I am new to R. I was trying to install the plot3D package. The package doesn't work even after successful instalment. I am using Mac OS. following are the codes used :-
install.packages('plot3D')
library(plot3D)
I got the following error:-
xcrun: error: invalid active developer path
(/Library/Developer/CommandLineTools), missing xcrun at:
/Library/Developer/CommandLineTools/usr/bin/xcrun Error: package or
namespace load failed for ‘plot3D’: .onLoad failed in loadNamespace()
for 'tcltk', details: call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/tcltk/libs/tcltk.so,
0x000A): Library not loaded: /opt/X11/lib/libX11.6.dylib Referenced
from:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/tcltk/libs/tcltk.so
Reason: tried: '/opt/X11/lib/libX11.6.dylib' (no such file),
'/Library/Frameworks/R.framework/Resources/lib/libX11.6.dylib' (no
such file), '/Users/mayank/lib/libX11.6.dylib' (no such file),
'/usr/local/lib/libX11.6.dylib' (no such file),
'/usr/lib/libX11.6.dylib' (no such file), '/lib/libX11.6.dylib' (no
such file),
'/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home/jre/lib/server/libX11.6.dylib'
(no such file), '/var/folders/2j/3rpp744j739 In addition: Warning
message: In system2("/usr/bin/otool", c("-L", shQuote(DSO)), stdout =
TRUE) : running command ''/usr/bin/otool' -L
'/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so''
had status 1
Related
Error: package or namespace load failed for 'DESeq2' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so, 0x0006): Library not loaded: '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib'
Referenced from: '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so'
Reason: tried: '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib' (no such file), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file)
1. Install xcode.
2. Indtal XQuarz
Follow the instruction on this website to install Deseq2: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
This code is important:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
Please post more details if it doesn't work.
I installed ChemmineR and ChemmineOB on my MacOSX (MaxOS Ventura; R version 4.2.1) and got this:
library(ChemmineOB)
Error: package or namespace load failed for ‘ChemmineOB’:
.onLoad failed in loadNamespace() for 'ChemmineOB', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ChemmineOB/libs/ChemmineOB.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ChemmineOB/libs/ChemmineOB.so, 0x000A): Library not loaded: /usr/local/opt/open-babel/lib/libopenbabel.7.dylib
Referenced from: <77D86F2D-1FC2-3CDF-81D4-73A54E882F99> /Library/Frameworks/R.framework/Versions/4.2/Resources/library/ChemmineOB/libs/ChemmineOB.so
Reason: tried: '/usr/local/opt/open-babel/lib/libopenbabel.7.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/opt/open-babel/lib/libopenbabel.7.dylib' (no such file), '/usr/local/opt/open-babel/lib/libopenbabel.7.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libopenbabel.7.dylib' (no such file), '/Users/hanyan/l
So, I tried to install a package ConvergenceConcepts in RStudio and it threw me an error message:
ERROR: lazy loading failed for package ‘ConvergenceConcepts’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ConvergenceConcepts’
and a warning, that the package had non-zero exit status. How could I resolve this?
Error loading ConvergenceConcepts library:
Loading required package: tcltk
xcrun: error: active developer path ("/Library/Developer/CommandLineTools") does not exist
Use `sudo xcode-select --switch path/to/Xcode.app` to specify the Xcode that you wish to use for command line developer tools, or use `xcode-select --install` to install the standalone command line developer tools.
See `man xcode-select` for more details.
Error: package or namespace load failed for ‘tcltk’:
.onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /opt/X11/lib/libX11.6.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/tcltk/libs/tcltk.so
Reason: image not found
Error: package ‘tcltk’ could not be loaded
In addition: Warning message:
In system2("/usr/bin/otool", c("-L", shQuote(DSO)), stdout = TRUE) :
running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' had status 1
Error when I try to add tcltk library:
library(tcltk)
xcrun: error: active developer path ("/Library/Developer/CommandLineTools") does not exist
Use `sudo xcode-select --switch path/to/Xcode.app` to specify the Xcode that you wish to use for command line developer tools, or use `xcode-select --install` to install the standalone command line developer tools.
See `man xcode-select` for more details.
Error: package or namespace load failed for ‘tcltk’:
.onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /opt/X11/lib/libX11.6.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/tcltk/libs/tcltk.so
Reason: image not found
In addition: Warning message:
In system2("/usr/bin/otool", c("-L", shQuote(DSO)), stdout = TRUE) :
running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' had status 1
The following error is displayed:
Unable to find any JVMs matching version "(null)".
No Java runtime present, try --request to install.
Error: package or namespace load failed for ‘qdap’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
Reason: image not found
In addition: Warning message:
In system("/usr/libexec/java_home", intern = TRUE) :
running command '/usr/libexec/java_home' had status 1
I am trying to get extension R to work with mediawiki but have run into a roadblock with the following error:
REngine.php: sh: /usr/bin/R: No such file or directory
Does anyone know how to correct this issue? If I look at mediawiki/Special:Version, I can see R listed under extensions as version 0.14, but if I try to use <R>1:10</R> it throws that error.
After the comment to add a symlink below I was able to get a little further. I added the following symlink to my brew installation of R:
ln -s /usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/bin/R /usr/bin/R
and this was the output:
REngine.php: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library/grDevices/libs/grDevices.so':
dlopen(/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library/grDevices/libs/grDevices.so, 6): Symbol not found: __cg_jpeg_resync_to_restart
Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
Expected in: /mediWiki/common/lib/libJPEG.dylib
in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library/grDevices/libs/grDevices.so':
dlopen(/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library/grDevices/libs/grDevices.so, 6): Symbol not found: __cg_jpeg_resync_to_restart
Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
Expected in: /mediWiki/common/lib/libJPEG.dylib
in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
In addition: Warning message:
package 'grDevices' in options("defaultPackages") was not found
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library/grDevices/libs/grDevices.so':
dlopen(/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library/grDevices/libs/grDevices.so, 6): Symbol not found: __cg_jpeg_resync_to_restart
Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
Expected in: /mediWiki/common/lib/libJPEG.dylib
in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
In addition: Warning message:
package 'graphics' in options("defaultPackages") was not found
During startup - Warning message:
package 'stats' in options("defaultPackages") was not found
<!--- Start of program --->
[1] 1 2 3 4 5 6 7 8 9 10
<!--- End of program --->
Error: could not find function "dev.cur"
Execution halted
Also the code I hae on the mediawiki page is:
Test
<R>1:10</R>