Trying to get language server to work in latest build of VS Code, R 4.6.0,
Project dependencies are managed with renv. I have verified I have renv installed in both local and project library.
When launching VS Code, I get the following stack trace from the OUTPUT tab for R Language Server:
R Language Server (5068) started
R library paths: F:/Programs/R/R-4.6.0/library
[2026-05-25 23:14:23.818] Error: ! Could not start R session, timed out
Call: [1] "rs_init(self, private, super, options, wait, wait_timeout)"
Stack trace:
1: throw(new_error("Could not start R session, timed out"))
2: rs_init(self, private, super, options, wait, wait_timeout)
3: initialize(...)
4: callr::r_session$new(options = callr::r_session_options(system_profile = TRUE,
user_profile = TRUE), wait = TRUE)
5: private$find_or_create_session()
6: self$diagnostics_task_manager$run_tasks()
7: self$process_events()
[2026-05-25 23:14:23.820] exiting
[Error - 11:14:23 PM] Client R Language Server: connection to server is erroring.
read ECONNRESET
[Error - 11:14:23 PM] Client R Language Server: connection to server is erroring.
read ECONNRESET
[Error - 11:14:23 PM] Connection to server got closed. Server will not be restarted.
R Language Server (5068) exited with exit code null
Any ideas? I believe it's due to the renv environment being activated because when I comment out the source file added to my .Rprofile project file, it works fine. But when renv activation script is sourced in .Rprofile (source("renv/activate.R"), it throws this error. I could not find any way to adjust timeout settings. I timed a launch of my CLI (Git Bash), it takes approximately 5 seconds with the activation script. Without the activation sourced, it's essentially instant.
So is it an issue with how long it's taking renv to scan files in my environment? I have added all non .R scripts to my .renvignore to speed the process up.
> renv::diagnostics()
Diagnostics Report [renv 1.2.3]
===============================
# Session Info ---------------------------------------------------------------
R version 4.6.0 (2026-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=English_United Kingdom.utf8
[2] LC_CTYPE=English_United Kingdom.utf8
[3] LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.27 compiler_4.6.0 tools_4.6.0
[4] renv_1.2.3
# Project --------------------------------------------------------------------
Project path: "F:/Documents/GitProjects/project"
# Status ---------------------------------------------------------------------
No issues found -- the project is in a consistent state.
# Packages -------------------------------------------------------------------
Library Source Lockfile Source Path Dependency
AnnotationDbi 1.74.0 Bioconductor 3.23 1.74.0 Bioconductor 3.23 [1] indirect
AnnotationHub 4.2.0 Bioconductor 3.23 4.2.0 Bioconductor 3.23 [1] indirect
BH 1.90.0-1 CRAN 1.90.0-1 CRAN [1] indirect
Biobase 2.72.0 https://bioc-release.r-universe.dev 2.72.0 https://bioc-release.r-universe.dev [1] indirect
BiocBaseUtils 1.14.0 https://bioc-release.r-universe.dev 1.14.0 https://bioc-release.r-universe.dev [1] indirect
BiocFileCache 3.2.0 https://bioc-release.r-universe.dev 3.2.0 https://bioc-release.r-universe.dev [1] indirect
BiocGenerics 0.58.1 https://bioc-release.r-universe.dev 0.58.1 https://bioc-release.r-universe.dev [1] indirect
BiocIO 1.22.0 https://bioc-release.r-universe.dev 1.22.0 https://bioc-release.r-universe.dev [1] indirect
BiocManager 1.30.27 CRAN 1.30.27 CRAN [1] indirect
BiocParallel 1.46.0 https://bioc-release.r-universe.dev 1.46.0 https://bioc-release.r-universe.dev [1] indirect
BiocSingular 1.28.0 https://bioc-release.r-universe.dev 1.28.0 https://bioc-release.r-universe.dev [1] indirect
BiocVersion 3.23.1 https://bioc.r-universe.dev 3.23.1 https://bioc.r-universe.dev [1] indirect
Biostrings 2.80.1 Bioconductor 3.23 2.80.1 Bioconductor 3.23 [1] indirect
BumpyMatrix 1.20.0 https://bioc-release.r-universe.dev 1.20.0 https://bioc-release.r-universe.dev [1] indirect
ComplexHeatmap 2.28.0 https://bioc-release.r-universe.dev 2.28.0 https://bioc-release.r-universe.dev [1] direct
CoreGx 2.16.0 https://bioc-release.r-universe.dev 2.16.0 https://bioc-release.r-universe.dev [1] indirect
DBI 1.3.0 CRAN 1.3.0 CRAN [1] indirect
DESeq2 1.52.0 https://bioc-release.r-universe.dev 1.52.0 https://bioc-release.r-universe.dev [1] direct
DOSE 4.6.0 Bioconductor 3.23 4.6.0 Bioconductor 3.23 [1] indirect
DT 0.34.0 CRAN 0.34.0 CRAN [1] indirect
DelayedArray 0.38.1 https://bioc-release.r-universe.dev 0.38.1 https://bioc-release.r-universe.dev [1] indirect
DelayedMatrixStats 1.34.0 https://bioc-release.r-universe.dev 1.34.0 https://bioc-release.r-universe.dev [1] indirect
Deriv 4.2.0 CRAN 4.2.0 CRAN [1] indirect
EDASeq 2.46.0 https://bioc-release.r-universe.dev 2.46.0 https://bioc-release.r-universe.dev [1] direct
ExperimentHub 3.2.0 https://bioc-release.r-universe.dev 3.2.0 https://bioc-release.r-universe.dev [1] direct
Formula 1.2-5 CRAN 1.2-5 CRAN [1] indirect
GGally 2.4.0 CRAN 2.4.0 CRAN [1] direct
GO.db 3.23.1 Bioconductor 3.23.1 Bioconductor [1] indirect
GOSemSim 2.38.0 https://bioc-release.r-universe.dev 2.38.0 https://bioc-release.r-universe.dev [1] indirect
GSEABase 1.74.0 https://bioc-release.r-universe.dev 1.74.0 https://bioc-release.r-universe.dev [1] indirect
GSVA 2.6.2 https://bioc-release.r-universe.dev 2.6.2 https://bioc-release.r-universe.dev [1] direct
GenomicAlignments 1.48.0 https://bioc-release.r-universe.dev 1.48.0 https://bioc-release.r-universe.dev [1] indirect
GenomicFeatures 1.64.0 https://bioc-release.r-universe.dev 1.64.0 https://bioc-release.r-universe.dev [1] indirect
GenomicRanges 1.64.0 https://bioc-release.r-universe.dev 1.64.0 https://bioc-release.r-universe.dev [1] indirect
GetoptLong 1.1.1 CRAN 1.1.1 CRAN [1] indirect
GlobalOptions 0.1.4 CRAN 0.1.4 CRAN [1] indirect
HDF5Array 1.40.0 https://bioc-release.r-universe.dev 1.40.0 https://bioc-release.r-universe.dev [1] indirect
IRanges 2.46.0 https://bioc-release.r-universe.dev 2.46.0 https://bioc-release.r-universe.dev [1] indirect
KEGGREST 1.52.0 Bioconductor 3.23 1.52.0 Bioconductor 3.23 [1] indirect
KernSmooth 2.23-26 CRAN 2.23-26 CRAN [2] indirect
MASS 7.3-65 CRAN 7.3-65 CRAN [1] direct
Matrix 1.7-5 CRAN 1.7-5 CRAN [2] indirect
MatrixGenerics 1.24.0 https://bioc-release.r-universe.dev 1.24.0 https://bioc-release.r-universe.dev [1] indirect
MatrixModels 0.5-4 CRAN 0.5-4 CRAN [1] indirect
ModelMetrics 1.2.2.2 CRAN 1.2.2.2 CRAN [1] indirect
MultiAssayExperiment 1.38.0 https://bioc-release.r-universe.dev 1.38.0 https://bioc-release.r-universe.dev [1] indirect
NISTunits 1.0.1 CRAN 1.0.1 CRAN [1] indirect
PCAtools 2.24.0 https://bioc-release.r-universe.dev 2.24.0 https://bioc-release.r-universe.dev [1] direct
PharmacoGx 3.16.0 https://bioc-release.r-universe.dev 3.16.0 https://bioc-release.r-universe.dev [1] direct
R.cache 0.17.0 CRAN <NA> <NA> [1] <NA>
R.methodsS3 1.8.2 CRAN 1.8.2 CRAN [1] indirect
R.oo 1.27.1 CRAN 1.27.1 CRAN [1] indirect
R.utils 2.13.0 CRAN 2.13.0 CRAN [1] indirect
R6 2.6.1 CRAN 2.6.1 CRAN [1] indirect
RANN 2.6.2 CRAN 2.6.2 CRAN [1] indirect
RColorBrewer 1.1-3 CRAN 1.1-3 CRAN [1] direct
RCurl 1.98-1.18 CRAN 1.98-1.18 CRAN [1] indirect
RSQLite 3.53.1 CRAN 3.53.1 CRAN [1] indirect
RSpectra 0.16-2 CRAN 0.16-2 CRAN [1] indirect
Rcpp 1.1.1-1.1 CRAN 1.1.1-1.1 CRAN [1] indirect
RcppArmadillo 15.2.6-1 CRAN 15.2.6-1 CRAN [1] indirect
RcppEigen 0.3.4.0.2 CRAN 0.3.4.0.2 CRAN [1] indirect
RcppParallel 5.1.11-2 CRAN 5.1.11-2 CRAN [1] indirect
RcppTOML 0.2.3 CRAN 0.2.3 CRAN [1] indirect
Rdpack 2.6.6 CRAN 2.6.6 CRAN [1] indirect
Rhdf5lib 2.0.0 https://bioc-release.r-universe.dev 2.0.0 https://bioc-release.r-universe.dev [1] indirect
Rhtslib 3.8.0 https://bioc-release.r-universe.dev 3.8.0 https://bioc-release.r-universe.dev [1] indirect
Rsamtools 2.28.0 https://bioc-release.r-universe.dev 2.28.0 https://bioc-release.r-universe.dev [1] indirect
S4Arrays 1.12.0 https://bioc-release.r-universe.dev 1.12.0 https://bioc-release.r-universe.dev [1] indirect
S4Vectors 0.50.1 https://bioc-release.r-universe.dev 0.50.1 https://bioc-release.r-universe.dev [1] indirect
S7 0.2.2 CRAN 0.2.2 CRAN [1] indirect
SQUAREM 2026.1 CRAN 2026.1 CRAN [1] indirect
STRINGdb 2.24.0 https://bioc-release.r-universe.dev 2.24.0 https://bioc-release.r-universe.dev [1] direct
ScaledMatrix 1.20.0 https://bioc-release.r-universe.dev 1.20.0 https://bioc-release.r-universe.dev [1] indirect
Seqinfo 1.2.0 https://bioc-release.r-universe.dev 1.2.0 https://bioc-release.r-universe.dev [1] indirect
ShortRead 1.70.0 https://bioc-release.r-universe.dev 1.70.0 https://bioc-release.r-universe.dev [1] indirect
SingleCellExperiment 1.34.0 https://bioc-release.r-universe.dev 1.34.0 https://bioc-release.r-universe.dev [1] indirect
SnowballC 0.7.1 CRAN 0.7.1 CRAN [1] indirect
SparseArray 1.12.2 https://bioc-release.r-universe.dev 1.12.2 https://bioc-release.r-universe.dev [1] indirect
SparseM 1.84-2 CRAN 1.84-2 CRAN [1] indirect
SpatialExperiment 1.22.0 https://bioc-release.r-universe.dev 1.22.0 https://bioc-release.r-universe.dev [1] indirect
SummarizedExperiment 1.42.0 https://bioc-release.r-universe.dev 1.42.0 https://bioc-release.r-universe.dev [1] indirect
TH.data 1.1-5 CRAN 1.1-5 CRAN [1] indirect
UpSetR 1.4.0 CRAN 1.4.0 CRAN [1] direct
XML 3.99-0.23 CRAN 3.99-0.23 CRAN [1] indirect
XVector 0.52.0 https://bioc-release.r-universe.dev 0.52.0 https://bioc-release.r-universe.dev [1] indirect
abind 1.4-8 CRAN 1.4-8 CRAN [1] indirect
aisdk 1.1.0 CRAN 1.1.0 CRAN [1] indirect
annotate 1.90.0 https://bioc-release.r-universe.dev 1.90.0 https://bioc-release.r-universe.dev [1] indirect
ape 5.8-1 CRAN 5.8-1 CRAN [1] indirect
aplot 0.2.9 CRAN 0.2.9 CRAN [1] indirect
aroma.light 3.42.0 https://bioc-release.r-universe.dev 3.42.0 https://bioc-release.r-universe.dev [1] indirect
askpass 1.2.1 CRAN 1.2.1 CRAN [1] indirect
assorthead 1.6.1 https://bioc-release.r-universe.dev 1.6.1 https://bioc-release.r-universe.dev [1] indirect
backports 1.5.1 CRAN 1.5.1 CRAN [1] indirect
base64enc 0.1-6 CRAN 0.1-6 CRAN [1] indirect
beachmat 2.28.0 https://bioc-release.r-universe.dev 2.28.0 https://bioc-release.r-universe.dev [1] indirect
beeswarm 0.4.0 CRAN 0.4.0 CRAN [1] indirect
bench 1.1.4 CRAN 1.1.4 CRAN [1] indirect
biocmake 1.4.0 https://bioc-release.r-universe.dev 1.4.0 https://bioc-release.r-universe.dev [1] indirect
biomaRt 2.68.0 https://bioc-release.r-universe.dev 2.68.0 https://bioc-release.r-universe.dev [1] direct
bit 4.6.0 CRAN 4.6.0 CRAN [1] indirect
bit64 4.8.2 CRAN 4.8.2 CRAN [1] indirect
bitops 1.0-9 CRAN 1.0-9 CRAN [1] indirect
blob 1.3.0 CRAN 1.3.0 CRAN [1] indirect
boot 1.3-32 CRAN 1.3-32 CRAN [2] indirect
brew 1.0-10 CRAN <NA> <NA> [1] <NA>
broom 1.0.13 CRAN 1.0.13 CRAN [1] indirect
bslib 0.11.0 CRAN 0.11.0 CRAN [1] indirect
caTools 1.18.3 CRAN 1.18.3 CRAN [1] indirect
cachem 1.1.0 CRAN 1.1.0 CRAN [1] indirect
callr 3.7.6 CRAN 3.7.6 CRAN [1] indirect
car 3.1-5 CRAN 3.1-5 CRAN [1] direct
carData 3.0-6 CRAN 3.0-6 CRAN [1] indirect
caret 7.0-1 CRAN 7.0-1 CRAN [1] direct
celestial 1.5.8 CRAN 1.5.8 CRAN [1] indirect
cellranger 1.1.0 CRAN 1.1.0 CRAN [1] indirect
checkmate 2.3.4 CRAN 2.3.4 CRAN [1] indirect
chron 2.3-62 CRAN 2.3-62 CRAN [1] indirect
cigarillo 1.2.0 https://bioc-release.r-universe.dev 1.2.0 https://bioc-release.r-universe.dev [1] indirect
circlize 0.4.18 CRAN 0.4.18 CRAN [1] direct
class 7.3-23 CRAN 7.3-23 CRAN [2] indirect
cli 3.6.6 CRAN 3.6.6 CRAN [1] indirect
clipr 0.8.1 CRAN 0.8.1 CRAN [1] indirect
clock 0.7.4 CRAN 0.7.4 CRAN [1] indirect
clue 0.3-68 CRAN 0.3-68 CRAN [1] indirect
cluster 2.1.8.2 CRAN 2.1.8.2 CRAN [2] indirect
clusterProfiler 4.20.0 https://bioc-release.r-universe.dev 4.20.0 https://bioc-release.r-universe.dev [1] direct
codetools 0.2-20 CRAN 0.2-20 CRAN [2] indirect
collections 0.3.12 CRAN <NA> <NA> [1] <NA>
colorspace 2.1-2 CRAN 2.1-2 CRAN [1] indirect
commonmark 2.0.0 CRAN 2.0.0 CRAN [1] indirect
compiler <NA> <NA> <NA> <NA> [2] indirect
conflicted 1.2.0 CRAN 1.2.0 CRAN [1] indirect
coop 0.6-3 CRAN 0.6-3 CRAN [1] indirect
corrplot 0.95 CRAN 0.95 CRAN [1] indirect
cowplot 1.2.0 CRAN 1.2.0 CRAN [1] direct
cpp11 0.5.5 CRAN 0.5.5 CRAN [1] indirect
crayon 1.5.3 CRAN 1.5.3 CRAN [1] indirect
crosstalk 1.2.2 CRAN 1.2.2 CRAN [1] indirect
curl 7.1.0 CRAN 7.1.0 CRAN [1] indirect
data.table 1.18.4 CRAN 1.18.4 CRAN [1] direct
data.tree 1.2.0 CRAN 1.2.0 CRAN [1] indirect
datasets <NA> <NA> <NA> <NA> [2] indirect
dbplyr 2.5.2 CRAN 2.5.2 CRAN [1] indirect
deldir 2.0-4 CRAN 2.0-4 CRAN [1] indirect
dendextend 1.19.1 CRAN 1.19.1 CRAN [1] direct
desc 1.4.3 CRAN <NA> <NA> [1] <NA>
diagram 1.6.5 CRAN 1.6.5 CRAN [1] indirect
digest 0.6.39 CRAN 0.6.39 CRAN [1] direct
dir.expiry 1.20.0 https://bioc-release.r-universe.dev 1.20.0 https://bioc-release.r-universe.dev [1] indirect
doBy 4.7.1 CRAN 4.7.1 CRAN [1] indirect
doParallel 1.0.17 CRAN 1.0.17 CRAN [1] indirect
downloader 0.4.1 CRAN 0.4.1 CRAN [1] indirect
dplyr 1.2.1 CRAN 1.2.1 CRAN [1] direct
dqrng 0.4.1 CRAN 0.4.1 CRAN [1] indirect
drc 3.0-1 CRAN 3.0-1 CRAN [1] direct
dtplyr 1.3.3 CRAN 1.3.3 CRAN [1] indirect
e1071 1.7-17 CRAN 1.7-17 CRAN [1] indirect
edgeR 4.10.0 https://bioc-release.r-universe.dev 4.10.0 https://bioc-release.r-universe.dev [1] direct
emmeans 2.0.3 CRAN 2.0.3 CRAN [1] direct
enrichit 0.1.4 CRAN 0.1.4 CRAN [1] indirect
enrichplot 1.32.0 Bioconductor 3.23 1.32.0 Bioconductor 3.23 [1] indirect
estimability 1.5.1 CRAN 1.5.1 CRAN [1] indirect
evaluate 1.0.5 CRAN 1.0.5 CRAN [1] indirect
farver 2.1.2 CRAN 2.1.2 CRAN [1] indirect
fastmap 1.2.0 CRAN 1.2.0 CRAN [1] indirect
fastmatch 1.1-8 CRAN 1.1-8 CRAN [1] indirect
fgsea 1.38.0 https://bioc-release.r-universe.dev 1.38.0 https://bioc-release.r-universe.dev [1] direct
filelock 1.0.3 CRAN 1.0.3 CRAN [1] indirect
fitdistrplus 1.2-6 CRAN 1.2-6 CRAN [1] direct
fontBitstreamVera 0.1.1 CRAN 0.1.1 CRAN [1] indirect
fontLiberation 0.1.0 CRAN 0.1.0 CRAN [1] indirect
fontawesome 0.5.3 CRAN 0.5.3 CRAN [1] indirect
fontquiver 0.2.1 CRAN 0.2.1 CRAN [1] indirect
forcats 1.0.1 CRAN 1.0.1 CRAN [1] indirect
foreach 1.5.2 CRAN 1.5.2 CRAN [1] indirect
forecast 9.0.2 CRAN 9.0.2 CRAN [1] indirect
foreign 0.8-91 CRAN <NA> <NA> [2] <NA>
formatR 1.14 CRAN 1.14 CRAN [1] indirect
fracdiff 1.5-4 CRAN 1.5-4 CRAN [1] indirect
fs 2.1.0 CRAN 2.1.0 CRAN [1] indirect
futile.logger 1.4.9 CRAN 1.4.9 CRAN [1] indirect
futile.options 1.0.1 CRAN 1.0.1 CRAN [1] indirect
future 1.70.0 CRAN 1.70.0 CRAN [1] indirect
future.apply 1.20.2 CRAN 1.20.2 CRAN [1] indirect
gargle 1.6.1 CRAN 1.6.1 CRAN [1] indirect
gdtools 0.5.0 CRAN 0.5.0 CRAN [1] indirect
generics 0.1.4 CRAN 0.1.4 CRAN [1] indirect
ggbeeswarm 0.7.3 CRAN 0.7.3 CRAN [1] direct
ggforce 0.5.0 CRAN 0.5.0 CRAN [1] indirect
ggfun 0.2.0 CRAN 0.2.0 CRAN [1] indirect
ggiraph 0.9.6 CRAN 0.9.6 CRAN [1] indirect
ggnewscale 0.5.2 CRAN 0.5.2 CRAN [1] indirect
ggplot2 4.0.3 CRAN 4.0.3 CRAN [1] direct
ggplotify 0.1.3 CRAN 0.1.3 CRAN [1] indirect
ggpubr 0.6.3 CRAN 0.6.3 CRAN [1] direct
ggrepel 0.9.8 CRAN 0.9.8 CRAN [1] direct
ggsci 5.0.0 CRAN 5.0.0 CRAN [1] indirect
ggsignif 0.6.4 CRAN 0.6.4 CRAN [1] direct
ggstance 0.3.7 CRAN 0.3.7 CRAN [1] direct
ggstats 0.13.0 CRAN 0.13.0 CRAN [1] indirect
ggtangle 0.1.2 CRAN 0.1.2 CRAN [1] indirect
ggtree 4.2.0 https://bioc-release.r-universe.dev 4.2.0 https://bioc-release.r-universe.dev [1] indirect
globals 0.19.1 CRAN 0.19.1 CRAN [1] indirect
glue 1.8.1 CRAN 1.8.1 CRAN [1] indirect
googledrive 2.1.2 CRAN 2.1.2 CRAN [1] indirect
googlesheets4 1.1.2 CRAN 1.1.2 CRAN [1] indirect
gower 1.0.2 CRAN 1.0.2 CRAN [1] indirect
gplots 3.3.0 CRAN 3.3.0 CRAN [1] indirect
grDevices <NA> <NA> <NA> <NA> [2] indirect
graph 1.90.0 https://bioc-release.r-universe.dev 1.90.0 https://bioc-release.r-universe.dev [1] indirect
graphics <NA> <NA> <NA> <NA> [2] indirect
grid <NA> <NA> <NA> <NA> [2] direct
gridExtra 2.3 CRAN 2.3 CRAN [1] direct
gridGraphics 0.5-1 CRAN 0.5-1 CRAN [1] indirect
gson 0.1.0 CRAN 0.1.0 CRAN [1] indirect
gsubfn 0.7 CRAN 0.7 CRAN [1] indirect
gtable 0.3.6 CRAN 0.3.6 CRAN [1] indirect
gtools 3.9.5 CRAN 3.9.5 CRAN [1] indirect
h5mread 1.4.0 https://bioc-release.r-universe.dev 1.4.0 https://bioc-release.r-universe.dev [1] indirect
hardhat 1.4.3 CRAN 1.4.3 CRAN [1] indirect
hash 2.2.6.4 CRAN 2.2.6.4 CRAN [1] indirect
haven 2.5.5 CRAN 2.5.5 CRAN [1] indirect
here 1.0.2 CRAN 1.0.2 CRAN [1] indirect
highr 0.12 CRAN 0.12 CRAN [1] indirect
hms 1.1.4 CRAN 1.1.4 CRAN [1] indirect
htmltools 0.5.9 CRAN 0.5.9 CRAN [1] indirect
htmlwidgets 1.6.4 CRAN 1.6.4 CRAN [1] indirect
httpuv 1.6.17 CRAN 1.6.17 CRAN [1] indirect
httr 1.4.8 CRAN 1.4.8 CRAN [1] indirect
httr2 1.2.2 CRAN 1.2.2 CRAN [1] indirect
hwriter 1.3.2.1 CRAN 1.3.2.1 CRAN [1] indirect
ids 1.0.1 CRAN 1.0.1 CRAN [1] indirect
igraph 2.3.1 CRAN 2.3.1 CRAN [1] indirect
interp 1.1-6 CRAN 1.1-6 CRAN [1] indirect
ipred 0.9-15 CRAN 0.9-15 CRAN [1] indirect
irlba 2.3.7 CRAN 2.3.7 CRAN [1] indirect
irr 0.84.1 CRAN 0.84.1 CRAN [1] direct
isoband 0.3.0 CRAN 0.3.0 CRAN [1] indirect
iterators 1.0.14 CRAN 1.0.14 CRAN [1] indirect
jpeg 0.1-11 CRAN 0.1-11 CRAN [1] indirect
jquerylib 0.1.4 CRAN 0.1.4 CRAN [1] indirect
jsonlite 2.0.0 CRAN 2.0.0 CRAN [1] direct
knitr 1.51 CRAN 1.51 CRAN [1] indirect
labeling 0.4.3 CRAN 0.4.3 CRAN [1] indirect
lambda.r 1.2.4 CRAN 1.2.4 CRAN [1] indirect
languageserver 0.3.18 CRAN <NA> <NA> [1] <NA>
later 1.4.8 CRAN 1.4.8 CRAN [1] indirect
latex2exp 0.9.8 CRAN 0.9.8 CRAN [1] direct
lattice 0.22-9 CRAN 0.22-9 CRAN [1] indirect
latticeExtra 0.6-31 CRAN 0.6-31 CRAN [1] indirect
lava 1.9.1 CRAN 1.9.1 CRAN [1] indirect
lazyeval 0.2.3 CRAN 0.2.3 CRAN [1] indirect
lifecycle 1.0.5 CRAN 1.0.5 CRAN [1] indirect
limma 3.68.3 https://bioc-release.r-universe.dev 3.68.3 https://bioc-release.r-universe.dev [1] direct
lintr 3.3.0-1 CRAN <NA> <NA> [1] <NA>
listenv 0.10.1 CRAN 0.10.1 CRAN [1] indirect
lme4 2.0-1 CRAN 2.0-1 CRAN [1] direct
lmtest 0.9-40 CRAN 0.9-40 CRAN [1] direct
locfit 1.5-9.12 CRAN 1.5-9.12 CRAN [1] indirect
logisticPCA 0.2 CRAN 0.2 CRAN [1] direct
lpSolve 5.6.23 CRAN 5.6.23 CRAN [1] indirect
lsa 0.73.4 CRAN 0.73.4 CRAN [1] indirect
lubridate 1.9.5 CRAN 1.9.5 CRAN [1] indirect
magicaxis 2.5.1 CRAN 2.5.1 CRAN [1] indirect
magick 2.9.1 CRAN 2.9.1 CRAN [1] indirect
magrittr 2.0.5 CRAN 2.0.5 CRAN [1] indirect
mapproj 1.2.12 CRAN 1.2.12 CRAN [1] indirect
maps 3.4.3 CRAN 3.4.3 CRAN [1] indirect
marray 1.90.0 https://bioc-release.r-universe.dev 1.90.0 https://bioc-release.r-universe.dev [1] indirect
matrixStats 1.5.0 CRAN 1.5.0 CRAN [1] indirect
memoise 2.0.1 CRAN 2.0.1 CRAN [1] indirect
memuse 4.2-3 CRAN 4.2-3 CRAN [1] indirect
methods <NA> <NA> <NA> <NA> [2] indirect
mgcv 1.9-4 CRAN 1.9-4 CRAN [2] indirect
miRBaseConverter 1.36.0 https://bioc-release.r-universe.dev 1.36.0 https://bioc-release.r-universe.dev [1] direct
microbenchmark 1.5.0 CRAN 1.5.0 CRAN [1] indirect
mime 0.13 CRAN 0.13 CRAN [1] indirect
minqa 1.2.8 CRAN 1.2.8 CRAN [1] indirect
modelr 0.1.11 CRAN 0.1.11 CRAN [1] indirect
moments 0.14.1 CRAN 0.14.1 CRAN [1] direct
msigdb 1.20.0 Bioconductor 3.23 1.20.0 Bioconductor 3.23 [1] direct
multcomp 1.4-30 CRAN 1.4-30 CRAN [1] indirect
multiMiR 1.34.0 https://bioc-release.r-universe.dev 1.34.0 https://bioc-release.r-universe.dev [1] direct
mvtnorm 1.3-7 CRAN 1.3-7 CRAN [1] indirect
ncf 1.3-3 CRAN 1.3-3 CRAN [1] direct
networkD3 0.4.1 CRAN 0.4.1 CRAN [1] direct
nlme 3.1-169 CRAN 3.1-169 CRAN [1] direct
nloptr 2.2.1 CRAN 2.2.1 CRAN [1] indirect
nnet 7.3-20 CRAN 7.3-20 CRAN [2] indirect
numDeriv 2016.8-1.1 CRAN 2016.8-1.1 CRAN [1] indirect
openssl 2.4.1 CRAN 2.4.1 CRAN [1] direct
org.Hs.eg.db 3.23.1 Bioconductor 3.23.1 Bioconductor [1] direct
org.Mm.eg.db 3.23.0 Bioconductor 3.23.0 Bioconductor [1] indirect
otel 0.2.0 CRAN 0.2.0 CRAN [1] indirect
pROC 1.19.0.1 CRAN 1.19.0.1 CRAN [1] direct
parallel <NA> <NA> <NA> <NA> [2] direct
parallelDist 0.2.7 CRAN 0.2.7 CRAN [1] direct
parallelly 1.47.0 CRAN 1.47.0 CRAN [1] indirect
patchwork 1.3.2 CRAN 1.3.2 CRAN [1] indirect
pbapply 1.7-4 CRAN 1.7-4 CRAN [1] direct
pbkrtest 0.5.5 CRAN 0.5.5 CRAN [1] indirect
piano 2.28.0 https://bioc-release.r-universe.dev 2.28.0 https://bioc-release.r-universe.dev [1] indirect
pillar 1.11.1 CRAN 1.11.1 CRAN [1] indirect
pkgbuild 1.4.8 CRAN <NA> <NA> [1] <NA>
pkgconfig 2.0.3 CRAN 2.0.3 CRAN [1] indirect
pkgload 1.5.2 CRAN <NA> <NA> [1] <NA>
plotly 4.12.0 CRAN 4.12.0 CRAN [1] direct
plotrix 3.8-14 CRAN 3.8-14 CRAN [1] indirect
plyr 1.8.9 CRAN 1.8.9 CRAN [1] indirect
png 0.1-9 CRAN 0.1-9 CRAN [1] indirect
polyclip 1.10-7 CRAN 1.10-7 CRAN [1] indirect
polynom 1.4-1 CRAN 1.4-1 CRAN [1] indirect
pracma 2.4.6 CRAN 2.4.6 CRAN [1] indirect
prettyunits 1.2.0 CRAN 1.2.0 CRAN [1] indirect
processx 3.9.0 CRAN 3.9.0 CRAN [1] indirect
prodlim 2026.03.11 CRAN 2026.03.11 CRAN [1] indirect
profmem 0.7.0 CRAN 0.7.0 CRAN [1] indirect
progress 1.2.3 CRAN 1.2.3 CRAN [1] indirect
progressr 0.19.0 CRAN 0.19.0 CRAN [1] indirect
promises 1.5.0 CRAN 1.5.0 CRAN [1] indirect
proto 1.0.0 CRAN 1.0.0 CRAN [1] indirect
proxy 0.4-29 CRAN 0.4-29 CRAN [1] indirect
ps 1.9.3 CRAN 1.9.3 CRAN [1] indirect
purrr 1.2.2 CRAN 1.2.2 CRAN [1] direct
pwalign 1.8.0 https://bioc-release.r-universe.dev 1.8.0 https://bioc-release.r-universe.dev [1] indirect
qs2 0.2.1 CRAN 0.2.1 CRAN [1] direct
quantreg 6.1 CRAN 6.1 CRAN [1] indirect
qvalue 2.44.0 https://bioc-release.r-universe.dev 2.44.0 https://bioc-release.r-universe.dev [1] indirect
ragg 1.5.2 CRAN 1.5.2 CRAN [1] indirect
rappdirs 0.3.4 CRAN 0.3.4 CRAN [1] indirect
rbibutils 2.4.1 CRAN 2.4.1 CRAN [1] indirect
readr 2.2.0 CRAN 2.2.0 CRAN [1] indirect
readxl 1.5.0 CRAN 1.5.0 CRAN [1] direct
recipes 1.3.2 CRAN 1.3.2 CRAN [1] indirect
reformulas 0.4.4 CRAN 0.4.4 CRAN [1] indirect
relations 0.6-17 CRAN 0.6-17 CRAN [1] indirect
rematch 2.0.0 CRAN 2.0.0 CRAN [1] indirect
rematch2 2.1.2 CRAN 2.1.2 CRAN [1] indirect
renv 1.2.3 CRAN 1.2.3 CRAN [1] direct
reprex 2.1.1 CRAN 2.1.1 CRAN [1] indirect
reshape2 1.4.5 CRAN 1.4.5 CRAN [1] indirect
restfulr 0.0.16 CRAN 0.0.16 CRAN [1] indirect
reticulate 1.46.0 CRAN 1.46.0 CRAN [1] indirect
rex 1.2.2 CRAN <NA> <NA> [1] <NA>
rhdf5 2.56.0 https://bioc-release.r-universe.dev 2.56.0 https://bioc-release.r-universe.dev [1] indirect
rhdf5filters 1.24.0 https://bioc-release.r-universe.dev 1.24.0 https://bioc-release.r-universe.dev [1] indirect
rjson 0.2.23 CRAN 0.2.23 CRAN [1] indirect
rlang 1.2.0 CRAN 1.2.0 CRAN [1] direct
rmarkdown 2.31 CRAN 2.31 CRAN [1] indirect
roxygen2 8.0.0 CRAN <NA> <NA> [1] <NA>
rpart 4.1.27 CRAN 4.1.27 CRAN [2] indirect
rprojroot 2.1.1 CRAN 2.1.1 CRAN [1] indirect
rstatix 0.7.3 CRAN 0.7.3 CRAN [1] direct
rstudioapi 0.18.0 CRAN 0.18.0 CRAN [1] indirect
rsvd 1.0.5 CRAN 1.0.5 CRAN [1] indirect
rtracklayer 1.72.0 https://bioc-release.r-universe.dev 1.72.0 https://bioc-release.r-universe.dev [1] indirect
rvest 1.0.5 CRAN 1.0.5 CRAN [1] indirect
sandwich 3.1-1 CRAN 3.1-1 CRAN [1] indirect
sass 0.4.10 CRAN 0.4.10 CRAN [1] indirect
scales 1.4.0 CRAN 1.4.0 CRAN [1] direct
scatterpie 0.2.6 CRAN 0.2.6 CRAN [1] indirect
selectr 0.5-1 CRAN 0.5-1 CRAN [1] indirect
sets 1.0-25 CRAN 1.0-25 CRAN [1] indirect
shape 1.4.6.1 CRAN 1.4.6.1 CRAN [1] indirect
shiny 1.13.0 CRAN 1.13.0 CRAN [1] indirect
shinydashboard 0.7.3 CRAN 0.7.3 CRAN [1] indirect
shinyjs 2.1.1 CRAN 2.1.1 CRAN [1] indirect
sitmo 2.0.2 CRAN 2.0.2 CRAN [1] indirect
slam 0.1-55 CRAN 0.1-55 CRAN [1] indirect
sm 2.2-6.0 CRAN 2.2-6.0 CRAN [1] indirect
snow 0.4-4 CRAN 0.4-4 CRAN [1] indirect
sourcetools 0.1.7-2 CRAN 0.1.7-2 CRAN [1] indirect
sparseMatrixStats 1.24.0 https://bioc-release.r-universe.dev 1.24.0 https://bioc-release.r-universe.dev [1] indirect
sparsevctrs 0.3.6 CRAN 0.3.6 CRAN [1] indirect
spatial 7.3-18 CRAN <NA> <NA> [2] <NA>
splines <NA> <NA> <NA> <NA> [2] indirect
sqldf 0.4-12 CRAN 0.4-12 CRAN [1] indirect
statmod 1.5.2 CRAN 1.5.2 CRAN [1] indirect
stats <NA> <NA> <NA> <NA> [2] direct
stats4 <NA> <NA> <NA> <NA> [2] indirect
stringfish 0.19.0 CRAN 0.19.0 CRAN [1] indirect
stringi 1.8.7 CRAN 1.8.7 CRAN [1] indirect
stringr 1.6.0 CRAN 1.6.0 CRAN [1] direct
styler 1.11.0 CRAN <NA> <NA> [1] <NA>
survival 3.8-6 CRAN 3.8-6 CRAN [2] indirect
svglite 2.2.2 CRAN 2.2.2 CRAN [1] direct
sys 3.4.3 CRAN 3.4.3 CRAN [1] indirect
systemfonts 1.3.2 CRAN 1.3.2 CRAN [1] indirect
textshaping 1.0.5 CRAN 1.0.5 CRAN [1] indirect
tibble 3.3.1 CRAN 3.3.1 CRAN [1] direct
tidydr 0.0.6 CRAN 0.0.6 CRAN [1] indirect
tidyr 1.3.2 CRAN 1.3.2 CRAN [1] direct
tidyselect 1.2.1 CRAN 1.2.1 CRAN [1] direct
tidytree 0.4.7 CRAN 0.4.7 CRAN [1] indirect
tidyverse 2.0.0 CRAN 2.0.0 CRAN [1] direct
timeDate 4052.112 CRAN 4052.112 CRAN [1] indirect
timechange 0.4.0 CRAN 0.4.0 CRAN [1] indirect
tinytex 0.59 CRAN 0.59 CRAN [1] indirect
tools <NA> <NA> <NA> <NA> [2] direct
treeio 1.36.1 https://bioc-release.r-universe.dev 1.36.1 https://bioc-release.r-universe.dev [1] indirect
tweenr 2.0.3 CRAN 2.0.3 CRAN [1] indirect
tzdb 0.5.0 CRAN 0.5.0 CRAN [1] indirect
umap 0.2.10.0 CRAN 0.2.10.0 CRAN [1] direct
urca 1.3-4 CRAN 1.3-4 CRAN [1] indirect
utf8 1.2.6 CRAN 1.2.6 CRAN [1] indirect
utils <NA> <NA> <NA> <NA> [2] indirect
uuid 1.2-2 CRAN 1.2-2 CRAN [1] indirect
vctrs 0.7.3 CRAN 0.7.3 CRAN [1] indirect
vipor 0.4.7 CRAN 0.4.7 CRAN [1] indirect
viridis 0.6.5 CRAN 0.6.5 CRAN [1] direct
viridisLite 0.4.3 CRAN 0.4.3 CRAN [1] indirect
visNetwork 2.1.4 CRAN 2.1.4 CRAN [1] indirect
vroom 1.7.1 CRAN 1.7.1 CRAN [1] indirect
webshot 0.5.5 CRAN 0.5.5 CRAN [1] direct
withr 3.0.2 CRAN 3.0.2 CRAN [1] indirect
xfun 0.57 CRAN 0.57 CRAN [1] indirect
xml2 1.5.2 CRAN 1.5.2 CRAN [1] indirect
xmlparsedata 1.0.5 CRAN <NA> <NA> [1] <NA>
xtable 1.8-8 CRAN 1.8-8 CRAN [1] indirect
yaml 2.3.12 CRAN 2.3.12 CRAN [1] indirect
yulab.utils 0.2.4 CRAN 0.2.4 CRAN [1] indirect
zoo 1.8-15 CRAN 1.8-15 CRAN [1] indirect
[1]: F:/Documents/GitProjects/project/renv/library/windows/R-4.6/x86_64-w64-mingw32
[2]: C:/Users/bgkin/AppData/Local/R/cache/R/renv/sandbox/windows/R-4.6/x86_64-w64-mingw32/e9f0da3f
# R CMD config --all ---------------------------------------------------------
CC = gcc
CFLAGS = -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign
CPICFLAGS =
CPPFLAGS =
CC17 = gcc
C17FLAGS = -O2 -Wall -std=gnu17 -mfpmath=sse -msse2 -mstackrealign
CC23 = gcc
C23FLAGS = -O2 -Wall -std=gnu23 -mfpmath=sse -msse2 -mstackrealign
CC90 = gcc
C90FLAGS = -O2 -Wall -std=gnu90 -mfpmath=sse -msse2 -mstackrealign
CC99 = gcc
C99FLAGS = -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign
CXX = g++ -std=gnu++20
CXXFLAGS = -O2 -Wall -mfpmath=sse -msse2 -mstackrealign
CXXPICFLAGS =
CXX17 = g++
CXX17STD = -std=gnu++17
CXX17FLAGS = -O2 -Wall -mfpmath=sse -msse2 -mstackrealign
CXX17PICFLAGS =
CXX20 = g++
CXX20STD = -std=gnu++20
CXX20FLAGS = -O2 -Wall -mfpmath=sse -msse2 -mstackrealign
CXX20PICFLAGS =
CXX23 = g++
CXX23STD = -std=gnu++23
CXX23FLAGS = -O2 -Wall -mfpmath=sse -msse2 -mstackrealign
CXX23PICFLAGS =
CXX26 = g++
CXX26STD = -std=gnu++26
CXX26FLAGS = -O2 -Wall -mfpmath=sse -msse2 -mstackrealign
CXX26PICFLAGS =
DYLIB_EXT = .dll
DYLIB_LD = gcc
DYLIB_LDFLAGS = -shared
FC = gfortran
FFLAGS = -O2 -mfpmath=sse -msse2 -mstackrealign
FPICFLAGS =
FLIBS = -lgfortran -lquadmath
FCFLAGS = -O2 -mfpmath=sse -msse2 -mstackrealign
SAFE_FFLAGS = -O2 -msse2 -mfpmath=sse
OBJC = gcc
OBJCFLAGS = -O2
JAVA =
JAVAC =
JAVAH =
JAR =
JAVA_HOME =
JAVA_LIBS = -L/bin/client -ljvm -ljvm-w32
JAVA_CPPFLAGS = -I/../include -I/../include/win32
LDFLAGS =
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = g++ -std=gnu++20
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX17LD = g++
SHLIB_CXX17LDFLAGS = -shared
SHLIB_CXX20LD = g++
SHLIB_CXX20LDFLAGS = -shared
SHLIB_CXX23LD = g++
SHLIB_CXX23LDFLAGS = -shared
SHLIB_CXX26LD = g++
SHLIB_CXX26LDFLAGS = -shared
SHLIB_EXT = .dll
SHLIB_FFLAGS =
SHLIB_LD = gcc
SHLIB_LDFLAGS = -shared
TCLTK_CPPFLAGS = -I F:/Programs/R/R-4.6.0/Tcl/include -DWin32
TCLTK_LIBS = -LF:/Programs/R/R-4.6.0/Tcl/bin -ltcl86 -ltk86
BLAS_LIBS = -LF:/Programs/R/R-4.6.0/bin/x64 -lRblas
LAPACK_LIBS = -LF:/Programs/R/R-4.6.0/bin/x64 -lRlapack
MAKE = make
LIBnn = lib
AR = ar
NM = nm
RANLIB = ranlib
LTO =
LTO_FC =
LTO_LD =
LOCAL_SOFT = F:/Programs/R/rtools45/x86_64-w64-mingw32.static.posix
R_TOOLS_SOFT = F:/Programs/R/rtools45/x86_64-w64-mingw32.static.posix
COMPILED_BY = gcc-14.3.0
OBJDUMP = objdump
## The following variables are defunct
CPP CXXCPP CXX11 CXX11STD CXX11FLAGS CXX11PICFLAGS CXX14 CXX14STD CXX14FLAGS CXX14PICFLAGS SHLIB_CXX11LD SHLIB_CXX11LDFLAGS SHLIB_CXX14LD SHLIB_CXX14LDFLAGS
# User Profile ---------------------------------------------------------------
[no user profile detected]
# Settings -------------------------------------------------------------------
List of 15
$ bioconductor.version : NULL
$ external.libraries : chr(0)
$ ignored.packages : chr(0)
$ lockfile.sanitize : logi TRUE
$ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
$ ppm.enabled : NULL
$ ppm.ignored.urls : chr(0)
$ r.version : NULL
$ snapshot.dev : logi FALSE
$ snapshot.type : chr "implicit"
$ use.cache : logi TRUE
$ vcs.ignore.cellar : logi TRUE
$ vcs.ignore.library : logi TRUE
$ vcs.ignore.local : logi TRUE
$ vcs.manage.ignores : logi TRUE
# Options --------------------------------------------------------------------
List of 9
$ defaultPackages : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
$ download.file.method : NULL
$ download.file.extra : NULL
$ install.packages.compile.from.source: chr "interactive"
$ pkgType : chr "both"
$ repos : Named chr [1:6] "https://bioconductor.org/packages/3.23/bioc" "https://bioconductor.org/packages/3.23/data/annotation" "https://bioconductor.org/packages/3.23/data/experiment" "https://bioconductor.org/packages/3.23/workflows" ...
..- attr(*, "names")= chr [1:6] "BioCsoft" "BioCann" "BioCexp" "BioCworkflows" ...
$ renv.consent : logi TRUE
$ renv.project.path : chr "F:/Documents/GitProjects/project"
$ renv.verbose : logi TRUE
# Environment Variables ------------------------------------------------------
CC = <NA>
CFLAGS = <NA>
CPPFLAGS = <NA>
CXX = <NA>
CXXFLAGS = <NA>
HOME = C:\Users\bgkin
LANG = en_US.UTF-8
LDFLAGS = <NA>
MAKE = <NA>
R_LIBS = <NA>
R_LIBS_SITE = F:/Programs/R/R-4.6.0/site-library
R_LIBS_USER = F:/Documents/GitProjects/project/renv/library/windows/R-4.6/x86_64-w64-mingw32
RENV_DEFAULT_R_ENVIRON = <NA>
RENV_DEFAULT_R_ENVIRON_USER = <NA>
RENV_DEFAULT_R_LIBS = <NA>
RENV_DEFAULT_R_LIBS_SITE = F:/Programs/R/R-4.6.0/site-library
RENV_DEFAULT_R_LIBS_USER = C:\Users\bgkin\AppData\Local/R/win-library/4.6
RENV_DEFAULT_R_PROFILE = <NA>
RENV_DEFAULT_R_PROFILE_USER = <NA>
RENV_PROJECT = F:/Documents/GitProjects/project
# PATH -----------------------------------------------------------------------
- <programs on path go here>
# Cache ----------------------------------------------------------------------
There are a total of 228 packages installed in the renv cache.
Cache path: "~/AppData/Local/R/cache/R/renv/cache/v5/windows/R-4.6/x86_64-w64-mingw32"
Trying to get language server to work in latest build of VS Code, R 4.6.0,
Project dependencies are managed with renv. I have verified I have renv installed in both local and project library.
When launching VS Code, I get the following stack trace from the OUTPUT tab for R Language Server:
Any ideas? I believe it's due to the renv environment being activated because when I comment out the source file added to my .Rprofile project file, it works fine. But when renv activation script is sourced in .Rprofile (
source("renv/activate.R"), it throws this error. I could not find any way to adjust timeout settings. I timed a launch of my CLI (Git Bash), it takes approximately 5 seconds with the activation script. Without the activation sourced, it's essentially instant.So is it an issue with how long it's taking renv to scan files in my environment? I have added all non .R scripts to my .renvignore to speed the process up.