I recently updated to data.table 1.9.6 and get the following error when using fread:
fread("Aug14.csv")
Error in fread("Aug14.csv") :
4 arguments passed to .Internal(nchar) which requires 3
Another post discusses this error in another context, but this worked fine prior to upgrading to data.table 1.9.6. Any advice?
Here's my set up:
sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.9.6 Matrix_1.2-2
loaded via a namespace (and not attached):
[1] modeltools_0.2-21 tools_3.2.0 splines_3.2.0 grid_3.2.0 chron_2.3-47 stats4_3.2.0 lattice_0.20-33
This seems to be a wider problem affecting other packages too and something similar was raised on r-devel here :
http://r.789695.n4.nabble.com/Error-generated-by-Internal-nchar-disappears-when-debugging-td4713138.html
If I understand correctly, CRAN provides one Windows binary for the R 3.2.* series. I guess this binary is built using the latest version of R in that series, currently R 3.2.2. As Andriy T. pointed out in a comment here, the base R function nchar gained an extra argument in R 3.2.1. Since data.table uses the R function nchar and it sets ByteCompile:TRUE in its DESCRIPTION file, the CRAN binary package for Windows doesn't seem to be compatible with R 3.2.0. I guess binary incompatible changes to R itself are supposed to be made to the .0 version only for this reason, but I'm not sure on that. Where packages are compiled on install (e.g. Ubuntu) this isn't an issue.
If you are using R < 3.2.0 on any platform, there shouldn't be a problem.
If you are using R >= 3.2.1 on any platform, there shouldn't be a problem.
If you are using R 3.2.0 on Windows and installing the binary .zip from CRAN (i.e. the default method) then you'll need to either upgrade to R >= 3.2.1, or, build data.table (and potentially any other package using nchar that also set ByteCompile:TRUE) yourself using Rtools.
Related
I am having some issue with installing a package in R 4.0.2 from binaries. Here is my attempt:
> install.packages("C:/Users/MNestor/Downloads/libSBML_5.18.0.zip", repos = NULL, type = "win.binary")
Installing package into ‘C:/Users/MNestor/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)
package ‘libSBML’ successfully unpacked and MD5 sums checked
Warning messages:
1: multiple methods tables found for ‘type’
2: multiple methods tables found for ‘type<-’
Next I load library:
> library('libSBML')
Error: package or namespace load failed for ‘libSBML’:
package ‘libSBML’ was installed before R 4.0.0: please re-install it
This error is confusing to me because I am working in R 4.0.2 and have clearly just done a fresh install.
I have tried
deleting the library folder and reinstalling
running remove.packages('libSBML') and reinstalling
For reference here are my library directories:
> .libPaths()
[1] "C:/Users/MNestor/Documents/R/win-library/4.0"
[2] "C:/Program Files/R/R-4.0.2/library"
The libSMBL folder is located in the first library path, and not the second (as expected).
Here is session info:
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
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] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] rsbml_2.46.0 BiocGenerics_0.34.0
loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.2 tools_4.0.2 remotes_2.2.0
[5] stats4_4.0.2 SBMLR_1.84.0 graph_1.66.0
The error message is maybe a bit confusing, but it's saying the package is already compiled for an earlier version of R. (That's what the option "win.binary" means).
R 4.0 and earlier binaries are not compatible because of updated compilers and build tools.
You'll need to install the package from source, which likely means installing R tools (https://cran.r-project.org/bin/windows/Rtools/) or you'll need to use a version that is pre-built for R 4.0 or later.
I need a packages witch is located on Github. And I am aware that there are multiple solutions to install the package in R.
I am trying to install the package on a Windows server. This is what I tried:
Solution 1 (which is based on the Vignette)
install.packages("devtools")
library("devtools")
devtools::install_github("bmschmidt/wordVectors")
Error: Could not find tools necessary to compile a package
In addition: Warning messages:
1: In strptime(xx, f, tz = tz): unable to identify current timezone 'C':
Please set environment variable 'TZ'
I tried many things to solve this:
Reinstalling Devtools, use the CRAN devtools version
Reinstalling R and Rstudio (installing the latest versions as admin) (Error : Could not find build tools necessary to build)
But still the same error...
So I tried a workaround to install the packages on my computer:
Solution two
Download ZIP file from (https://github.com/bmschmidt/wordVectors)
Unzip the ZIP file
But the result is an error again:
library(devtools)
install("path/to/unzipped/file")
library("wordVectors")
Error there is no packages called wordVectors.
Anyone an idea what is going on? I struggled the whole day with this issue. Help is really appreciated! Thanks!
Edit
Also Rtools is (re)installed (the latest version...)
Edit 2
As requested in the comments (#DJV):
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server >= 2012 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.2 tools_3.5.2
I want to update an R package using Microsoft R Open via Microsoft R Server. I can see in MRAN package repo that the package version is 1.2.0 but when I try an update in RStudio it says all packages up to date although respective package is still on version 1.1.0 (dbplyr in my case). Why is R not updating the package? RStudio points to C:\Program Files\Microsoft\ML Server\R_SERVER.
sessionInfo()
#>R version 3.4.1 (2017-06-30)
#>Platform: x86_64-w64-mingw32/x64 (64-bit)
#>Running under: Windows 7 x64 (build 7601) Service Pack 1
#Matrix products: default
#>locale:
#>[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
#>[4] LC_NUMERIC=C LC_TIME=English_United States.1252
#>attached base packages:
#>[1] stats graphics grDevices utils datasets methods base
#>other attached packages:
#>[1] RevoUtilsMath_10.0.0 RevoUtils_10.0.5 RevoMods_11.0.0 MicrosoftML_1.5.0 mrsdeploy_1.1.2 RevoScaleR_9.2.1
#>[7] lattice_0.20-35 rpart_4.1-11
#>loaded via a namespace (and not attached):
#>[1] codetools_0.2-15 CompatibilityAPI_1.1.0 foreach_1.4.4 grid_3.4.1 R6_2.2.0
#>[6] jsonlite_1.4 curl_2.6 iterators_1.0.8 tools_3.4.1 yaml_2.1.14
#>[11] compiler_3.4.1 mrupdate_1.0.1
packageVersion("dbplyr")
#>‘1.1.0’
RStudio IDE has as mirror Global (CDN) - RStudio but I guess this is overruled by MRAN?
So you are running Microsoft R Server, and that has an R version of 3.4.1. I believe what happens is that when you try to upgrade using MRAN, the upgrade takes into consideration which version of R you're on - and (I believe again) the latest version of dbplyr for R 3.4.1 was 1.1.0. You can read more about snapshots and checkpoints here.
What you can do if you want is to install the package straight from the CRAN repo, using code something like so:
install.packages("dbplyr", repos = "https://cloud.r-project.org/", dependencies=TRUE, lib = pkg.dir)
Hope this helps!
Niels
This question already has answers here:
How can I load dependencies in an R package?
(2 answers)
Closed 5 years ago.
RESOLVED
In my description file, I changed
Imports: dplyr (>= 0.4.3), ggplot2 (>= 2.1.0), lazyeval (>= 0.1.10)
to
Depends: dplyr (>= 0.4.3), ggplot2 (>= 2.1.0), lazyeval (>= 0.1.10)
This worked for me. "Imports:" may be depreciated?
---
I'm writing a package in RStudio. One of my dependencies is dplyr. When I build and reload the package, I get the following error when running a function:
> library(my_package)
> my_package::get_survey(...)
Error in get_survey(import_dir) : could not find function "%>%"
However, I've documented my dependencies in my DESCRIPTION file:
Imports: dplyr (>= 0.4.3), ggplot2 (>= 2.1.0), lazyeval (>= 0.1.10)
The libraries are installed on my system, however I want my package to work out of the box without requiring users to run
library(dplyr)
library(ggplot2)
library(lazyeval)
before using it. How can I fix this?
Here's my sessionInfo():
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices
[4] utils datasets methods
[7] base
other attached packages:
[1] my_package_0.0.0.9000
loaded via a namespace (and not attached):
[1] tools_3.3.0
Thanks in advance for any help!
Since there's no answer yet...
J_F writes
Have you tried to put the three packages under "Depends" in your DESCRIPTON?
I ran into this recently and Depends still seems to work where Imports does not.
I am having trouble running Rcpp on my PC in RStudio. Whenever I sourceCpp() a cpp file, even the Hello World file that comes with Rcpp::Rcpp.package.skeleton(), I get the warning
In normalizePath(path.expand(path), winslash, mustWork) :
path[1]=".../anRpackage/src/../inst/include": The system cannot find the path specified
I searched Stackoverflow and it looks like some people get this warning if they don't have Depends: Rcpp in the DESCRIPTION of their package, but I am just running sourceCpp() so the DESCRIPTION file shouldn't matter (I also changed my DESCRIPTION file).
It is just a warning so the class and functions I wrote do appear in R, but RStudio frequently crashes after I use the functions in R a few times, which may or may not be related.
My session info:
R version 3.1.3 (2015-03-09)
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
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rcpp_0.12.1 RevoUtilsMath_7.4.1 RevoUtils_7.4.1 RevoMods_7.4.1 RevoScaleR_7.4.1 lattice_0.20-30 rpart_4.1-9
loaded via a namespace (and not attached):
[1] codetools_0.2-10 foreach_1.4.2 grid_3.1.3 iterators_1.0.7 tools_3.1.3
I suppose it is possible that Revolution R is the culprit here, but I have no way of knowing. I would appreciate help, because I don't want to ignore this warning, and it's obviously not ideal for RStudio to crash repeatedly.
Kind Regards
This is still relevant today, so here's my discoveries.
Rcpp can generate interfaces to and from C++ and R.
These are generated with the help of attributes specified in source-files.
From these attributes, the call to Rcpp::compileAttributes() produces the headers. Whilst at it, this also create the folder <package directory>/inst/include. If you have specified no attributes, anywhere, then compileAttributes() does not create these directories.
In order to get rid of this warning, create the <package directory>/inst/include.
For more on attributes, see Rcpp attributes vignette.