I'm using renv for my private package (mdTools). devtools::install() works, but when I devtools::check(), it fails to find the DBI package, which is installed in my renv user cache.
devtools::check() error message
checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'mdTools' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called 'DBI'
Execution halted
This was a previous similar problem not using renv:
devtools::install() works but devtools::check() does not, so it is possible that this is not a renv problem. The answer there was to use the system library which doesn't seem like what I want to do.
What I've tried none of which resolved the issue
- renv::remove("DBI") and renv::install("DBI")
- renv::deactivate() and renv::init()
- renv::clean()
- renv::hydrate()
- renv::purge("DBI") and renv::install("DBI")
- renv::repair("DBI")
> renv::diagnostics()
Diagnostics Report [renv 0.16.0]
================================
# Session Info =======================
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] mdTools_0.0.0.9000
loaded via a namespace (and not attached):
[1] qpdf_1.3.0 xfun_0.36 tidyselect_1.2.0
[4] janitor_2.1.0 purrr_1.0.0 rJava_1.0-6
[7] snakecase_0.11.0 vctrs_0.5.1 generics_0.1.3
[10] htmltools_0.5.4 utf8_1.2.2 docxtractr_0.6.5
[13] blob_1.2.3 rlang_1.0.6 pillar_1.8.1
[16] glue_1.6.2 DBI_1.1.3 re2_0.1.2
[19] rappdirs_0.3.3 bit64_4.0.5 readxl_1.4.1
[22] rptTools_0.0.0.9000 uuid_1.1-0 lifecycle_1.0.3
[25] stringr_1.5.0 cellranger_1.1.0 zip_2.2.2
[28] AzureGraph_1.3.2 evaluate_0.19 knitr_1.41
[31] fastmap_1.1.0 tzdb_0.3.0 fansi_1.0.3
[34] xlsxjars_0.6.1 pdftools_3.3.2 Rcpp_1.0.9
[37] readr_2.1.3 openssl_2.0.5 renv_0.16.0
[40] xlsx_0.6.5 bit_4.0.5 digest_0.6.31
[43] hms_1.1.2 askpass_1.1 stringi_1.7.8
[46] openxlsx_4.2.5.1 keyring_1.3.1 dplyr_1.0.10
[49] rprojroot_2.0.3 here_1.0.1 cli_3.6.0
[52] odbc_1.3.3 tools_4.2.2 magrittr_2.0.3
[55] AzureAuth_1.3.3 tibble_3.1.8 pkgconfig_2.0.3
[58] ellipsis_0.3.2 data.table_1.14.6 xml2_1.3.3
[61] lubridate_1.9.0 timechange_0.1.1 rmarkdown_2.19
[64] assertthat_0.2.1 httr_1.4.4 Microsoft365R_2.3.4
[67] officer_0.5.1 rstudioapi_0.14 R6_2.5.1
[70] compiler_4.2.2
# Project ============================
Project path: "C:/RStudio_Projects/R_projects/mdTools"
# Status =============================
* The project is already synchronized with the lockfile.
# Packages ===========================
Library Source Lockfile Source Path Dependency
AzureAuth 1.3.3 CRAN 1.3.3 CRAN [1] indirect
AzureGraph 1.3.2 CRAN 1.3.2 CRAN [1] indirect
DBI 1.1.3 CRAN 1.1.3 CRAN [1] direct
KernSmooth 2.23-20 CRAN <NA> <NA> [2] <NA>
MASS 7.3-58.1 CRAN <NA> <NA> [2] <NA>
Matrix 1.5-1 CRAN <NA> <NA> [2] <NA>
Microsoft365R 2.3.4 CRAN 2.3.4 CRAN [1] direct
R6 2.5.1 CRAN 2.5.1 CRAN [1] indirect
Rcpp 1.0.9 CRAN 1.0.9 CRAN [1] indirect
askpass 1.1 CRAN 1.1 CRAN [1] indirect
assertthat 0.2.1 CRAN 0.2.1 CRAN [1] indirect
base64enc 0.1-3 CRAN 0.1-3 CRAN [1] indirect
bit 4.0.5 CRAN 4.0.5 CRAN [1] indirect
bit64 4.0.5 CRAN 4.0.5 CRAN [1] indirect
blob 1.2.3 CRAN 1.2.3 CRAN [1] indirect
boot 1.3-28 CRAN <NA> <NA> [2] <NA>
brew 1.0-8 CRAN <NA> <NA> [1] indirect
brio 1.1.3 CRAN <NA> <NA> [1] indirect
bslib 0.4.2 CRAN 0.4.2 CRAN [1] indirect
cachem 1.0.6 CRAN 1.0.6 CRAN [1] indirect
callr 3.7.3 CRAN <NA> <NA> [1] indirect
cellranger 1.1.0 CRAN 1.1.0 CRAN [1] indirect
class 7.3-20 CRAN <NA> <NA> [2] <NA>
cli 3.6.0 CRAN 3.6.0 CRAN [1] indirect
clipr 0.8.0 CRAN 0.8.0 CRAN [1] indirect
cluster 2.1.4 CRAN <NA> <NA> [2] <NA>
codetools 0.2-18 CRAN <NA> <NA> [2] <NA>
commonmark 1.8.1 CRAN <NA> <NA> [1] indirect
cpp11 0.4.3 CRAN 0.4.3 CRAN [1] indirect
crayon 1.5.2 CRAN 1.5.2 CRAN [1] indirect
credentials 1.3.2 CRAN <NA> <NA> [1] indirect
curl 4.3.3 CRAN 4.3.3 CRAN [1] indirect
data.table 1.14.6 CRAN 1.14.6 CRAN [1] direct
desc 1.4.2 CRAN <NA> <NA> [1] indirect
devtools 2.4.5 CRAN <NA> <NA> [1] direct
diffobj 0.3.5 CRAN <NA> <NA> [1] indirect
digest 0.6.31 CRAN 0.6.31 CRAN [1] indirect
docxtractr 0.6.5 CRAN 0.6.5 CRAN [1] direct
downlit 0.4.2 CRAN <NA> <NA> [1] indirect
dplyr 1.0.10 CRAN 1.0.10 CRAN [1] indirect
ellipsis 0.3.2 CRAN 0.3.2 CRAN [1] indirect
evaluate 0.19 CRAN 0.19 CRAN [1] indirect
fansi 1.0.3 CRAN 1.0.3 CRAN [1] indirect
fastmap 1.1.0 CRAN 1.1.0 CRAN [1] indirect
filelock 1.0.2 CRAN 1.0.2 CRAN [1] indirect
fontawesome 0.4.0 CRAN <NA> <NA> [1] indirect
foreign 0.8-83 CRAN <NA> <NA> [2] <NA>
fs 1.5.2 CRAN 1.5.2 CRAN [1] indirect
generics 0.1.3 CRAN 0.1.3 CRAN [1] indirect
gert 1.9.2 CRAN <NA> <NA> [1] indirect
gh 1.3.1 CRAN <NA> <NA> [1] indirect
gitcreds 0.1.2 CRAN <NA> <NA> [1] indirect
glue 1.6.2 CRAN 1.6.2 CRAN [1] direct
grDevices <NA> <NA> <NA> <NA> [2] indirect
graphics <NA> <NA> <NA> <NA> [2] indirect
here 1.0.1 CRAN 1.0.1 CRAN [1] direct
highr 0.10 CRAN 0.10 CRAN [1] indirect
hms 1.1.2 CRAN 1.1.2 CRAN [1] indirect
htmltools 0.5.4 CRAN 0.5.4 CRAN [1] indirect
htmlwidgets 1.6.1 CRAN <NA> <NA> [1] indirect
httpuv 1.6.7 CRAN <NA> <NA> [1] indirect
httr 1.4.4 CRAN 1.4.4 CRAN [1] indirect
ini 0.3.1 CRAN <NA> <NA> [1] indirect
janitor 2.1.0 CRAN 2.1.0 CRAN [1] direct
jose 1.2.0 CRAN 1.2.0 CRAN [1] indirect
jquerylib 0.1.4 CRAN 0.1.4 CRAN [1] indirect
jsonlite 1.8.4 CRAN 1.8.4 CRAN [1] indirect
keyring 1.3.1 CRAN 1.3.1 CRAN [1] direct
knitr 1.41 CRAN 1.41 CRAN [1] direct
later 1.3.0 CRAN <NA> <NA> [1] indirect
lattice 0.20-45 CRAN <NA> <NA> [2] <NA>
lifecycle 1.0.3 CRAN 1.0.3 CRAN [1] indirect
lubridate 1.9.0 CRAN 1.9.0 CRAN [1] indirect
magrittr 2.0.3 CRAN 2.0.3 CRAN [1] indirect
mdTools <NA> <NA> <NA> <NA> [1] direct
memoise 2.0.1 CRAN 2.0.1 CRAN [1] indirect
methods <NA> <NA> <NA> <NA> [2] indirect
mgcv 1.8-41 CRAN <NA> <NA> [2] <NA>
mime 0.12 CRAN 0.12 CRAN [1] indirect
miniUI 0.1.1.1 CRAN <NA> <NA> [1] indirect
nlme 3.1-160 CRAN <NA> <NA> [2] <NA>
nnet 7.3-18 CRAN <NA> <NA> [2] <NA>
odbc 1.3.3 CRAN 1.3.3 CRAN [1] direct
officer 0.5.1 CRAN 0.5.1 CRAN [1] direct
openssl 2.0.5 CRAN 2.0.5 CRAN [1] indirect
openxlsx 4.2.5.1 CRAN 4.2.5.1 CRAN [1] direct
pdftools 3.3.2 CRAN 3.3.2 CRAN [1] indirect
pillar 1.8.1 CRAN 1.8.1 CRAN [1] indirect
pkgbuild 1.4.0 CRAN <NA> <NA> [1] indirect
pkgconfig 2.0.3 CRAN 2.0.3 CRAN [1] indirect
pkgdown 2.0.7 CRAN <NA> <NA> [1] indirect
pkgload 1.3.2 CRAN <NA> <NA> [1] indirect
praise 1.0.0 CRAN <NA> <NA> [1] indirect
prettyunits 1.1.1 CRAN 1.1.1 CRAN [1] indirect
processx 3.8.0 CRAN <NA> <NA> [1] indirect
profvis 0.3.7 CRAN <NA> <NA> [1] indirect
progress 1.2.2 CRAN 1.2.2 CRAN [1] indirect
promises 1.2.0.1 CRAN <NA> <NA> [1] indirect
ps 1.7.2 CRAN <NA> <NA> [1] indirect
purrr 1.0.0 CRAN 1.0.0 CRAN [1] indirect
qpdf 1.3.0 CRAN 1.3.0 CRAN [1] indirect
rJava 1.0-6 CRAN 1.0-6 CRAN [1] indirect
ragg 1.2.4 CRAN <NA> <NA> [1] indirect
rappdirs 0.3.3 CRAN 0.3.3 CRAN [1] indirect
rcmdcheck 1.4.0 CRAN <NA> <NA> [1] indirect
re2 0.1.2 CRAN 0.1.2 CRAN [1] direct
readr 2.1.3 CRAN 2.1.3 CRAN [1] direct
readxl 1.4.1 CRAN 1.4.1 CRAN [1] direct
rematch 1.0.1 CRAN 1.0.1 CRAN [1] indirect
rematch2 2.1.2 CRAN <NA> <NA> [1] indirect
remotes 2.4.2 CRAN <NA> <NA> [1] indirect
renv 0.16.0 CRAN 0.16.0 CRAN [1] direct
rlang 1.0.6 CRAN 1.0.6 CRAN [1] indirect
rmarkdown 2.19 CRAN 2.19 CRAN [1] direct
roxygen2 7.2.3 CRAN <NA> <NA> [1] direct
rpart 4.1.19 CRAN <NA> <NA> [2] <NA>
rprojroot 2.0.3 CRAN 2.0.3 CRAN [1] indirect
rptTools 0.0.0.9000 Git 0.0.0.9000 Git [1] direct
rstudioapi 0.14 CRAN <NA> <NA> [1] indirect
rversions 2.1.2 CRAN <NA> <NA> [1] indirect
sass 0.4.4 CRAN 0.4.4 CRAN [1] indirect
sessioninfo 1.2.2 CRAN <NA> <NA> [1] indirect
shiny 1.7.4 CRAN <NA> <NA> [1] indirect
snakecase 0.11.0 CRAN 0.11.0 CRAN [1] indirect
sodium 1.2.1 CRAN 1.2.1 CRAN [1] indirect
sourcetools 0.1.7 CRAN <NA> <NA> [1] indirect
spatial 7.3-15 CRAN <NA> <NA> [2] <NA>
stats <NA> <NA> <NA> <NA> [2] indirect
stringi 1.7.8 CRAN 1.7.8 CRAN [1] indirect
stringr 1.5.0 CRAN 1.5.0 CRAN [1] indirect
survival 3.4-0 CRAN <NA> <NA> [2] <NA>
sys 3.4.1 CRAN 3.4.1 CRAN [1] indirect
systemfonts 1.0.4 CRAN <NA> <NA> [1] indirect
testthat 3.1.6 CRAN <NA> <NA> [1] indirect
textshaping 0.3.6 CRAN <NA> <NA> [1] indirect
tibble 3.1.8 CRAN 3.1.8 CRAN [1] indirect
tidyr 1.2.1 CRAN 1.2.1 CRAN [1] indirect
tidyselect 1.2.0 CRAN 1.2.0 CRAN [1] indirect
timechange 0.1.1 CRAN 0.1.1 CRAN [1] indirect
tinytex 0.43 CRAN 0.43 CRAN [1] indirect
tools <NA> <NA> <NA> <NA> [2] indirect
tzdb 0.3.0 CRAN 0.3.0 CRAN [1] indirect
urlchecker 1.0.1 CRAN <NA> <NA> [1] indirect
usethis 2.1.6 CRAN <NA> <NA> [1] indirect
utf8 1.2.2 CRAN 1.2.2 CRAN [1] indirect
utils <NA> <NA> <NA> <NA> [2] direct
uuid 1.1-0 CRAN 1.1-0 CRAN [1] indirect
vctrs 0.5.1 CRAN 0.5.1 CRAN [1] indirect
vroom 1.6.0 CRAN 1.6.0 CRAN [1] indirect
waldo 0.4.0 CRAN <NA> <NA> [1] indirect
whisker 0.4.1 CRAN <NA> <NA> [1] indirect
withr 2.5.0 CRAN 2.5.0 CRAN [1] indirect
xfun 0.36 CRAN 0.36 CRAN [1] indirect
xlsx 0.6.5 CRAN 0.6.5 CRAN [1] direct
xlsxjars 0.6.1 CRAN 0.6.1 CRAN [1] indirect
xml2 1.3.3 CRAN 1.3.3 CRAN [1] indirect
xopen 1.0.0 CRAN <NA> <NA> [1] indirect
xtable 1.8-4 CRAN <NA> <NA> [1] indirect
yaml 2.3.6 CRAN 2.3.6 CRAN [1] indirect
zip 2.2.2 CRAN 2.2.2 CRAN [1] indirect
[1]: C:/Users/dlucey/AppData/Local/R/cache/R/renv/library/mdTools-fbe1603d/R-4.2/x86_64-w64-mingw32
[2]: C:/Users/dlucey/AppData/Local/Temp/RtmpEXMKbd/renv-system-library
# ABI ================================
* ABI conflict checks are not yet implemented on Windows.
# User Profile =======================
[no user profile detected]
# Settings ===========================
List of 10
$ bioconductor.version : chr(0)
$ 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.cellar : logi TRUE
$ vcs.ignore.library : logi TRUE
$ vcs.ignore.local : logi TRUE
# Options ============================
List of 9
$ defaultPackages : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
$ download.file.method : chr "libcurl"
$ download.file.extra : NULL
$ install.packages.compile.from.source: chr "interactive"
$ pkgType : chr "both"
$ repos : Named chr "https://cran.rstudio.com"
..- attr(*, "names")= chr "CRAN"
$ renv.consent : logi TRUE
$ renv.project.path : chr "C:/RStudio_Projects/R_projects/mdTools"
$ renv.verbose : logi TRUE
# Environment Variables ==============
HOME = C:/Users/dlucey/OneDrive - South Bronx Classical Charter School/Documents
LANG = <NA>
MAKE = <NA>
R_LIBS = <NA>
R_LIBS_SITE = C:/PROGRA~1/R/R-42~1.2/site-library
R_LIBS_USER = C:/Users/dlucey/AppData/Local/R/cache/R/renv/library/mdTools-fbe1603d/R-4.2/x86_64-w64-mingw32;C:/Users/dlucey/AppData/Local/Temp/RtmpEXMKbd/renv-system-library
RENV_DEFAULT_R_ENVIRON = <NA>
RENV_DEFAULT_R_ENVIRON_USER = <NA>
RENV_DEFAULT_R_LIBS = <NA>
RENV_DEFAULT_R_LIBS_SITE = C:/PROGRA~1/R/R-42~1.2/site-library
RENV_DEFAULT_R_LIBS_USER = C:\Users\dlucey\AppData\Local/R/win-library/4.2
RENV_DEFAULT_R_PROFILE = <NA>
RENV_DEFAULT_R_PROFILE_USER = <NA>
RENV_PROJECT = C:/RStudio_Projects/R_projects/mdTools
# PATH ===============================
- C:\RBuildTools\rtools42/x86_64-w64-mingw32.static.posix/bin
- C:\RBuildTools\rtools42/usr/bin
- C:\Program Files\R\R-4.2.2\bin\x64
- C:\Program Files (x86)\Common Files\Oracle\Java\javapath
- C:\WINDOWS\system32
- C:\WINDOWS
- C:\WINDOWS\System32\Wbem
- C:\WINDOWS\System32\WindowsPowerShell\v1.0\
- C:\WINDOWS\System32\OpenSSH\
- C:\Program Files\Intel\WiFi\bin\
- C:\Program Files\Common Files\Intel\WirelessCommon\
- C:\Program Files\Docker\Docker\resources\bin
- C:\Program Files\Microsoft SQL Server\150\Tools\Binn\
- C:\Program Files\Microsoft SQL Server\Client SDK\ODBC\170\Tools\Binn\
- C:\Program Files\dotnet\
- C:\ProgramData\chocolatey\bin
- C:\Program Files\Git\cmd
- C:\Users\dlucey\AppData\Local\Microsoft\WindowsApps
-
- C:\Program Files\RStudio\resources\app\bin\rpostback
- C:\Program Files\RStudio\resources\app\bin\postback
- C:/Program Files/RStudio/resources/app/bin/quarto/bin
# Cache ==============================
There are a total of 294 package(s) installed in the renv cache.
Cache path: "C:/Users/dlucey/AppData/Local/R/cache/R/renv/cache/v5/R-4.2/x86_64-w64-mingw32"`\
renv user cache (EDITED)
> renv:::renv_cache_list(packages = "DBI")
[1] "C:\\Users\\dlucey\\AppData\\Local/R/cache/R/renv/cache/v5/R-4.2/x86_64-w64-mingw32/DBI/1.1.3/b2866e62bab9378c3cc9476a1954226b/DBI"
System user library (EDITED)
I've read that renv uses symlinks to my main user library where DBI is also installed:
> list.files("C:/Users/dlucey/AppData/Local/R/win-library/4.2")
[46] "DBI" "dbplyr" "deldir"
```
