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.
Related
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'))"
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.
Im building an R package and when testing the package using devtools::check() I get an error when the test reaches the installation phase, saying:
Error: .onLoad failed in loadNamespace() for 'pillar', details:
call: utils::packageVersion("vctrs")
error: there is no package called 'vctrs'
Execution halted
ERROR: lazy loading failed for package
Neither pillar nor vctrs are mentioned in my description file, so they must be dependents of some other package that I depend on. Both pillar and vctrs are installed and I've also tried reinstalling them. They are stored in the the first .libPath entry. I tried installing pillar from github as was suggested by mfox9 here, but this failed for me, giving this error:
> devtools::install_github("r-lib/pillar")
Downloading GitHub repo r-lib/pillar#master
√ checking for file 'C:\Users\DESCRIPTION' (337ms)
- preparing 'pillar': (664ms)
√ checking DESCRIPTION meta-information ...
- installing the package to process help pages
- checking for LF line-endings in source and make files and shell scripts (8.5s)
- checking for empty or unneeded directories
- building 'pillar_1.4.2.9001.tar.gz'
Installing package into ‘Z:/’
(as ‘lib’ is unspecified)
The filename, directory name, or volume label syntax is incorrect.
Error: Failed to install 'pillar' from GitHub:
(converted from warning) installation of package ‘C:/Users/Temp/RtmpgjFfZl/file32586b634e28/pillar_1.4.2.9001.tar.gz’ had non-zero exit status
(note: z:/ is my correct R library address)
Can someone please help?
´´´
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pillar_1.4.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 rstudioapi_0.10 magrittr_1.5 usethis_1.5.1
[5] devtools_2.2.0 pkgload_1.0.2 R6_2.4.0 rlang_0.4.0
[9] tools_3.6.1 pkgbuild_1.0.5 DT_0.8 packrat_0.5.0
[13] sessioninfo_1.1.1 cli_1.1.0 withr_2.1.2 remotes_2.1.0
[17] htmltools_0.3.6 ellipsis_0.2.0.1 assertthat_0.2.1 digest_0.6.20
[21] rprojroot_1.3-2 crayon_1.3.4 processx_3.4.1 callr_3.3.1
[25] fs_1.3.1 htmlwidgets_1.3 ps_1.3.0 curl_4.0
[29] testthat_2.2.1 glue_1.3.1 memoise_1.1.0 compiler_3.6.1
[33] desc_1.2.0 backports_1.1.4 prettyunits_1.0.2
´´´
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
I tried installing all the dependant packages and also tried another repo source as recommended in another post here.
R version 3.2.0 x64
install.packages("fracdiff")
install.packages("Rcpp")
install.packages("RcppArmadillo")
install.packages("colorspace")
install.packages("forecast", dep=T)
install.packages("forecast", repos=c("http://cran.rstudio.com"),dep=T)
library("forecast")
then I get
Loading required package: zoo
Attaching package: ‘zoo’
The following objects are masked from ‘package:base’:
as.Date, as.Date.numeric
Loading required package: timeDate
Error : .onAttach failed in attachNamespace() for 'forecast', details:
call: fun(libname, pkgname)
error: 4 arguments passed to .Internal(nchar) which requires 3
In addition: Warning message:
package ‘forecast’ was built under R version 3.2.1
Error: package or namespace load failed for ‘forecast’
sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] Hmisc_3.16-0 ggplot2_1.0.1 Formula_1.2-1 survival_2.38-1 lattice_0.20-31 zoo_1.7-12 timeSeries_3012.99 timeDate_3012.100
loaded via a namespace (and not attached):
[1] Rcpp_0.11.6 cluster_2.0.1 magrittr_1.5 MASS_7.3-41 splines_3.2.0 forecast_6.1 munsell_0.4.2
[8] colorspace_1.2-6 quadprog_1.5-5 stringr_1.0.0 plyr_1.8.3 tools_3.2.0 nnet_7.3-9 parallel_3.2.0
[15] gtable_0.1.2 latticeExtra_0.6-26 tseries_0.10-34 digest_0.6.8 gridExtra_0.9.1 RColorBrewer_1.1-2 reshape2_1.4.1
[22] acepack_1.3-3.3 rpart_4.1-9 fracdiff_1.4-2 stringi_0.4-1 scales_0.2.5 foreign_0.8-63 proto_0.3-10
I tried to reproduce. I get no message about either loading timeDate or the error you see. I do get a message about loading pkg:zoo. The package loads and announces its version number. Try updating to R version 3.2.1, since that is where a new argument to nchar was introduced:
new$Text[ grep("nchar", news$Text) ]
• nchar(x, *) and nzchar(x) gain a new argument keepNA which governs how the result for NAs in x is determined. For the R 3.2.x series, the default remains FALSE which is fully back compatible. From R 3.3.0, the default will change to keepNA = NA and you are advised to consider this for code portability.