-3.5/x86_64-pc-linux-gnu"

If the error is triggered by a call to renv::status(), do you then see the error or any extra context if you run:

trace(readRDS, quote(print(ls.str())))
options(error = quote(print(sys.calls())))
renv::status()

And one more thing. I had a package that was preventing a successful renv::snapshot(). The package was dbx, and there was a suggestion made by renv about reinstalling. Instead, I placed renv::settings$ignored.packages("dbx", persist = FALSE) in my .Rprofile. After reopening the project, I was able to successfully renv::snapshot().

I did receive that error.

This is from the Console:

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

[Workspace loaded from ~/fbar-ovdp/.RData]

> library(readr)
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> trace(readRDS, quote(print(ls.str())))
Tracing function "readRDS" in package "base"
[1] "readRDS"
> options(error = quote(print(sys.calls())))
> results <- capture.output(renv::status()) %>% 
+     write_lines("renv_output.txt")
Error in readRDS(file) : error reading from connection

The tracing output does not contain the error, but I've attached it: renv_output.txt

Can you try the following to narrow it down?

pkgdirs <- list.files(.libPaths(), full.names = TRUE)
rdsfiles <- file.path(pkgdirs, "Meta/package.rds")
for (file in rdsfiles)
  if (file.exists(file))
    readRDS(file)
print(file)

It seems like renv is failing to read the package.rds file associated with one of your installed packages...

It's the dbx package, as mentioned in the earlier post:

And one more thing. I had a package that was preventing a successful renv::snapshot(). The package was dbx, and there was a suggestion made by renv about reinstalling. Instead, I placed renv::settings$ignored.packages("dbx", persist = FALSE) in my .Rprofile. After reopening the project, I was able to successfully renv::snapshot().

Here's the Console output:

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

[Workspace loaded from ~/fbar-ovdp/.RData]

> pkgdirs <- list.files(.libPaths(), full.names = TRUE)
> rdsfiles <- file.path(pkgdirs, "Meta/package.rds")
> for (file in rdsfiles)
+     if (file.exists(file))
+         readRDS(file)
Error in readRDS(file) : error reading from connection
> print(file)
[1] "/opt/R/R-3.5.3/lib64/R/library/dbx/Meta/package.rds"

The package.rds file is empty/blank/zeroKB, if you didn't already know.

Thanks. The real question here, of course, is how this happened in the first place...

I'll see if there's something renv could be doing here to better report packages that find themselves in this state.

Just to update you, I installed renv 0.13.2. I also commented out RENV_CONFIG_SANDBOX_ENABLED = FALSE and commented out RENV_CONFIG_EXTERNAL_LIBRARIES in my user .Renviron. In my user .Rprofile I still have renv::settings$ignored.packages("dbx", persist = TRUE). So, it appears that my projects are now completely isolated. Everything seems to be working fine, but I do still get the Error in readRDS(file) : error reading from connection message upon opening the project. Below is the output from renv::status() and renv::diagnostics(). FYI . . .

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

Error in readRDS(file) : error reading from connection
* Project '~/fbar-ovdp' loaded. [renv 0.13.2]
[Workspace loaded from ~/fbar-ovdp/.RData]

> renv::status()
* The project is already synchronized with the lockfile.
> renv::diagnostics()
Diagnostics Report [renv 0.13.2]
================================

# Session Info =======================
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default
BLAS: /opt/R/R-3.5.3/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-3.5.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

loaded via a namespace (and not attached):
 [1] compiler_3.5.3  htmltools_0.5.1 tools_3.5.3     yaml_2.2.1     
 [5] rmarkdown_1.18  knitr_1.31      xfun_0.20       digest_0.6.27  
 [9] rlang_0.4.10    renv_0.13.2     evaluate_0.14  

# Project ============================
Project path: "~/fbar-ovdp"

# Status =============================
* The project is already synchronized with the lockfile.

# Packages ===========================
                 Library Source  Lockfile Source Path Dependency
BH              1.72.0-3   CRAN  1.72.0-3   CRAN  [1]   indirect
DBI                1.1.0   CRAN     1.1.0   CRAN  [1]   indirect
Formula            1.2-4   CRAN     1.2-4   CRAN  [1]   indirect
Hmisc              4.5-0   CRAN     4.5-0   CRAN  [1]   indirect
KernSmooth       2.23-15   CRAN      <NA>   <NA>  [2]       <NA>
MASS            7.3-53.1   CRAN  7.3-53.1   CRAN  [1]   indirect
Matrix            1.2-14   CRAN    1.2-14   CRAN  [1]   indirect
R6                 2.5.0   CRAN     2.5.0   CRAN  [1]   indirect
RColorBrewer       1.1-2   CRAN     1.1-2   CRAN  [1]   indirect
Rcpp               1.0.6   CRAN     1.0.6   CRAN  [1]   indirect
XML            3.98-1.10   CRAN 3.98-1.10   CRAN  [1]   indirect
askpass              1.1   CRAN       1.1   CRAN  [1]   indirect
assertthat         0.2.1   CRAN     0.2.1   CRAN  [1]   indirect
backports          1.1.2   CRAN     1.1.2   CRAN  [1]   indirect
base64enc          0.1-3   CRAN     0.1-3   CRAN  [1]   indirect
boot              1.3-20   CRAN      <NA>   <NA>  [2]       <NA>
broom              0.5.4   CRAN     0.5.4   CRAN  [1]   indirect
callr              3.6.0   CRAN     3.6.0   CRAN  [1]   indirect
cellranger         1.1.0   CRAN     1.1.0   CRAN  [1]   indirect
checkmate          2.0.0   CRAN     2.0.0   CRAN  [1]   indirect
class             7.3-15   CRAN      <NA>   <NA>  [2]       <NA>
cli                2.4.0   CRAN     2.4.0   CRAN  [1]   indirect
cluster            2.1.2   CRAN     2.1.2   CRAN  [1]   indirect
codetools         0.2-16   CRAN    0.2-16   CRAN  [1]   indirect
colorspace         1.3-2   CRAN     1.3-2   CRAN  [1]   indirect
compiler            <NA>   <NA>      <NA>   <NA>  [2]   indirect
crayon             1.4.1   CRAN     1.4.1   CRAN  [1]   indirect
curl                 3.2   CRAN       3.2   CRAN  [1]   indirect
data.table        1.14.0   CRAN    1.14.0   CRAN  [1]   indirect
dbplyr             1.4.2   CRAN     1.4.2   CRAN  [1]   indirect
digest            0.6.27   CRAN    0.6.27   CRAN  [1]   indirect
dplyr              1.0.4   CRAN     1.0.4   CRAN  [1]     direct
easyr              0.5-2   CRAN     0.5-2   CRAN  [1]     direct
ellipsis           0.3.1   CRAN     0.3.1   CRAN  [1]   indirect
evaluate            0.14   CRAN      0.14   CRAN  [1]   indirect
fansi              0.4.2   CRAN     0.4.2   CRAN  [1]   indirect
farver             2.0.3   CRAN     2.0.3   CRAN  [1]   indirect
forcats            0.3.0   CRAN     0.3.0   CRAN  [1]   indirect
foreign           0.8-76   CRAN    0.8-76   CRAN  [1]   indirect
formattable      0.2.0.1   CRAN   0.2.0.1   CRAN  [1]     direct
furrr              0.1.0   CRAN     0.1.0   CRAN  [1]     direct
future            1.21.0   CRAN    1.21.0   CRAN  [1]   indirect
generics           0.1.0   CRAN     0.1.0   CRAN  [1]   indirect
ggplot2            3.3.3   CRAN     3.3.3   CRAN  [1]   indirect
globals           0.14.0   CRAN    0.14.0   CRAN  [1]   indirect
glue               1.4.2   CRAN     1.4.2   CRAN  [1]   indirect
grDevices           <NA>   <NA>      <NA>   <NA>  [2]   indirect
graphics            <NA>   <NA>      <NA>   <NA>  [2]   indirect
grid                <NA>   <NA>      <NA>   <NA>  [2]   indirect
gridExtra            2.3   CRAN       2.3   CRAN  [1]   indirect
gtable             0.2.0   CRAN     0.2.0   CRAN  [1]   indirect
haven              1.1.1   CRAN     1.1.1   CRAN  [1]   indirect
highr                0.6   CRAN       0.6   CRAN  [1]   indirect
hms                1.0.0   CRAN     1.0.0   CRAN  [1]   indirect
htmlTable          2.1.0   CRAN     2.1.0   CRAN  [1]   indirect
htmltools          0.5.1   CRAN     0.5.1   CRAN  [1]   indirect
htmlwidgets        1.5.3   CRAN     1.5.3   CRAN  [1]   indirect
httr               1.3.1   CRAN     1.3.1   CRAN  [1]   indirect
isoband            0.2.4   CRAN     0.2.4   CRAN  [1]   indirect
jsonlite           1.7.2   CRAN     1.7.2   CRAN  [1]   indirect
knitr               1.31   CRAN      1.31   CRAN  [1]   indirect
labeling           0.4.2   CRAN     0.4.2   CRAN  [1]   indirect
lattice          0.20-41   CRAN   0.20-41   CRAN  [1]   indirect
latticeExtra      0.6-28   CRAN    0.6-28   CRAN  [1]   indirect
lazyeval           0.2.1   CRAN     0.2.1   CRAN  [1]   indirect
lifecycle          1.0.0   CRAN     1.0.0   CRAN  [1]   indirect
listenv            0.8.0   CRAN     0.8.0   CRAN  [1]   indirect
lubridate         1.7.10   CRAN    1.7.10   CRAN  [1]     direct
magrittr           2.0.1   CRAN     2.0.1   CRAN  [1]   indirect
markdown             0.8   CRAN       0.8   CRAN  [1]   indirect
matrixStats       0.58.0   CRAN    0.58.0   CRAN  [1]   indirect
methods             <NA>   <NA>      <NA>   <NA>  [2]   indirect
mgcv              1.8-23   CRAN    1.8-23   CRAN  [1]   indirect
microbenchmark     1.4-4   CRAN     1.4-4   CRAN  [1]     direct
mime                 0.5   CRAN       0.5   CRAN  [1]   indirect
modelr             0.1.1   CRAN     0.1.1   CRAN  [1]   indirect
munsell            0.5.0   CRAN     0.5.0   CRAN  [1]   indirect
nlme             3.1-137   CRAN   3.1-137   CRAN  [1]   indirect
nnet              7.3-15   CRAN    7.3-15   CRAN  [1]   indirect
openssl            1.4.3   CRAN     1.4.3   CRAN  [1]   indirect
ore                1.6.3   CRAN     1.6.3   CRAN  [1]   indirect
parallel            <NA>   <NA>      <NA>   <NA>  [2]   indirect
parallelly        1.23.0   CRAN    1.23.0   CRAN  [1]   indirect
pdftools           2.3.1   CRAN     2.3.1   CRAN  [1]     direct
pillar             1.5.0   CRAN     1.5.0   CRAN  [1]   indirect
pkgconfig          2.0.1   CRAN     2.0.1   CRAN  [1]   indirect
plyr               1.8.4   CRAN     1.8.4   CRAN  [1]   indirect
prettyunits        1.1.1   CRAN     1.1.1   CRAN  [1]   indirect
processx           3.5.1   CRAN     3.5.1   CRAN  [1]   indirect
progress           1.2.2   CRAN     1.2.2   CRAN  [1]   indirect
ps                 1.6.0   CRAN     1.6.0   CRAN  [1]   indirect
purrr              0.3.4   CRAN     0.3.4   CRAN  [1]     direct
qpdf                 1.1   CRAN       1.1   CRAN  [1]   indirect
readr              1.1.1   CRAN     1.1.1   CRAN  [1]     direct
readxl             1.3.1   CRAN     1.3.1   CRAN  [1]   indirect
rematch            1.0.1   CRAN     1.0.1   CRAN  [1]   indirect
renv              0.13.2   CRAN    0.13.2   CRAN  [1]     direct
reprex             0.1.2   CRAN     0.1.2   CRAN  [1]   indirect
reshape2           1.4.3   CRAN     1.4.3   CRAN  [1]   indirect
rlang             0.4.10   CRAN    0.4.10   CRAN  [1]   indirect
rmarkdown           1.18   CRAN      1.18   CRAN  [1]     direct
rpart             4.1-15   CRAN    4.1-15   CRAN  [1]   indirect
rprojroot          2.0.2   CRAN     2.0.2   CRAN  [1]   indirect
rstudioapi          0.13   CRAN      0.13   CRAN  [1]   indirect
rvest              0.3.2   CRAN     0.3.2   CRAN  [1]   indirect
scales             1.1.1   CRAN     1.1.1   CRAN  [1]   indirect
selectr            0.4-1   CRAN     0.4-1   CRAN  [1]   indirect
spatial           7.3-11   CRAN      <NA>   <NA>  [2]       <NA>
splines             <NA>   <NA>      <NA>   <NA>  [2]   indirect
stats               <NA>   <NA>      <NA>   <NA>  [2]   indirect
strex              1.1.0   CRAN     1.1.0   CRAN  [1]     direct
stringi            1.5.4   WORK     1.5.4   WORK  [1]   indirect
stringr            1.4.0   CRAN     1.4.0   CRAN  [1]   indirect
survival          3.2-10   CRAN    3.2-10   CRAN  [1]   indirect
sys                  3.4   CRAN       3.4   CRAN  [1]   indirect
tibble             3.1.0   CRAN     3.1.0   CRAN  [1]   indirect
tidyr              0.8.0   CRAN     0.8.0   CRAN  [1]   indirect
tidyselect         1.1.0   CRAN     1.1.0   CRAN  [1]   indirect
tidyverse          1.2.1   CRAN     1.2.1   CRAN  [1]     direct
tinytex             0.31   CRAN      0.31   CRAN  [1]   indirect
tools               <NA>   <NA>      <NA>   <NA>  [2]   indirect
utf8               1.1.4   CRAN     1.1.4   CRAN  [1]   indirect
utils               <NA>   <NA>      <NA>   <NA>  [2]   indirect
vctrs              0.3.6   CRAN     0.3.6   CRAN  [1]   indirect
viridis            0.5.1   CRAN     0.5.1   CRAN  [1]   indirect
viridisLite        0.3.0   CRAN     0.3.0   CRAN  [1]   indirect
whisker            0.3-2   CRAN     0.3-2   CRAN  [1]   indirect
withr              2.4.1   CRAN     2.4.1   CRAN  [1]   indirect
xfun                0.20   CRAN      0.20   CRAN  [1]   indirect
xml2               1.2.0   CRAN     1.2.0   CRAN  [1]   indirect
yaml               2.2.1   CRAN     2.2.1   CRAN  [1]   indirect

[1]: /home/user/fbar-ovdp/renv/library/R-3.5/x86_64-pc-linux-gnu
[2]: /tmp/RtmphYs9ji/renv-system-library                         

# User Profile =======================
                 Source Package Require Version   Dev
1 /home/user/.Rprofile    renv                 FALSE

# Settings ===========================
List of 8
 $ external.libraries       : chr(0) 
 $ ignored.packages         : chr "dbx"
 $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
 $ r.version                : chr(0) 
 $ snapshot.type            : chr "implicit"
 $ use.cache                : logi TRUE
 $ vcs.ignore.library       : logi TRUE
 $ vcs.ignore.local         : logi TRUE

# Options ============================
List of 6
 $ defaultPackages     : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
 $ download.file.method: NULL
 $ download.file.extra : NULL
 $ repos               : Named chr [1:2] "file://projects/Analysts/R" "xx.xxx.xx.xxx/R"
  ..- attr(*, "names")= chr [1:2] "WORK" "SYSTEM"
 $ renv.consent        : logi TRUE
 $ renv.verbose        : logi TRUE

# Environment Variables ==============
HOME                        = /home/user
LANG                        = en_US.UTF-8
R_LIBS                      = <NA>
R_LIBS_SITE                 = 
R_LIBS_USER                 = /home/user/fbar-ovdp/renv/library/R-3.5/x86_64-pc-linux-gnu:/tmp/RtmphYs9ji/renv-system-library
RENV_DEFAULT_R_ENVIRON      = <NA>
RENV_DEFAULT_R_ENVIRON_USER = <NA>
RENV_DEFAULT_R_LIBS         = <NA>
RENV_DEFAULT_R_LIBS_SITE    = 
RENV_DEFAULT_R_LIBS_USER    = /projects/Analysts/R/x86_64-pc-linux-gnu-library/3.5
RENV_DEFAULT_R_PROFILE      = <NA>
RENV_DEFAULT_R_PROFILE_USER = <NA>
RENV_PROJECT                = /home/user/fbar-ovdp

# PATH ===============================
- /opt/R/R-3.5.3/bin
- /opt/Python-3.7.4/bin
- /usr/local/sbin
- /usr/local/bin
- /usr/sbin
- /usr/bin
- /opt/app/SybaseIQ/IQ-16_1/bin64

# Cache ==============================
There are a total of 289 package(s) installed in the renv cache.
Cache path: "~/.local/share/renv/cache/v5/R-3.5/x86_64-pc-linux-gnu"

Given that this issue is over 2 years old, and there hasn't been other reports of similar problems, I think either the root cause has been fixed, or it's sufficiently rare that it affects vanishingly few people.

rstudio / renv

issue at project startup: "Error in readRDS(file) : error reading from connection" #700