thanks for checking out my very first post. please bear with my formatting.
Issue summary: I have been using tdplyr to access teradata database with no issue until I tested another package called dplyr.teradata for potential performance enhancement. However I can no longer connect to the database due to the following error messages:
Error: package or namespace load failed for 'tdplyr':.onLoad failed
in loadNamespace() for 'tdplyr', details:
call: parent.env(from)
error: argument is not an environment
so I deleted the dplyr.teradata package, thought that would allow my original tdplyr to work, but I still get the same error message above. then I deleted the tdplyr package without backup, trying to reinstall using the original script below:
install.packages('tdplyr',repos=c('https://teradata-download.s3.amazonaws.com','https://cloud.r-
project.org'))
but fail to install because of the same error again. Hope someone could advise on fix.
My sessioninfo is below:
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)
Matrix products: default
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] rlang_0.4.10 teradatasql_17.0.0.8 odbc_1.3.0 dplyr_1.0.2
[5] dbplyr_2.0.0 digest_0.6.27 DBI_1.1.0 hms_0.5.3
[9] bit64_4.0.5 bit_4.0.4
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 rstudioapi_0.13 magrittr_1.5 tidyselect_1.1.0 R6_2.4.1
[6] blob_1.2.1 tools_4.0.3 xfun_0.20 tinytex_0.28 ellipsis_0.3.1
[11] assertthat_0.2.1 tibble_3.0.4 lifecycle_0.2.0 crayon_1.3.4 zip_2.1.1
[16] purrr_0.3.4 vctrs_0.3.6 glue_1.4.2 openxlsx_4.2.3 stringi_1.5.3
[21] compiler_4.0.3 pillar_1.4.6 generics_0.0.2 pkgconfig_2.0.3
found the answer myself. Pasting the answer below.
The Teradata R package is incompatible with dbplyr v2.0.0 and its later versions, which introduced some breaking changes. To use tdplyr, the version of dbplyr package must be v1.4.4. tdplyr should be installed using the following commands from your Terminal (for Linux and Mac) or Command Prompt (for Windows), till a new version that is compatible with dbplyr v2.0.0 and its later versions is released:
Install dbplyr v1.4.4 first. There are various ways to install a specific version of a R package. Teradata recommends using the following command:
Rscript -e "remotes::install_version('dbplyr',version='1.4.4',repos='https://cloud.r-project.org')"
Note: To run this above command, the R package remotes should be present on the client machine.
Next to download and install tdplyr and dependencies automatically, if minimum required versions are not met, specify the Teradata R package repository and CRAN in the repos argument for install.packages.
Rscript -e "install.packages('tdplyr',repos=c('https://teradata-download.s3.amazonaws.com','https://cloud.r-project.org'))"
Related
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.
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.
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.
Every time I try to download a package from GitHub using devtools I get an error. I'm currently trying to open the elan package:
library(devtools)
devtools::install_github("dalejbarr/elan")
I get the following error:
Installing package into ‘C:/Users/Daniel &
Catherine/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified)
Error: no packages specified The system cannot find the path
specified. Error: Failed to install 'elan' from GitHub: (converted
from warning) installation of package
‘C:/rtemp/Rtmp0gabkG/file5580567f6ac9/elan_0.1.tar.gz’ had non-zero
exit status
I've tried the solutions suggested here and here, but neither fix the problem. I understand that there might be a problem with the spaces in the path name, but there's not much I can do about that (I don't want to set up a new user on my computer just to run devtools).
My SessionInfo() is:
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_2.2.2 usethis_1.5.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 rstudioapi_0.10 magrittr_1.5 pkgload_1.0.2 R6_2.4.0 rlang_0.4.0 tools_3.6.1 pkgbuild_1.0.3 sessioninfo_1.1.1 cli_1.1.0 withr_2.1.2 ellipsis_0.3.0
[13] remotes_2.1.1 assertthat_0.2.1 digest_0.6.21 rprojroot_1.3-2 crayon_1.3.4 processx_3.4.0 callr_3.3.0 fs_1.3.1 ps_1.3.0 curl_3.3 testthat_2.2.1 memoise_1.1.0
[25] glue_1.3.1 compiler_3.6.1 desc_1.2.0 backports_1.1.5 prettyunits_1.0.2
Looking at the source code at https://github.com/dalejbarr/elan/blob/master/DESCRIPTION I found a potential error of format. You could try to clone the repository and debug it manually by removing the extra spaces in front on the XML package import :
DESCRIPTION file
Package: elan
Title: Read ELAN XML files
Version: 0.1
Authors#R: "Dale Barr <dalejbarr3#gmail.com> [aut, cre]"
Description: Read ELAN XML files to tidy output
Depends:
R (>= 3.1.1),
dplyr
Imports:
XML,
plyr
License:
LazyData: true
RoxygenNote: 7.0.2
I tried it in a minimal package and this raise a problem (but the package still compiles without the scripts).
Alternatively you could use the XML(which this small package uses) or the xml2 (as here) package to parse your XML files.
I have been running a bash script (under Ubuntu) that calls and runs some R scripts to plot some maps with ggplot2. As it is a production system I don't update any new R or package releases. But recently I tried to install plotly with an error message output.
Now, when trying to run the script (calling a php webpage trhough a browser; that was running fine for a lot of time) an error with crayon package halts and exits the script without plotting the maps.
'/usr/lib/R/bin/R --slave --no-restore --no-save --no-restore --file=./RAMS-mapa-onades-zones-manual.R'
Loading required package: sp
Loading required package: methods
Checking rgeos availability: TRUE
Error : .onLoad failed in loadNamespace() for 'pillar', details:
call: loadNamespace(name)
error: there is no package called 'crayon'
Error: package or namespace load failed for 'ggplot2'
Execution halted
But if I run from a terminal or with RStudio server crayon package is loaded, ggplot2 is also properly loaded, and the maps are produced.
crayon package (located at /home/meteo/R/i686-pc-linux-gnu-library/3.1) called as
library("crayon", lib.loc= c("/home/meteo/R/i686-pc-linux-gnu-library/3.1", "/usr/local/lib/R/site-library", "/usr/lib/R/library"))
R session info on Rstudio Server:
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu precise (12.04.5 LTS)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] crayon_1.3.4 rgdal_0.9-1 rgeos_0.3-8 raster_2.3-24 gpclib_1.5-5 mapproj_1.2-2 maps_2.3-9
[8] stringr_0.6.2 plyr_1.8.1 ggplot2_3.2.0 maptools_0.8-34 sp_1.2-3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 magrittr_1.5 tidyselect_0.2.5 munsell_0.5.0 colorspace_1.2-4 lattice_0.20-33 R6_2.4.0
[8] rlang_0.3.4 dplyr_0.8.1 tools_3.2.2 gtable_0.1.2 withr_2.1.2 digest_0.6.8 lazyeval_0.2.2
[15] assertthat_0.2.1 tibble_2.1.3 purrr_0.3.2 glue_1.3.1 labeling_0.3 pillar_1.4.1 scales_1.0.0
[22] foreign_0.8-66 pkgconfig_2.0.2
Maybe there is a version conflict? How do I check?
what version of R is in /usr/lib/R/bin/R? Basically it appears you are in a slight "dependency hell" I would run /usr/lib/R/bin/R and check to see if crayon is installed there. #Alexis is correct though, it is not wise to mix versions like that. Let R handle library location unless you are trying to separate packages. Check the libraries for 3.2.2 and see if crayon is installed. you may have switched your R version since plotly depends on R >=3.2.0 https://cran.r-project.org/web/packages/plotly/
I think the easy fix would be to correct your .libpaths() i.e not call the 3.1 library and install the correct version of the packages you need.
OR
switch from R 3.2 back to R 3.1