I am using bioconductor for WES pipeline and I am using tk_choose.dir for selection of directory (and store it for further use) where user has stored input files. Here the command lines
library(tcltk)
dataDir <- dirname(tk_choose.dir(default = " ", caption = "Select Directory for input fastq files"))
But these command lines shows some error, shown below (although library(tcltk) is working fine)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :
[tcl] invalid command name "tk_chooseDirectory".
Any hint guys, I am not able to figure out if library is already installed and loaded then why this command is not working. I am using R version 3.4.3 and bioconductor version 3.2
Thanks.
Related
I'm trying to load papaja in R (version 3.6.0). I'm running Windows 10 on my computer. When I try to run devtools::install_github("crsh/papaja") I get the following error message:
package ‘markdown’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\My
Name\AppData\Local\Temp\RtmpKCmBDG\downloaded_packages
ERROR
cannot change to directory 'C:\Users\My'
The system cannot find the path specified.
Error in (function (command = NULL, args = character(), error_on_status =
TRUE, :
System command error
From some research, including this post and this post, I realise that this is a common issue, but none of the answers I can find help me work around this in papaja.
For info, I don't have this problem when installing other packages using install.packages().
I have managed to solve this problem after hours and hours of googling. The problem is not papaja; it is the presence of spaces in the path, which devtools does not deal with well.
To solve this, I first changed my library path:
.libPaths("C:/Program Files/R/R-3.6.1/library") # for R v.3.6.1
At first I couldn't get this to work - I kept getting the error 'lib = "C:/Program Files/R/R-3.6.1/library"' is not writable. Basically, this is because I did not have permission to write into this folder. To fix this, you simply close RStudio, go to the folder where the programme is saved and right click, then select 'Run as administrator'.
In this tutorial, there is a command pymol.dccm(cij, pdb, type="launch"). But I was told
> pymol.dccm(cij, pdb, type="launch")
Error in pymol.dccm(cij, pdb, type = "launch") :
Launching external program failed
make sure 'C:/python27/PyMOL/pymol.exe' is in your search path
In addition: Warning message:
running command 'C:/python27/PyMOL/pymol.exe -cq' had status 127
I already have pymol installed on my PC. Can I ask how to add another search path to R?
Now I think pymol is a sub-package in bio3d. But I already installed bio3d and other commands can work (e.g. pdb <- read.pdb()). But why the pymol command could not work?
I tried
> .libPaths("path/to/pymol2/")
> .libPaths("path/to/pymol2/PyMOL")
> .libPaths("path/to/pymol2/PyMOL/PyMOLWin.exe")
> pymol.dccm(cij, pdb, type="launch")
Error in pymol.dccm(cij, pdb, type = "launch") :
Launching external program failed
make sure 'C:/python27/PyMOL/pymol.exe' is in your search path
In addition: Warning message:
running command 'C:/python27/PyMOL/pymol.exe -cq' had status 127
> PyMOLWin.dccm(cij, pdb, type="launch")
Error: could not find function "PyMOLWin.dccm"
So the .libPaths did not return error. But pymol.dccm and PyMOLWin.dccm did not work.
I also tried to install pymol package in R
> install.packages("pymol")
Warning in install.packages :
package ‘pymol’ is not available (for R version 3.2.2)
There's a mistake in the tutorial command itself. The correct syntax for dccm is
pymol(cij, pdb, type="launch",exefile="C:/Program Files/pymol")
where exefile = file path to the ‘PYMOL’ program on your system (i.e. how is ‘PYMOL’ invoked). If NULL, use OS-dependent default path to the program.
Try the following code, it worked perfectly for me:
pymol(cm, pdb.open, type="launch", exefile="%userprofile%/PyMOL/PyMOLWin.exe")
.libPaths("path/to/package/library") probably does what you need.
.libPaths gets/sets the library trees within which packages are looked for.
Set the path to the parent directory of the directory with the package name rather than the package directory itself.
I recently updated R to the latest release: 3.4.0. R is installed on a network location H:/. Now something weird is happening when I try to install a local binary package:
filename <- paste0("R:/path/independeR_", versions, ".zip")
install.packages(filename,
repos = NULL, type = "source",
lib = gsub("\\\\\\\\networkpath/home/[[:alpha:]]*/",
"H:/", .libPaths()[1]))
Both H:/ and R:/ are network locations. In .libPaths() the default location is in the H:/ location, but it shows with the entire network adress. In the call to install.packages I substituted this.
The code above fails, with the following output:
'\\networkpath\home\JDUB~PN6\DOCU~UZL\R\R-34~TN4.0' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"//networkpath/home/JDUB~PN6/DOCU~UZL/R/R-34~TN4.0/bin/x64/R" CMD INSTALL -l "H:\Documents\R\R-3.4.0\library" "R:/path/independeR_0.1.8.zip"' had status 1
Warning in install.packages :
installation of package ‘R:/path/independeR_0.1.8.zip’ had non-zero exit status
There is two things that surprise me here. The directorynames are all jumbled up (DOCU~UZL instead of Documents etc), but for some reason Command promt seems fine with that. The more interesting thing is the following:
When I try to put the command "//networkpath/home/JDUB~PN6/DOCU~UZL/R/R-34~TN4.0/bin/x64/R" CMD INSTALL -l "H:\Documents\R\R-3.4.0\library" "R:/path/independeR_0.1.8.zip" directly into Command Prompt, the output is very similar:
C:\Users\jdubbeldam>"//networkpath/home/JDUB~PN6/DOCU~UZL/R/R-34~TN4.0/b
in/x64/R" CMD INSTALL -l "H:\Documents\R\R-3.4.0\library" "R:/path/independeR_0.1.8.zip"
'\\networkpath\home\JDUB~PN6\DOCU~UZL\R\R-34~TN4.0' is not recognized as
an internal or external command,
operable program or batch file.
For some reason CMD seems to cut off the path to the command halfway through. I guess that this is because the command is too long. When I try the same command, but with H:/Documents/R/R-3.4.0/bin/x64/R, the installation goes just fine.
I would like to be able to automatically install this package from a script, so I would like a solution to this problem from within R. Is there a way to get R to use the shorter H:/Documents/R/R-3.4.0/bin/x64/R?
I was having problems with updating packages, while searching I found that there is a reported bug affecting getting the timestamps from files in Windows 10:
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17261
Starting in R 3.4.0, file.info sometimes returns for mtime,
atime and ctime for directories. It seems to have something to do
with sharing. This affects functions that use file.mtime like
update.packages.
Reproduce:
Try file.info() with a random directory. If it returns a legitimate
file time, open a windows explorer window and navigate to the
directory, then run the call again and it will return s.
In some cases it returns s even if the directory is not open (or
in the path of an open explorer window), but this is not consistent.
With a comment of Tomas Kalibera:
Thank you for the report, this is a known bug that has been fixed
recently in R-devel
I found that when I closed the file explorer windows the timestamps worked correctly and didn't show up as NA's.
This may be a lead for why your code isn't working.
I managed to make the following work. However, I think it is extremely ugly, and would still like to see if it is possible to do it someway else.
filename <- paste0("R:/path/independeR_", versions, ".zip")
cmd <- file.path(gsub("//networkpath/home/[[:alnum:]]*/", "H:/",
gsub("//networkpath/home/[[:alnum:]]*~[[:alnum:]]*/",
"H:/", R.home())), "bin/x64/R")
libname <- gsub("\\\\\\\\networkpath/home/[[:alpha:]]*/",
"H:/", .libPaths()[1])
call <- paste(paste0('"', cmd, '"'),
"CMD",
"INSTALL",
"-l",
paste0('"', libname, '"'),
"--no-lock",
paste0('"', filename, '"'),
sep = " ")
system(call)
To avoid the irregular parameter error caused by the directory including space and set workspace and tool path at once, I tried to compile R package in R console. My goal is compile the new version of "text2vec-0.4" which downloaded from https://github.com/dselivanov/text2vec/tree/0.4
setwd("E:/packbuild/")
builder <- "D:/Program Files/R/R-3.3.1/bin/x64/Rcmd.exe"
para <- "INSTALL --build"
packname <- "text2vec-0.4"
system(paste(shQuote(builder), para, packname, sep = " "), wait = FALSE)
When I run this program, it runs “successfully” no errors or warnings, but when I check the workspace"E:/packbuild/", there is no zip files generated and no new files installed in the R library. Rtools has completely installed in “D:/Rtools/” and its default path set has done.
Does Rtools can’t call by a meta program like this?
Or if we use command line, and don’t write directory of “Rcmd” into
path, how to do is right?
OS- Windows 7
R version 3.0.3
What I typed on R console :
if(!file.exists("data")){dir.create("data")}
fileUrl <- "https://data.baltimorecity.gov/api/views/dz54-2aru/rows.xlsx?accessType=DOWNLOAD"
download.file(fileUrl,destfile="./data/cameras.xlsx",method="curl")
dateDownloaded <- date()
What I got on R console
Warning messages:
1: running command 'curl "https://data.baltimorecity.gov/api/views/dz54-2aru/rows.xlsx?accessType=DOWNLOAD" -o "./data/cameras.xlsx"' had status 127
2: In download.file(fileUrl, destfile = "./data/cameras.xlsx", method = "curl") :
download had nonzero exit status
How do I make it right ?
Your code works for me. You probably don't have cURL installed on your system. See ?download.file:
For methods "wget", "curl" and "lynx" a system call is made to the tool given by method, and the respective program must be installed on your system and be in the search path for executables.
Install cURL and make sure it is in your path.
After removing the method="curl" parameter, it works well on Windows.