Upon opening a project on rstudio i have the following Warning:
Warning message:
renv 0.12.0 was loaded from project library, but renv 0.11.0 is recorded in lockfile.
Use `renv::record("renv@0.12.0")` to record this version in the lockfile.
Use `renv::restore(packages = "renv")` to install renv 0.11.0 into the project library.
When running renv::record("renv@0.12.0") i get this message:
Error: no lockfile exists at path "~/Documents/GitHub/CIMMYT/renv.lock"
And when running renv::restore() i get this:
* The library is already synchronized with the lockfile.
I assume there is a lockfile but it's not in that path so I looked for the lockfile on the parent directory. My OS is Ubuntu 20.04
find . -type f -iname 'renv.lock'
But there is no lockfile under this folder. What am I missing here ? Could not find any useful answer on that googling.
Update: renv::diagnostics() as requested
Diagnostics Report -- renv [0.12.0]
===================================
# Session Info =======================
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_HK.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_HK.UTF-8 LC_COLLATE=en_HK.UTF-8
[5] LC_MONETARY=en_HK.UTF-8 LC_MESSAGES=en_HK.UTF-8
[7] LC_PAPER=en_HK.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_HK.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] gtools_3.8.2 here_0.1 adegenet_2.1.3 ade4_1.7-15
loaded via a namespace (and not attached):
[1] splines_4.0.2 shiny_1.5.0 expm_0.999-5 sp_1.4-2
[5] renv_0.12.0 LearnBayes_2.15.1 pillar_1.4.6 backports_1.1.9
[9] lattice_0.20-41 glue_1.4.2 digest_0.6.25 promises_1.1.1
[13] colorspace_1.4-1 htmltools_0.5.0 httpuv_1.5.4 Matrix_1.2-18
[17] plyr_1.8.6 pkgconfig_2.0.3 raster_3.3-13 gmodels_2.18.1
[21] purrr_0.3.4 xtable_1.8-4 scales_1.1.1 gdata_2.18.0
[25] later_1.1.0.1 tibble_3.0.3 mgcv_1.8-33 generics_0.0.2
[29] ggplot2_3.3.2 ellipsis_0.3.1 magrittr_1.5 crayon_1.3.4
[33] mime_0.9 deldir_0.1-29 nlme_3.1-149 MASS_7.3-53
[37] class_7.3-17 vegan_2.5-6 tools_4.0.2 lifecycle_0.2.0
[41] stringr_1.4.0 munsell_0.5.0 cluster_2.1.0 compiler_4.0.2
[45] e1071_1.7-3 tinytex_0.25 rlang_0.4.7 classInt_0.4-3
[49] units_0.6-7 grid_4.0.2 rstudioapi_0.11 igraph_1.2.5
[53] boot_1.3-25 gtable_0.3.0 codetools_0.2-16 DBI_1.1.0
[57] reshape2_1.4.4 R6_2.4.1 dplyr_1.0.2 fastmap_1.0.1
[61] seqinr_3.6-1 rprojroot_1.3-2 spdep_1.1-5 KernSmooth_2.23-17
[65] permute_0.9-5 ape_5.4-1 stringi_1.5.3 parallel_4.0.2
[69] Rcpp_1.0.5 vctrs_0.3.4 sf_0.9-6 spData_0.3.8
[73] tidyselect_1.1.0 xfun_0.17 coda_0.19-3
# Project ============================
Project path: "~/Documents/GitHub/CIMMYT"
# Status =============================
* This project has not yet been snapshotted -- 'renv.lock' does not exist.
The following package(s) are installed but not recorded in the lockfile:
_
utf8 [1.1.4]
clipr [0.7.0]
tidyselect [1.1.0]
lme4 [1.1-23]
FactoMineR [2.3]
maptools [1.0-2]
cpp11 [0.2.1]
sourcetools [0.1.7]
munsell [0.5.0]
units [0.6-7]
statmod [1.4.34]
withr [2.2.0]
colorspace [1.4-1]
highr [0.8]
knitr [1.29]
leaps [3.1]
rstudioapi [0.11]
ggsignif [0.6.0]
labeling [0.3]
farver [2.0.3]
rprojroot [1.3-2]
coda [0.19-3]
LearnBayes [2.15.1]
vctrs [0.3.4]
generics [0.0.2]
xfun [0.17]
adegenet [2.1.3]
R6 [2.4.1]
markdown [1.1]
RcppEigen [0.3.3.7.0]
isoband [0.2.2]
RcppArmadillo [0.9.900.3.0]
assertthat [0.2.1]
promises [1.1.1]
scales [1.1.1]
nnet [7.3-14]
gtable [0.3.0]
conquer [1.0.2]
processx [3.4.4]
rlang [0.4.7]
MatrixModels [0.4-1]
scatterplot3d [0.3-41]
rstatix [0.6.0]
selectr [0.4-2]
broom [0.7.0]
yaml [2.2.1]
reshape2 [1.4.4]
abind [1.4-5]
modelr [0.1.8]
backports [1.1.9]
httpuv [1.5.4]
spData [0.3.8]
gaston [1.5.6]
ggplot2 [3.3.2]
ellipsis [0.3.1]
raster [3.3-13]
RColorBrewer [1.1-2]
polynom [1.4-0]
Rcpp [1.0.5]
plyr [1.8.6]
base64enc [0.1-3]
progress [1.2.2]
classInt [0.4-3]
purrr [0.3.4]
ps [1.3.4]
prettyunits [1.1.1]
ggpubr [0.4.0]
openssl [1.4.2]
deldir [0.1-29]
viridis [0.5.1]
cowplot [1.1.0]
ggrepel [0.8.2]
haven [2.3.1]
cluster [2.1.0]
fs [1.5.0]
here [0.1]
factoextra [1.0.7]
tinytex [0.25]
magrittr [1.5]
data.table [1.13.0]
pixmap [0.4-11]
openxlsx [4.1.5]
SparseM [1.78]
gmodels [2.18.1]
reprex [0.3.0]
whisker [0.4]
matrixStats [0.56.0]
pkgload [1.1.0]
hms [0.5.3]
mime [0.9]
evaluate [0.14]
xtable [1.8-4]
pbkrtest [0.4-8.6]
rio [0.5.16]
jpeg [0.1-8.1]
readxl [1.3.1]
gridExtra [2.3]
testthat [2.3.2]
ellipse [0.4.2]
tibble [3.0.3]
KernSmooth [2.23-17]
crayon [1.3.4]
minqa [1.2.4]
htmltools [0.5.0]
segmented [1.2-0]
mgcv [1.8-33]
later [1.1.0.1]
spdep [1.1-5]
tidyr [1.1.2]
expm [0.999-5]
RcppParallel [5.0.2]
lubridate [1.7.9]
DBI [1.1.0]
corrplot [0.84]
praise [1.0.0]
dbplyr [1.4.4]
MASS [7.3-53]
sf [0.9-6]
boot [1.3-25]
sys [3.4]
Matrix [1.2-18]
ade4 [1.7-15]
car [3.0-9]
readr [1.3.1]
permute [0.9-5]
cli [2.0.2]
gdata [2.18.0]
igraph [1.2.5]
forcats [0.5.0]
pkgconfig [2.0.3]
flashClust [1.01-2]
foreign [0.8-80]
sp [1.4-2]
xml2 [1.3.2]
BH [1.72.0-3]
rematch [1.0.1]
rvest [0.3.6]
stringr [1.4.0]
callr [3.4.4]
digest [0.6.25]
vegan [2.5-6]
rmarkdown [2.3]
cellranger [1.1.0]
dendextend [1.14.0]
curl [4.3]
shiny [1.5.0]
gtools [3.8.2]
commonmark [1.7]
quantreg [5.67]
nloptr [1.2.2.2]
hierfstat [0.5-7]
lifecycle [0.2.0]
nlme [3.1-149]
jsonlite [1.7.1]
carData [3.0-4]
seqinr [3.6-1]
desc [1.2.0]
viridisLite [0.3.0]
askpass [1.1]
fansi [0.4.1]
pillar [1.4.6]
ggsci [2.9]
lattice [0.20-41]
fastmap [1.0.1]
httr [1.4.2]
pkgbuild [1.1.0]
glue [1.4.2]
zip [2.1.1]
png [0.1-7]
class [7.3-17]
stringi [1.5.3]
blob [1.2.1]
latticeExtra [0.6-29]
renv [0.12.0]
dplyr [1.0.2]
tidyverse [1.3.0]
e1071 [1.7-3]
ape [5.4-1]
Use `renv::snapshot()` to add these packages to your lockfile.
# Packages ===========================
This project has not yet been snapshotted: 'renv.lock' does not exist.
Library Source Lockfile Source Path Dependency
BH 1.72.0-3 CRAN <NA> <NA> [1] indirect
DBI 1.1.0 CRAN <NA> <NA> [1] indirect
FactoMineR 2.3 CRAN <NA> <NA> [1] indirect
KernSmooth 2.23-17 CRAN <NA> <NA> [2] indirect
LearnBayes 2.15.1 CRAN <NA> <NA> [1] indirect
MASS 7.3-53 CRAN <NA> <NA> [2] indirect
Matrix 1.2-18 CRAN <NA> <NA> [2] indirect
MatrixModels 0.4-1 CRAN <NA> <NA> [1] indirect
R6 2.4.1 CRAN <NA> <NA> [1] indirect
RColorBrewer 1.1-2 CRAN <NA> <NA> [1] indirect
Rcpp 1.0.5 CRAN <NA> <NA> [1] indirect
RcppArmadillo 0.9.900.3.0 CRAN <NA> <NA> [1] indirect
RcppEigen 0.3.3.7.0 CRAN <NA> <NA> [1] indirect
RcppParallel 5.0.2 CRAN <NA> <NA> [1] indirect
SparseM 1.78 CRAN <NA> <NA> [1] indirect
abind 1.4-5 CRAN <NA> <NA> [1] indirect
ade4 1.7-15 CRAN <NA> <NA> [1] indirect
adegenet 2.1.3 CRAN <NA> <NA> [1] direct
ape 5.4-1 CRAN <NA> <NA> [1] indirect
askpass 1.1 CRAN <NA> <NA> [1] indirect
assertthat 0.2.1 CRAN <NA> <NA> [1] indirect
backports 1.1.9 CRAN <NA> <NA> [1] indirect
base64enc 0.1-3 CRAN <NA> <NA> [1] indirect
blob 1.2.1 CRAN <NA> <NA> [1] indirect
boot 1.3-25 CRAN <NA> <NA> [2] indirect
broom 0.7.0 CRAN <NA> <NA> [1] indirect
callr 3.4.4 CRAN <NA> <NA> [1] indirect
car 3.0-9 CRAN <NA> <NA> [1] indirect
carData 3.0-4 CRAN <NA> <NA> [1] indirect
cellranger 1.1.0 CRAN <NA> <NA> [1] indirect
class 7.3-17 CRAN <NA> <NA> [2] indirect
classInt 0.4-3 CRAN <NA> <NA> [1] indirect
cli 2.0.2 CRAN <NA> <NA> [1] indirect
clipr 0.7.0 CRAN <NA> <NA> [1] indirect
cluster 2.1.0 CRAN <NA> <NA> [2] indirect
coda 0.19-3 CRAN <NA> <NA> [1] indirect
codetools 0.2-16 CRAN <NA> <NA> [2] <NA>
colorspace 1.4-1 CRAN <NA> <NA> [1] indirect
commonmark 1.7 CRAN <NA> <NA> [1] indirect
compiler <NA> <NA> <NA> <NA> [2] indirect
conquer 1.0.2 CRAN <NA> <NA> [1] indirect
corrplot 0.84 CRAN <NA> <NA> [1] indirect
cowplot 1.1.0 CRAN <NA> <NA> [1] indirect
cpp11 0.2.1 CRAN <NA> <NA> [1] indirect
crayon 1.3.4 CRAN <NA> <NA> [1] indirect
curl 4.3 CRAN <NA> <NA> [1] indirect
data.table 1.13.0 CRAN <NA> <NA> [1] indirect
datasets <NA> <NA> <NA> <NA> [2] indirect
dbplyr 1.4.4 CRAN <NA> <NA> [1] indirect
deldir 0.1-29 CRAN <NA> <NA> [1] indirect
dendextend 1.14.0 CRAN <NA> <NA> [1] indirect
desc 1.2.0 CRAN <NA> <NA> [1] indirect
digest 0.6.25 CRAN <NA> <NA> [1] indirect
dplyr 1.0.2 CRAN <NA> <NA> [1] direct
e1071 1.7-3 CRAN <NA> <NA> [1] indirect
ellipse 0.4.2 CRAN <NA> <NA> [1] indirect
ellipsis 0.3.1 CRAN <NA> <NA> [1] indirect
evaluate 0.14 CRAN <NA> <NA> [1] indirect
expm 0.999-5 CRAN <NA> <NA> [1] indirect
factoextra 1.0.7 CRAN <NA> <NA> [1] direct
fansi 0.4.1 CRAN <NA> <NA> [1] indirect
farver 2.0.3 CRAN <NA> <NA> [1] indirect
fastmap 1.0.1 CRAN <NA> <NA> [1] indirect
flashClust 1.01-2 CRAN <NA> <NA> [1] indirect
forcats 0.5.0 CRAN <NA> <NA> [1] indirect
foreign 0.8-80 CRAN <NA> <NA> [1] indirect
fs 1.5.0 CRAN <NA> <NA> [1] indirect
gaston 1.5.6 CRAN <NA> <NA> [1] indirect
gdata 2.18.0 CRAN <NA> <NA> [1] indirect
generics 0.0.2 CRAN <NA> <NA> [1] indirect
ggplot2 3.3.2 CRAN <NA> <NA> [1] direct
ggpubr 0.4.0 CRAN <NA> <NA> [1] indirect
ggrepel 0.8.2 CRAN <NA> <NA> [1] indirect
ggsci 2.9 CRAN <NA> <NA> [1] indirect
ggsignif 0.6.0 CRAN <NA> <NA> [1] indirect
glue 1.4.2 CRAN <NA> <NA> [1] indirect
gmodels 2.18.1 CRAN <NA> <NA> [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 <NA> <NA> [1] direct
gtable 0.3.0 CRAN <NA> <NA> [1] indirect
gtools 3.8.2 CRAN <NA> <NA> [1] direct
haven 2.3.1 CRAN <NA> <NA> [1] indirect
here 0.1 CRAN <NA> <NA> [1] direct
hierfstat 0.5-7 CRAN <NA> <NA> [1] direct
highr 0.8 CRAN <NA> <NA> [1] indirect
hms 0.5.3 CRAN <NA> <NA> [1] indirect
htmltools 0.5.0 CRAN <NA> <NA> [1] indirect
httpuv 1.5.4 CRAN <NA> <NA> [1] indirect
httr 1.4.2 CRAN <NA> <NA> [1] indirect
igraph 1.2.5 CRAN <NA> <NA> [1] indirect
isoband 0.2.2 CRAN <NA> <NA> [1] indirect
jpeg 0.1-8.1 CRAN <NA> <NA> [1] indirect
jsonlite 1.7.1 CRAN <NA> <NA> [1] indirect
knitr 1.29 CRAN <NA> <NA> [1] indirect
labeling 0.3 CRAN <NA> <NA> [1] indirect
later 1.1.0.1 CRAN <NA> <NA> [1] indirect
lattice 0.20-41 CRAN <NA> <NA> [2] direct
latticeExtra 0.6-29 CRAN <NA> <NA> [1] direct
leaps 3.1 CRAN <NA> <NA> [1] indirect
lifecycle 0.2.0 CRAN <NA> <NA> [1] indirect
lme4 1.1-23 CRAN <NA> <NA> [1] indirect
lubridate 1.7.9 CRAN <NA> <NA> [1] indirect
magrittr 1.5 CRAN <NA> <NA> [1] indirect
maptools 1.0-2 CRAN <NA> <NA> [1] indirect
markdown 1.1 CRAN <NA> <NA> [1] indirect
matrixStats 0.56.0 CRAN <NA> <NA> [1] indirect
methods <NA> <NA> <NA> <NA> [2] indirect
mgcv 1.8-33 CRAN <NA> <NA> [2] indirect
mime 0.9 CRAN <NA> <NA> [1] indirect
minqa 1.2.4 CRAN <NA> <NA> [1] indirect
modelr 0.1.8 CRAN <NA> <NA> [1] indirect
munsell 0.5.0 CRAN <NA> <NA> [1] indirect
nlme 3.1-149 CRAN <NA> <NA> [2] indirect
nloptr 1.2.2.2 CRAN <NA> <NA> [1] indirect
nnet 7.3-14 CRAN <NA> <NA> [2] indirect
openssl 1.4.2 CRAN <NA> <NA> [1] indirect
openxlsx 4.1.5 CRAN <NA> <NA> [1] indirect
parallel <NA> <NA> <NA> <NA> [2] indirect
pbkrtest 0.4-8.6 CRAN <NA> <NA> [1] indirect
permute 0.9-5 CRAN <NA> <NA> [1] indirect
pillar 1.4.6 CRAN <NA> <NA> [1] indirect
pixmap 0.4-11 CRAN <NA> <NA> [1] indirect
pkgbuild 1.1.0 CRAN <NA> <NA> [1] indirect
pkgconfig 2.0.3 CRAN <NA> <NA> [1] indirect
pkgload 1.1.0 CRAN <NA> <NA> [1] indirect
plyr 1.8.6 CRAN <NA> <NA> [1] indirect
png 0.1-7 CRAN <NA> <NA> [1] indirect
polynom 1.4-0 CRAN <NA> <NA> [1] indirect
praise 1.0.0 CRAN <NA> <NA> [1] indirect
prettyunits 1.1.1 CRAN <NA> <NA> [1] indirect
processx 3.4.4 CRAN <NA> <NA> [1] indirect
progress 1.2.2 CRAN <NA> <NA> [1] indirect
promises 1.1.1 CRAN <NA> <NA> [1] indirect
ps 1.3.4 CRAN <NA> <NA> [1] indirect
purrr 0.3.4 CRAN <NA> <NA> [1] indirect
quantreg 5.67 CRAN <NA> <NA> [1] indirect
raster 3.3-13 CRAN <NA> <NA> [1] indirect
readr 1.3.1 CRAN <NA> <NA> [1] indirect
readxl 1.3.1 CRAN <NA> <NA> [1] indirect
rematch 1.0.1 CRAN <NA> <NA> [1] indirect
renv 0.12.0 CRAN <NA> <NA> [1] <NA>
reprex 0.3.0 CRAN <NA> <NA> [1] indirect
reshape2 1.4.4 CRAN <NA> <NA> [1] indirect
rio 0.5.16 CRAN <NA> <NA> [1] indirect
rlang 0.4.7 CRAN <NA> <NA> [1] indirect
rmarkdown 2.3 CRAN <NA> <NA> [1] indirect
rpart 4.1-15 CRAN <NA> <NA> [2] <NA>
rprojroot 1.3-2 CRAN <NA> <NA> [1] indirect
rstatix 0.6.0 CRAN <NA> <NA> [1] indirect
rstudioapi 0.11 CRAN <NA> <NA> [1] indirect
rvest 0.3.6 CRAN <NA> <NA> [1] indirect
scales 1.1.1 CRAN <NA> <NA> [1] indirect
scatterplot3d 0.3-41 CRAN <NA> <NA> [1] indirect
segmented 1.2-0 CRAN <NA> <NA> [1] indirect
selectr 0.4-2 CRAN <NA> <NA> [1] indirect
seqinr 3.6-1 CRAN <NA> <NA> [1] indirect
sf 0.9-6 CRAN <NA> <NA> [1] indirect
shiny 1.5.0 CRAN <NA> <NA> [1] indirect
sourcetools 0.1.7 CRAN <NA> <NA> [1] indirect
sp 1.4-2 CRAN <NA> <NA> [1] indirect
spData 0.3.8 CRAN <NA> <NA> [1] indirect
spatial 7.3-12 CRAN <NA> <NA> [1] <NA>
spdep 1.1-5 CRAN <NA> <NA> [1] indirect
splines <NA> <NA> <NA> <NA> [2] indirect
[ reached 'max' / getOption("max.print") -- omitted 27 rows ]
[1]: /home/alex/Documents/GitHub/CIMMYT/renv/library/R-4.0/x86_64-pc-linux-gnu
[2]: /tmp/RtmpdZmmFV/renv-system-library
# User Profile =======================
[no user profile detected]
# Settings ===========================
List of 6
$ external.libraries : chr(0)
$ ignored.packages : chr(0)
$ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
$ snapshot.type : chr "implicit"
$ use.cache : logi TRUE
$ vcs.ignore.library : logi TRUE
# Options ============================
List of 2
$ renv.consent: logi TRUE
$ renv.verbose: logi TRUE
# Environment Variables ==============
HOME = /home/alex
LANG = en_HK.UTF-8
R_LIBS = <NA>
R_LIBS_SITE = /usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
R_LIBS_USER = /home/alex/Documents/GitHub/CIMMYT/renv/library/R-4.0/x86_64-pc-linux-gnu:/tmp/RtmpdZmmFV/renv-system-library
RENV_DEFAULT_R_ENVIRON = <NA>
RENV_DEFAULT_R_ENVIRON_USER = <NA>
RENV_DEFAULT_R_LIBS = <NA>
RENV_DEFAULT_R_LIBS_SITE = /usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
RENV_DEFAULT_R_LIBS_USER = ~/R/x86_64-pc-linux-gnu-library/4.0
RENV_DEFAULT_R_PROFILE = <NA>
RENV_DEFAULT_R_PROFILE_USER = <NA>
RENV_PROJECT = /home/alex/Documents/GitHub/CIMMYT
# PATH ===============================
- /usr/local/sbin
- /usr/local/bin
- /usr/sbin
- /usr/bin
- /sbin
- /bin
- /usr/games
- /usr/local/games
- /snap/bin
- /usr/lib/rstudio/bin/postback
# Cache ==============================
There are a total of 166 package(s) installed in the renv cache.
Cache path: "~/.local/share/renv/cache/v5/R-4.0/x86_64-pc-linux-gnu"
Again the lockfile seems to not exist
I think this is ultimately a small bug in renv. Here's my guess at what's happening:
While this project has been initialized as an renv project, it does not have a lockfile for some reason. (Perhaps renv::activate() was called to initialize renv without explicitly creating a lockfile?)
The project has an renv autoloader; this is from a script at renv/activate.R. That script is configured to load renv 0.11.0.
When the project is loaded, renv finds that renv 0.12.0 is installed in the project library, not the expected version 0.11.0. This causes the warning to be emitted. (Perhaps renv was updated in that project previously?)
So, ultimately, the warning is misleading here -- the request for renv 0.11.0 comes directly from the autoloader, not from the lockfile (which does not exist). As for why the lockfile does not exist, I'm not sure -- but it most likely implies the project was initialized via renv::activate(), and not by renv::init().
All that said -- you can safely re-generate the lockfile via renv::snapshot().