I have installed DESeq 2 and it gives this error message:
Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘Rcpp’
I have then tried to install RCPP but it gives the following error message:
1 error generated.
make: *** [api.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp’
Warning in install.packages :
installation of package ‘Rcpp’ had non-zero exit status
I have updated everything I could, R and R studio as well as my mac but the error persists.
Therefore when I try to run the following function of DESeq2 I can't run it and it gives me the following error which I guess is due to not having Rcpp:
dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
+ directory = getwd(),
+ design= ~ replicate + condition )
Error in DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = getwd(), :
could not find function "DESeqDataSetFromHTSeqCount"
Any help or solution on how to solve this?
Thanks a lot!!
Alerie
Related
I just updated the R version from 4.0.4 to 4.1.3.
I have successfully installed
install.packages("agricolae").
But, when I run the syntax
library(agricolae),
The output in RGUI shown:
Warning message: package ‘agricolae’ was built under R version 4.0.5.
Then, the output in RStudio shown:
Error: package or namespace load failed for ‘agricolae’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘magrittr’.
So, I tried to install the packages of "magrittr", but failed. The output in RStudio shown:
The system cannot find the path specified. make: \*\*\* \[pipe.o\] Error 1 ERROR: compilation failed for package 'magrittr'
* removing 'C:/Users/Anna/Documents/R/win-library/4.1/magrittr' Warning in install.packages : installation of package ‘magrittr’ had non-zero exit status\.
How can I install the package of agricolae?
here is the code I am using:
install.packages("jaccard")
library("jaccard")
The error code I receive is:
Error: package or namespace load failed for ‘jaccard’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘qvalue’
In addition: Warning message:
package ‘jaccard’ was built under R version 3.6.3
I try to install the package qvalue and receive the error:
Warning in install.packages :
package ‘qvalue’ is not available (for R version 3.6.2)
I've also tried installing jaccard and qvalue using the code:
install.packages("jaccard", repos="http://cran.rstudio.com/", dependencies=TRUE)
install.packages("qvalue", repos="http://cran.rstudio.com/", dependencies=TRUE)
None of this seems to work and I receive the same errors.
I am trying to do a scatter3d(y ~ x1+ x2), but I am getting the following error:
Loading required namespace: rgl
Failed with error: ‘there is no package called ‘shiny’’
Error in scatter3d(Vent ~ O2 + CO2) : rgl package missing
I have tried to install rgl in the following way:
install.packages("rgl", repos = c("http://rstudio.org/_packages", "http://cran.rstudio.com"))
install.packages("rgl", depositories = TRUE)
Getting this error:
Errore: package or namespace load failed for ‘rgl’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘shiny’
And if I try to install shiny in the same way that I did for rgl, I get the following
ERROR: dependency 'htmltools' is not available for package 'shiny'
* removing 'C:/Users/franc/Documents/R/win-library/3.5/shiny'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘shiny’ had non-zero exit status
ERROR: dependency 'shiny' is not available for package 'shinytest'
* removing 'C:/Users/franc/Documents/R/win-library/3.5/shinytest'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘shinytest’ had non-zero exit status
Does anyone know what is going on and how I can solve this?
Thank you in advance!
I'm trying to install the healthcare ai package after updating the version of R:
install.packages("healthcareai")
library(healthcareai)
But I'm getting the following error:
Error: package or namespace load failed for ‘healthcareai’ in
loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
vI[[j]]): there is no package called ‘ddalpha’
I tried installing the 'ddalpha' but another error
/var/folders/m8/y4hvcvrx4233n10636g64mlh0000gn/T//ccM1OugK.s:6664:2:
error: unknown directive
.stabd 68,0,144
^ /var/folders/m8/y4hvcvrx4233n10636g64mlh0000gn/T//ccM1OugK.s:6670:9:
error: unsupported directive '.stabs'
.stabs "cvkernsm_:F(0,3)",36,0,105,cvkernsm
make: *** [depth.fd.o] Error 1 ERROR: compilation failed for package
‘ddalpha’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ddalpha’
Warning in install.packages : installation of package ‘ddalpha’ had
non-zero exit status
Any help in resolving this issue would be greatly appreciated.
I am trying to install package called plm and i am getting the following error. I already have it installed and I am getting some messy error. any suggestions what I should do?
install.packages("plm", repos="http://R-Forge.R-project.org")
> Error in install.packages : Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
> library(plm)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace ‘pbkrtest’ 0.4-2 is being loaded, but >= 0.4.4 is required
In addition: Warning message:
package ‘plm’ was built under R version 3.2.5
Error: package or namespace load failed for ‘plm’
install.packages("plm", dependencies = TRUE)