Could not find function "printPerf"
Issue #75
resolved
Dear All,
I was trying to run the following codes but came across an error:
> source('http://portal.nersc.gov/dna/RD/Metagenome_RD/MetaBAT/Files/benchmark.R')
Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install
> # Recall: Genome completeness
> # Precision: contamination or purity
>
>
> # Set working directory
> setwd("/home/tanshiming/Downloads/tmp/sorted-bam/output-lineage")
>
> printPerf(list(calcPerfBySCG("CheckM.txt", removeStrain=F)),
+ rec=c(seq(.1,.9,.1),.95), prec=c(seq(.6,.9,.1),.95,.99))
Error in printPerf(list(calcPerfBySCG("CheckM.txt", removeStrain = F)), :
could not find function "printPerf"
I tried this as well:
> BiocManager::install("printPerf")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'printPerf'
installation path not writeable, unable to update packages: class, codetools, KernSmooth,
lattice, MASS, Matrix, mgcv, nlme, nnet, spatial, survival
Warning message:
package ‘printPerf’ is not available (for R version 3.6.1)
Is there a way I could download 'printPerf' without downgrading my version of R?
Thank you.
Comments (2)
-
-
- changed status to resolved
This benchmark.R file is now also in the repository under the opt subdirectory.
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Hi,
printPerf is implemented in this file, line #592
https://portal.nersc.gov/dna/RD/Metagenome_RD/MetaBAT/Files/benchmark.R
you can view it online and use it as you want.