I'm working in RStudio with R version 3.5.1.
Originally I tried installing the ChemmineR package using the following line of code.
>BiocManager::install("ChemmineR")
This ended up hanging so I had to stop the process and close out of RStudio.
I tried again, and now it is consistently hanging after the following step.
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/ChemmineR_3.32.1.zip'
Content type 'application/zip' length 2593605 bytes (2.5 MB)
downloaded 2.5 MB
Does anyone have any advice?
I would suggest skipping BiocManager package and just use biocLite():
> biocLite("ChemmineR")
> library('ChemmineR')
> packageVersion("ChemmineR")
[1] ‘2.30.2’
EDIT:
I re-read this question and realized you were on Windows and using a different version of R and a later version of ChemmineR. I re-tested this code and it still works:
R> biocLite("ChemmineR")
R> library("ChemmineR")
R> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows >= 8 x64 (build 9200)
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] ChemmineR_3.32.1 BiocInstaller_1.30.0
Related
I run memory.limit() on my 48G Windows 10 machine and it returned 1.759219e+13. This is head scratching. I am using R 3.6.1.
Is memory.limit() broken? Any other way to obtain memory limit?
Here is my 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_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
loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1
This is an issue with RStudio (hopefully fixed in the next update). It works well in RGui.
You can use disk.frame::df_ram_size() instead. It works on Windows 10 with RStudio and R 3.6.1.
You can install disk.frame using install.packages("disk.frame")
I need to obtain user input from the svDialogs R package, e.g. using svDialogs::dlgInput(). However, attempting to do this without attaching the package with library() or require() gives an error:
svDialogs::dlgInput("Example")
Error in svDialogs::dlgInput("Example") : attempt to apply non-function
The following works fine:
library(svDialogs)
svDialogs::dlgInput("Example")
Why might this be, and what might be a way around it? I have the current CRAN version of the package (0.9.57).
Update
I have tried installing previous versions of svDialogs, as well as comparing my code with the source code from the cgam package, which depends on svDialogs. Currently the entire svDialogs package is imported in my NAMESPACE, which is how it is used in cgam. But I still get the same error unless I first run library(svDialogs). Any tips?
Update 2
I also imported the entire svGUI package in my NAMESPACE, with no luck.
sessionInfo() R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
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] svDialogs_0.9-57 svGUI_0.9-55
loaded via a namespace (and not attached): [1] compiler_3.4.3
tools_3.4.3
I have used fread to read data. But the error has arisen:
showProgress is not type integer but type 'logical'. Please report.
Here is the reproducible script:
library(data.table)
x <- "sgsddsfsfsf"
write.csv2(x,"check.csv", row.names=FALSE)
fread("check.csv", stringsAsFactor=FALSE)
Example of printscreen:
> sessionInfo()
R version 3.3.2 (2016-10-31)
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
[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] data.table_1.9.8
loaded via a namespace (and not attached):
[1] tools_3.3.2
Just fixed. Please try again from dev. Thanks for reporting.
Fixed fread() error occurring for a subset of Windows users: showProgress is not type integer but type logical, #1944 and #1111. Our tests cover this usage (it is just default usage), pass on AppVeyor (Windows), win-builder (Windows) and CRAN's Windows so perhaps it only occurs on a specific and different version of Windows to all those. Thanks to #demydd for reporting. Fixed by using strictly logical type at R level and Rboolean at C level, consistently throughout.
I have a list that contain several large files. All the files have the same column names. I want to combine them into an rds file and save with the filename in a column. I have read some of the SO answers and have written the following code. But I ham getting error. This is my attempt:
list.nam<- list.files(pattern="*.I S")
list.fil <- lapply (list.nam, readRDS)
#listfil is 3.8 GB
# running this line gives error
for (i in 1:length(list.fil))
{list.fil[[i]]<-cbind(list.fil[[i]],list.nam[i])
}
data_rbind <- do.call("rbind", list.fil)
colnames(data_rbind)[c(1,2,3,4)]<-c("Time","MRP", "Lot", "Name")
saveRDS(data_rbind, "master.rds")
This is the error:
Error: cannot allocate vector of size 3.9 Mb
In addition: There were 22 warnings (use warnings() to see them)
> sessionInfo()
R version 3.2.2 (2015-08-14)
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
[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
loaded via a namespace (and not attached):
[1] tools_3.2.2
Please help.Is the problem I am facing is virtual address space limitation?
Is it possible to do the above operations on-disk using a package like ff? Any help is highly appreciated?
Before a project is open, R rapidly throws this error:
Surprisingly, I do not find anything related to this error with google. Even if, apparently, it does not cause problems to the working session, I am interested in its effects, to avoid possible future inconveniences.
> sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.2.4
Here an example of the subsequent working directory, even if this behaviour occurs for any project I open. It does not occurs when opening an isolated script.
getwd()
[1] "C:/Users/MaurizioLocale/OneDrive/Data_Science/10_Capstone_project/CP_Natural_Language"