I'm trying to download the package "Seurat" in R, the package is installed and it's now in my list of packages.
** testing if installed package keeps a record of temporary installation path
* DONE (patchwork)
The downloaded source packages are in
‘C:\Users\parnian\AppData\Local\Temp\RtmpAVgSd8\downloaded_packages’
But when I try to call it (library(Seurat)) I get the following error:
> library(Seurat)
Error: package or namespace load failed for ‘Seurat’:
object ‘wrap_plots’ is not exported by 'namespace:patchwork'
I read the similar questions and manually installed "patchwork":
> install.packages("patchwork")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/parnian/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
R also tells me to install Rtools whhich I have, but when I follow these commands:
> writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
but when I want to verify that make can be found (Sys.which("make")), I get this:
> Sys.which("make")
make
""
Also my downloaded packages are saved in a location that doesn't even exist in my computer!
How can I fix this?
Thank you
when you finish
> writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
you should restart R.
then Sys.which("make") may work.
Related
I'm trying to install XML Package to Rstudio Using the ribbon: Tools--> Install Packages --> Packages: to type XML, but the dropdown list opend had only this packages : xml2, XML2R, xml2relational, xmlparsedata, xmlr, xmlrpc2.
Next, I tried:
install.packages("XML")
but received the warning:
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘D:/BCDD/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘XML’ is not available (for R version 3.6.3)
So I followed the link above :https://cran.rstudio.com/bin/windows/Rtools/
and using these questions:
Why can't I install the XML package
Cannot install package XML to R
Then tried
install.packages("XML", repos = "http://www.omegahat.net/R",type="source")
but received the same warning and more:
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘D:/BCDD/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'http://www.omegahat.net/R/src/contrib/XML_3.99-0.tar.gz'
Content type 'application/x-gzip' length 1547930 bytes (1.5 MB)
downloaded 1.5 MB
* installing *source* package 'XML' ...
** using staged installation
Please define LIB_XML (and LIB_ZLIB, LIB_ICONV)
ERROR: configuration failed for package 'XML'
* removing 'D:/BCDD/Documents/R/win-library/3.6/XML'
Warning in install.packages :
installation of package ‘XML’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\BCDD\AppData\Local\Temp\RtmpAhAYpl\downloaded_packages’
Any help to how to install the package XML will be appreciated
You can download the version you want from here: https://cran.rstudio.com//src/contrib/Archive/XML/
According to their GitHub repo, version 3.99-0.3 should work for you, I can't try it out coz I have R4.0 and I can install only the most recent [3.99-0.5].
Alternatively, when you choose the version you want and run on your R console:
devtools::install_version("XML", version = "3.99-0.3") # or the version you want
Have a try. Let me know.
Check this RStudio Support post which covers how to install older versions of packages.
Be sure to install rtools35 from the archive
Going to R 4.0.2 is not a particularly bad idea at this point.
I'm trying to download the package "Seurat" in R, the package is installed and it's now in my list of packages.
** testing if installed package keeps a record of temporary installation path
* DONE (patchwork)
The downloaded source packages are in
‘C:\Users\parnian\AppData\Local\Temp\RtmpAVgSd8\downloaded_packages’
But when I try to call it (library(Seurat)) I get the following error:
> library(Seurat)
Error: package or namespace load failed for ‘Seurat’:
object ‘wrap_plots’ is not exported by 'namespace:patchwork'
I read the similar questions and manually installed "patchwork":
> install.packages("patchwork")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/parnian/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
R also tells me to install Rtools whhich I have, but when I follow these commands:
> writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
but when I want to verify that make can be found (Sys.which("make")), I get this:
> Sys.which("make")
make
""
Also the downloaded packages of Seurat are saved in a location that doesn't even exist in my computer! How is that possible?
How can I fix this? Is there something wrong with the address I write for the path?
Thank you
I've installed devtools for R, but when I call the library with:
library(devtools)
I get the following output:
WARNING: Rtools is required to build R packages, but is not currently installed.
Please download and install Rtools 3.1 from http://cran.r-project.org/bin/windows/Rtools/ and then run find_rtools().
So I executed the following code:
install.packages("Rtools", repos = "http://cran.r-project.org/bin/windows/Rtools/")
And I get the following output:
Installing package into ‘C:~/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository http://cran.r-project.org/bin/windows/Rtools/bin/windows/contrib/3.0
Warning message:
package ‘Rtools’ is not available (for R version 3.0.2)
I would appreciate any help that's out there to get Rtools onto my machine so I can call the devtools library. Thank you!
Rtools is not a package. See here: https://cran.r-project.org/bin/windows/Rtools/
I'm trying to install ROracle package on my Windows 7 client. I have Oracle Instant client and Rtools installed, DBI package is istalled, OCI32_LIB environmental variable has been set. But when I try to install from command line:
C:\Temp>R CMD INSTALL --build ROracle_1.1-10.tar.gz
* installing to library 'C:/Users/myaccount/Documents/R/win-library/3.0'
* installing *source* package 'ROracle' ...
** package 'ROracle' successfully unpacked and MD5 sums checked
ERROR: configuration failed for package 'ROracle'
* removing 'C:/Users/myaccount/Documents/R/win-library/3.0/ROracle'
C:\Temp>
When I try to install from source:
> install.packages("ROracle",type = "source")
Warning in install.packages :
package ‘ROracle’ is not available (for R version 3.0.0)
Installing package into ‘C:/Users/myaccount/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.at.r-project.org/src/contrib/ROracle_1.1-10.tar.gz'
Content type 'application/x-gzip' length 168193 bytes (164 Kb)
opened URL
downloaded 164 Kb
* installing *source* package 'ROracle' ...
** package 'ROracle' successfully unpacked and MD5 sums checked
ERROR: configuration failed for package 'ROracle'
* removing 'C:/Users/myaccount/Documents/R/win-library/3.0/ROracle'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-30~1.0/bin/i386/R" CMD INSTALL -l "C:\Users\myaccount\Documents\R\win-library\3.0" C:\Users\myaccount\AppData\Local\Temp\RtmpGggbyp/downloaded_packages/ROracle_1.1-10.tar.gz' had status 1
Warning in install.packages :
installation of package ‘ROracle’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\myaccount\AppData\Local\Temp\RtmpGggbyp\downloaded_packages’
What should I do, how to proceed?
From http://jgilfillan.github.io/2016/05/28/how-to-install-roracle-in-windows-7/
Download binary from oracle:
http://www.oracle.com/technetwork/database/database-technologies/r/roracle/downloads/index.html
The run the following command in r, substituting the file path:
setwd('xxxxx') # set to path of download
install.packages('ROracle_1.2-1.zip', repos = NULL)
Then load the library and use the package - you may have to change XXXX to whatever is in your TNS Names:
library('ROracle')
drv <- dbDriver("Oracle")
con <- dbConnect(drv, "USER GOES HERE", "PASSWORD GOES HERE", dbname='XXX')
test connection:
dbReadTable(con, 'DUAL')
Note that this has also been confirmed to work on Windows 10.
I had this exact problem as well, including the OCI_INC error. They actually talk about it in the INSTALL file in the .tar.gz package, you can read more there.
You have to set the OCI_INC variable to the include directory like this:
set OCI_INC=C:\oracle\product\11.2.0\client_2\oci\include
Or whereever your file is. Here was my complete setup to get things installed from an Admin privileged command line.
set OCI_LIB64=C:\oracle\product\11.2.0\client_2\BIN
set OCI_INC=C:\oracle\product\11.2.0\client_2\oci\include
set PATH=C:\oracle\product\11.2.0\client_2\BIN;C:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;%PATH%
"C:/PROGRA~1/R/R-30~1.1/bin/x64/R" CMD INSTALL --build "C:/Your/Path/To/ROracle_1.1-10.tar.gz"
Also, make sure to change client_2 to client_1 and OCI_LIB64 to OCI_LIB32 if you are trying to do a 32-bit install.
After following the steps (highlighted in red boxes).
I also ran commands below on R.
So, everything went through well on a Windows 7 64-bit, R 3.4 64bit environment.
Sys.setenv(OCI_LIB64="C:/Oracle/instantclient_12_2/")
Sys.setenv(OCI_INC="C:/Oracle/product/11.2.0/client_1/oci/include")
install.packages("ROracle", dep=T)
I had exactly this problem. It was caused because when installing RTools I did not check the 'edit PATH' checkbox. I uninstalled RTools and reinstalled it again, this time making sure the checkbox was checked, and it worked first time! Hope this helps.
I had a similar error when trying to install ROracle from source.1
After searching around a bit I had to undertake what others have mentioned as well as redownloading the tar.gz. When I double checked the download size it was 10KB instead of 234KB.
Re-Download source from: http://cran.r-project.org/web/packages/ROracle/index.html
Updated the following Environmental Varibles in windows
SET PATH=C:\Rtools\bin;C:\Rtools\gcc-4.6.3;%PATH%
SET OCI_INC=C:\Oracle_11G_ClientR2\product\11.2.0\client_1\oci\include
SET OCI_LIB32=C:\Oracle_11G_ClientR2\product\11.2.0\client_1\BIN
SET OCI_LIB64=C:\Oracle_11G_ClientR2\product\11.2.0\client_1\BIN
R CMD INSTALL --build "C:\temp\ROracle_1.1-12.tar.gz"
Output should look like the following:
1 Here is what the previous error looked like:
C:\Temp>R CMD INSTALL --build "C:\\temp\\ROracle_1.1-12.tar.gz"
Error in getOctD(x, offset, len) : invalid octal digit
Along with the 'Basic Package' and the 'ODBC Package', with Oracle 11g, you should copy unpacked files from the 'SDK package' into the subdirectory instantclient_11_2. In this case, you will not need to define the environment variable Sys.setenv (OCI_INC = "...").
This is what worked for me:
Sys.setenv(OCI_LIB32="C:/oracle/product/12.1.0/client_1/BIN/")
Sys.setenv(OCI_INC="C:/oracle/product/12.1.0/client_1/oci/include/")
install.packages("ROracle")
install.packages("P:/Strategic-Primary/documentation/R/Packages/DBI_1.0.0.zip", repos = NULL, type = "win.binary")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
package ‘DBI’ successfully unpacked and MD5 sums checked
> setwd('E:\R\packages')
Error: '\R' is an unrecognized escape in character string starting "'E:\R"
> setwd('E:\\R\\packages')
> install.packages('ROracle-1.3.2.zip')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘ROracle-1.3.2.zip’ is not available (for R version 3.6.0)
> install.packages('ROracle-1.3.1.zip')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘ROracle-1.3.1.zip’ is not available (for R version 3.6.0)
> Sys.setenv(OCI_LIB32="C:/oracle/product/12.1.0/client_1/BIN/")
> Sys.setenv(OCI_INC="C:/oracle/product/12.1.0/client_1/oci/include/")
> install.packages("ROracle")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘ROracle’
These will not be installed
> install.packages('ROracle-1.3.1.zip')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘ROracle-1.3.1.zip’ is not available (for R version 3.6.0)
> install.packages('ROracle-1.3.2.zip')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘ROracle-1.3.2.zip’ is not available (for R version 3.6.0)
I installed SDK, ODBC and basic install client (also set Env variable path) and it is still not working for me. Any advise pls?
I'm trying to install ROracle package on my Windows 7 client. I have Oracle Instant client and Rtools installed, DBI package is istalled, OCI32_LIB environmental variable has been set. But when I try to install from command line:
C:\Temp>R CMD INSTALL --build ROracle_1.1-10.tar.gz
* installing to library 'C:/Users/myaccount/Documents/R/win-library/3.0'
* installing *source* package 'ROracle' ...
** package 'ROracle' successfully unpacked and MD5 sums checked
ERROR: configuration failed for package 'ROracle'
* removing 'C:/Users/myaccount/Documents/R/win-library/3.0/ROracle'
C:\Temp>
When I try to install from source:
> install.packages("ROracle",type = "source")
Warning in install.packages :
package ‘ROracle’ is not available (for R version 3.0.0)
Installing package into ‘C:/Users/myaccount/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.at.r-project.org/src/contrib/ROracle_1.1-10.tar.gz'
Content type 'application/x-gzip' length 168193 bytes (164 Kb)
opened URL
downloaded 164 Kb
* installing *source* package 'ROracle' ...
** package 'ROracle' successfully unpacked and MD5 sums checked
ERROR: configuration failed for package 'ROracle'
* removing 'C:/Users/myaccount/Documents/R/win-library/3.0/ROracle'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-30~1.0/bin/i386/R" CMD INSTALL -l "C:\Users\myaccount\Documents\R\win-library\3.0" C:\Users\myaccount\AppData\Local\Temp\RtmpGggbyp/downloaded_packages/ROracle_1.1-10.tar.gz' had status 1
Warning in install.packages :
installation of package ‘ROracle’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\myaccount\AppData\Local\Temp\RtmpGggbyp\downloaded_packages’
What should I do, how to proceed?
From http://jgilfillan.github.io/2016/05/28/how-to-install-roracle-in-windows-7/
Download binary from oracle:
http://www.oracle.com/technetwork/database/database-technologies/r/roracle/downloads/index.html
The run the following command in r, substituting the file path:
setwd('xxxxx') # set to path of download
install.packages('ROracle_1.2-1.zip', repos = NULL)
Then load the library and use the package - you may have to change XXXX to whatever is in your TNS Names:
library('ROracle')
drv <- dbDriver("Oracle")
con <- dbConnect(drv, "USER GOES HERE", "PASSWORD GOES HERE", dbname='XXX')
test connection:
dbReadTable(con, 'DUAL')
Note that this has also been confirmed to work on Windows 10.
I had this exact problem as well, including the OCI_INC error. They actually talk about it in the INSTALL file in the .tar.gz package, you can read more there.
You have to set the OCI_INC variable to the include directory like this:
set OCI_INC=C:\oracle\product\11.2.0\client_2\oci\include
Or whereever your file is. Here was my complete setup to get things installed from an Admin privileged command line.
set OCI_LIB64=C:\oracle\product\11.2.0\client_2\BIN
set OCI_INC=C:\oracle\product\11.2.0\client_2\oci\include
set PATH=C:\oracle\product\11.2.0\client_2\BIN;C:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;%PATH%
"C:/PROGRA~1/R/R-30~1.1/bin/x64/R" CMD INSTALL --build "C:/Your/Path/To/ROracle_1.1-10.tar.gz"
Also, make sure to change client_2 to client_1 and OCI_LIB64 to OCI_LIB32 if you are trying to do a 32-bit install.
After following the steps (highlighted in red boxes).
I also ran commands below on R.
So, everything went through well on a Windows 7 64-bit, R 3.4 64bit environment.
Sys.setenv(OCI_LIB64="C:/Oracle/instantclient_12_2/")
Sys.setenv(OCI_INC="C:/Oracle/product/11.2.0/client_1/oci/include")
install.packages("ROracle", dep=T)
I had exactly this problem. It was caused because when installing RTools I did not check the 'edit PATH' checkbox. I uninstalled RTools and reinstalled it again, this time making sure the checkbox was checked, and it worked first time! Hope this helps.
I had a similar error when trying to install ROracle from source.1
After searching around a bit I had to undertake what others have mentioned as well as redownloading the tar.gz. When I double checked the download size it was 10KB instead of 234KB.
Re-Download source from: http://cran.r-project.org/web/packages/ROracle/index.html
Updated the following Environmental Varibles in windows
SET PATH=C:\Rtools\bin;C:\Rtools\gcc-4.6.3;%PATH%
SET OCI_INC=C:\Oracle_11G_ClientR2\product\11.2.0\client_1\oci\include
SET OCI_LIB32=C:\Oracle_11G_ClientR2\product\11.2.0\client_1\BIN
SET OCI_LIB64=C:\Oracle_11G_ClientR2\product\11.2.0\client_1\BIN
R CMD INSTALL --build "C:\temp\ROracle_1.1-12.tar.gz"
Output should look like the following:
1 Here is what the previous error looked like:
C:\Temp>R CMD INSTALL --build "C:\\temp\\ROracle_1.1-12.tar.gz"
Error in getOctD(x, offset, len) : invalid octal digit
Along with the 'Basic Package' and the 'ODBC Package', with Oracle 11g, you should copy unpacked files from the 'SDK package' into the subdirectory instantclient_11_2. In this case, you will not need to define the environment variable Sys.setenv (OCI_INC = "...").
This is what worked for me:
Sys.setenv(OCI_LIB32="C:/oracle/product/12.1.0/client_1/BIN/")
Sys.setenv(OCI_INC="C:/oracle/product/12.1.0/client_1/oci/include/")
install.packages("ROracle")
install.packages("P:/Strategic-Primary/documentation/R/Packages/DBI_1.0.0.zip", repos = NULL, type = "win.binary")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
package ‘DBI’ successfully unpacked and MD5 sums checked
> setwd('E:\R\packages')
Error: '\R' is an unrecognized escape in character string starting "'E:\R"
> setwd('E:\\R\\packages')
> install.packages('ROracle-1.3.2.zip')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘ROracle-1.3.2.zip’ is not available (for R version 3.6.0)
> install.packages('ROracle-1.3.1.zip')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘ROracle-1.3.1.zip’ is not available (for R version 3.6.0)
> Sys.setenv(OCI_LIB32="C:/oracle/product/12.1.0/client_1/BIN/")
> Sys.setenv(OCI_INC="C:/oracle/product/12.1.0/client_1/oci/include/")
> install.packages("ROracle")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘ROracle’
These will not be installed
> install.packages('ROracle-1.3.1.zip')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘ROracle-1.3.1.zip’ is not available (for R version 3.6.0)
> install.packages('ROracle-1.3.2.zip')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘ROracle-1.3.2.zip’ is not available (for R version 3.6.0)
I installed SDK, ODBC and basic install client (also set Env variable path) and it is still not working for me. Any advise pls?