Hi, I have a dataset from mogene20st platform. I am able to use the oligo package and read the celfiles and get the annotations. I am unable to use the brainarray CDF to read the celfiles. I realized that it's not added in pdInfobuilder. I referred to other posts where the cdf has been Pdinfobuilder. https://support.bioconductor.org/p/72378/
I followed the same steps and created z and seed. I am not able to install it. This is the error that R is throwing me.
> install.packages("pd.mogene21stmmense/", type="source",repos = NULL) * installing *source* package ‘pd.mogene21stmmense’ ... ** R ** byte-compile and prepare package for lazy loading Warning: package ‘Biostrings’ was built under R version 3.5.2 Error in eval(exprs[i], envir) : Unable to locate DB file Error : unable to load R code in package ‘pd.mogene21stmmense’ ERROR: lazy loading failed for package ‘pd.mogene21stmmense’ * removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/pd.mogene21stmmense’ Warning in install.packages : installation of package ‘pd.mogene21stmmense/’ had non-zero exit status
Here is my code.
library(pdInfoBuilder) library(ff) library(doMC) registerDoMC(10) download.file("http://mbni.org/customcdf/19.0.0/ense.download/mogene21st_Mm_ENSE_19.0.0.zip","tmp.zip") unzip("tmp.zip") dir() z <- cdf2table("mogene21st_Mm_ENSE.cdf") seed <- new("GenericPDInfoPkgSeed", table=z, author = "me", email = "email@example.com", species = "Mus musculus", pkgName = "pd.mogene21stmmense") makePdInfoPackage(seed) install.packages("pd.mogene21stmmense/", type="source",repos = NULL)
Thanks in advance