Use older version of ggplot in R script file - r

I have ggplot2 3.4.0 installed on Ubuntu 22.04, but for some reasons I would like to use older version ggplot2 3.3.6.
library(ggplot2, lib.loc="~/R/ggplot336/")
I worked fine when I started with a clean script file. However, when I use an existing script file like:
library(ggplot2, lib.loc="~/R/ggplot336/")
ggimage::geom_image()
I got the following error massage:
Error in value[3L] :
Package ‘ggplot2’ version 3.4.0 cannot be unloaded:
Error in unloadNamespace(package) : namespace ‘ggplot2’ is imported by ‘ggfun’, ‘ggplotify’, ‘ggimage’ so cannot be unloaded
Edit
Fresh start Rstudio
Open my R script file with following 3 lines:
sessionInfo()
library(ggplot2, lib.loc="~/R/ggplot336/")
ggimage::geom_image()
When I run the first line, sessionInfo() before doing anything else. We can see ggplot2_3.4.0 there. Could this be a Rstudio feature or an issue?
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8
[4] LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 highr_0.9 pillar_1.8.1 compiler_4.2.2
[5] R.utils_2.12.2 R.methodsS3_1.8.2 yulab.utils_0.0.5 tools_4.2.2
[9] digest_0.6.30 evaluate_0.18 jsonlite_1.8.3 lifecycle_1.0.3
[13] tibble_3.1.8 gtable_0.3.1 ggimage_0.3.1 R.cache_0.16.0
[17] pkgconfig_2.0.3 rlang_1.0.6 reprex_2.0.2 DBI_1.1.3
[21] cli_3.4.1 ggplotify_0.1.0 rstudioapi_0.14 magick_2.7.3
[25] yaml_2.3.6 xfun_0.35 fastmap_1.1.0 knitr_1.41
[29] withr_2.5.0 dplyr_1.0.10 styler_1.8.1 generics_0.1.3
[33] vctrs_0.5.1 fs_1.5.2 gridGraphics_0.5-1 grid_4.2.2
[37] tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 processx_3.8.0
[41] fansi_1.0.3 rmarkdown_2.18 clipr_0.8.0 callr_3.7.3
[45] ggplot2_3.4.0 purrr_0.3.5 magrittr_2.0.3 ps_1.7.2
[49] htmltools_0.5.3 scales_1.2.1 assertthat_0.2.1 colorspace_2.0-3
[53] utf8_1.2.2 munsell_0.5.0 ggfun_0.0.9 R.oo_1.25.0

It looks like R studio is loading in all of the previous libraries from a previous session. Maybe something leftover in .RData or .Rhistory. A fresh start of R should have far few loaded libraries.
Here is my fresh start:
sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.2 tools_4.2.2
In Rstudio's preference you should see this screen:
I would try unchecking all of the boxes and then quit and restart Rstudio to see if that clears up the problem.

After some experiments, I kind of worked out the problem. Since this has consumed so much time of my time, I thought this could be helpful to others.
The problem is :: (double colon) with packages using ggplot2, such as ggimage in my example. It appears that RStudio automatically load some dependent packages when a script file is open. One way to fix this problem for my work now is to remove ::, but use library() then function (geom_image) instead.
This fixed my problem but I still don't understand why RStudio behaves this way.
If :: (double colon) is necessary, comment lines containing ::, then after loading older version of ggplot2, uncomment those lines. A little awkward, but it works for me.

Related

Connection to IBM db2 in R fails - idaInit() error

I was recently forced to update R to the latest version of 4.1.2 and since then my connection to db2 is not working. I use ibmdbR. I follow the steps as recommended by IBM:
https://www.ibm.com/docs/en/db2-warehouse?topic=science-r-development-environment
it fails at step d, nitialising the analytics package by issuing the following R command.
The ODBC connection works (or seems to be working) but idaInit(con) fails with the following error:
> idaInit(con) #this fails
Error in assign("idaRGlobal", new.env(parent = baseenv()), envir = baseenv()) :
cannot add binding of 'idaRGlobal' to the base environment
The con object is created without an issue:
> con <- idaConnect(con.text) # this is successful and con is created
I've tested my ODBC connection using online reference (below) and it's successful.
https://www.ibm.com/docs/en/db2-warehouse?topic=programmatically-odbc-cli
More info on setup:
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ibmdbR_1.50.0 arules_1.7-2 Matrix_1.4-0 RODBC_1.3-19
loaded via a namespace (and not attached):
[1] magrittr_2.0.1 MASS_7.3-54 tidyselect_1.1.1 munsell_0.5.0 colorspace_2.0-2 lattice_0.20-45 R6_2.5.1 rlang_0.4.12 fansi_0.5.0 dplyr_1.0.7
[11] tools_4.1.2 parallel_4.1.2 grid_4.1.2 rpart.plot_3.1.0 gtable_0.3.0 utf8_1.2.2 ellipsis_0.3.2 tibble_3.1.6 lifecycle_1.0.1 crayon_1.4.2
[21] purrr_0.3.4 ggplot2_3.3.5 vctrs_0.3.8 rpart_4.1-15 glue_1.5.1 compiler_4.1.2 pillar_1.6.4 generics_0.1.1 scales_1.1.1 pkgconfig_2.0.3
It seems the error comes from executing this assignment in the code: assign("idaRGlobal", new.env(parent = baseenv()), envir=baseenv())
idaInit() code can be found here: rdrr.io/cran/ibmdbR/src/R/connection.R
I have completely removed R with all its libraries and installed everything from scratch, so I don't see how it could be a versioning issue. All packages seem to have the latest version. The only package that hasn't been updated after the release of R 4.2.1 are RODBC and IBMDBR.
Edit: Tried using RODBC directly and the connection works fine.

R Blogdown serve site: Error in !server$daemon : invalid argument type

My website used to work fine in my previous laptop, which used R 3.6.3. In my new laptop when I run blogdown::serve_site() I get the error Error in !server$daemon : invalid argument type. I tried doing what was suggested here but didn't help.
Here is the session info:
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.2.3
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 bookdown_0.22 digest_0.6.27 later_1.2.0 R6_2.5.0
[6] jsonlite_1.7.2 magrittr_2.0.1 evaluate_0.14 blogdown_1.3.2 rlang_0.4.11
[11] rstudioapi_0.13 promises_1.2.0.1 rmarkdown_2.9 tools_4.1.0 servr_0.22
[16] httpuv_1.6.1 xfun_0.24 yaml_2.2.1 compiler_4.1.0 htmltools_0.5.1.1
[21] knitr_1.33
This is the website link and you can find the Github repo here.
You should remove the quotes on interactive(). It should be
servr.daemon = interactive()
instead of
servr.daemon = "interactive()"
Actually servr.daemon = interactive() is the default, so you don't really need to set it explicitly (i.e., you can remove this setting).

Knitr keeps executing and cannot be cancelled after error

Every time I run into an error while knitting a script that stops execution, RStudio behaves in a weird way: In the R markdown tab it reads in red that the execution is stopped but in the R markdown tab I see the continuing progress circle still moving, suggesting that knitting is still ongoing. Also on the right hand I see that "stop" sign but clicking on it also does not stop executing. I can still write text in the script but I can no longer execute the script and can also not kick off a new knitting attempt.
The only way of going back to normal is top close Rstudio and re-start it. That means, everytime I run into any kind of error while knitting I have to restart Rstudio. This does not occur on my private PC with the same scripts.
I have installed a new version of Rstudio (the new 1.4 Preview) and I have re-installed R Markdown. Do you have any tips?
edit:
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] rmarkdown_2.5
loaded via a namespace (and not attached):
[1] rstudioapi_0.13 knitr_1.30 magrittr_2.0.1 tidyselect_1.1.0
[5] R6_2.5.0 rlang_0.4.9 dplyr_1.0.2 tools_4.0.3
[9] xfun_0.19 pacman_0.5.1 htmltools_0.5.0 ellipsis_0.3.1
[13] yaml_2.2.1 digest_0.6.27 tibble_3.0.4 lifecycle_0.2.0
[17] crayon_1.3.4 purrr_0.3.4 tidyr_1.1.2 vctrs_0.3.5
[21] clisymbols_1.2.0 glue_1.4.2 evaluate_0.14 compiler_4.0.3
[25] pillar_1.4.7 generics_0.1.0 pkgconfig_2.0.3 tidylog_1.0.2

save_kable does not work after installing R v4.0.2

I have successfully used save_kable() from kableExtra to export latex tables into *.png before. However, after updating R to the version 4.0.2, save_kable always ends with R fatal error (no specific error message is shown, the session is just aborted). I installed a clean version o R 3.6.3 and everything works fine again.
Next, I re-installed MikTEX, but this does not seem to be the problem because R Markdown can knit a .pdf file without an issue (in the 4.0.2 version). Also, using save_kable with "html" options works fine and exports the table into .png. The problem seems to be specific for latex.
Looking at sessionInfo(), the only difference is that R 3.6.3 automatically loads the 'magick' package, while R 4.0.2 does not. However, loading the magick package manually in the latter R version does not solve the problem. Then, of course, the sessions differ in the "compiler" package versions. Maybe this is the source of the problem?
Any help would be much appreciated. The problem can be reproduced with minimal code such as
kable(mtcars, "latex") %>% save_kable("test.png")
Here is the sessionInfo
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] magick_2.4.0 kableExtra_1.1.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 rstudioapi_0.11 knitr_1.29 xml2_1.3.2 magrittr_1.5
[6] hms_0.5.3 rvest_0.3.5 munsell_0.5.0 viridisLite_0.3.0 colorspace_1.4-1
[11] R6_2.4.1 rlang_0.4.7 stringr_1.4.0 httr_1.4.1 tools_4.0.2
[16] webshot_0.5.2 xfun_0.15 htmltools_0.5.0 ellipsis_0.3.1 digest_0.6.25
[21] tibble_3.0.3 lifecycle_0.2.0 crayon_1.3.4 readr_1.3.1 vctrs_0.3.2
[26] glue_1.4.1 evaluate_0.14 rmarkdown_2.3 stringi_1.4.6 compiler_4.0.2
[31] pillar_1.4.6 scales_1.1.1 pkgconfig_2.0.3
This seems to be a windows specific problem. I actually just asked a recent question here
kableExtra HTML styling in Rmarkdown and kable_save()
Some of the things I have seen mentioned as potential fixes are listed there such as updating ghostscript, not using tinytext, updating some latex packages including 'standalone', and editing the policy.xls document in ImageMagick ImageMagick security policy 'PDF' blocking conversion.
None of these worked for me and I get the same crashing issues the second I try to kable_save a latex format into png. However, some other Windows users have found success with the steps above so maybe try that out and see how it goes.

error "object ‘coef.cv.glmnet’ is not exported by 'namespace:glmnet' " while loading Lime package in R -

I've successfully installed Lime (and glmnet) in R but when I try loading it i receive an error:
> require(lime)
Loading required package: lime
Error: package or namespace load failed for ‘lime’:
object ‘coef.cv.glmnet’ is not exported by 'namespace:glmnet'
Searched online and can't seem to find a solution for this.
This is my sessioninfo()
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] glmnet_3.0 Matrix_1.2-17
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 rstudioapi_0.10 magrittr_1.5 tidyselect_0.2.5 munsell_0.5.0 colorspace_1.4-1 lattice_0.20-38 R6_2.4.0 rlang_0.4.1
[10] foreach_1.4.7 dplyr_0.8.3 tools_3.6.1 grid_3.6.1 gtable_0.3.0 iterators_1.0.12 lazyeval_0.2.2 assertthat_0.2.1 tibble_2.1.3
[19] crayon_1.3.4 purrr_0.3.3 ggplot2_3.2.1 codetools_0.2-16 shape_1.4.4 glue_1.3.1 compiler_3.6.1 pillar_1.4.2 scales_1.0.0
[28] pkgconfig_2.0.3
I've updated all my packages.
glmnet loads successfully
> library(glmnet)
Loaded glmnet 3.0
The recent major update of glmnet (which now does not export coef.cv.glmnet anymore) appears to have broken lime. You can see errors with the same cause in the CRAN tests. You can expect a fix by the package maintainer soon (or the package will be archived by CRAN). See also this bug report and the answer by the maintainer:
This is due to a recent breaking change in glmnet—lime will be updated soon to fix this

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