'Error: could not find function runmean' from an installed package: caTools?

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'Error: could not find function runmean' from an installed package: caTools?



I installed 'caTools' R package through the command line:


$ R
$ install.packages("caTools", lib="~/R/library")



Then, did this command:


INPUT=/home/user/file.bam
OUTPUT=/home/user/file_cor.bam
Rscript run_spp_nodups.R -c=$INPUT -savp -out=$OUTPUT



And got the error:


Error: could not find function "runmean"
Execution halted



The function 'runmean' belongs to package I installed, 'caTools'.
The R version is appropriate, as R in my machine is version 3.3.2 and 'caTools' depends on R (≥ 2.2.0).



The R code of 'run_spp_nodups.R' is to big to paste here. I show only the part with runmean:


# Smooth the cross-correlation curve if required
cc <- crosscorr$cross.correlation
crosscorr$min.cc <- crosscorr$cross.correlation[ length(crosscorr$cross.correlation$y) , ] # minimum value and shift of cross-correlation
cat("Minimum cross-correlation value", crosscorr$min.cc$y,"n",file=stdout())
cat("Minimum cross-correlation shift", crosscorr$min.cc$x,"n",file=stdout())
sbw <- 2*floor(ceiling(5/iparams$sep.range[2]) / 2) + 1 # smoothing bandwidth
cc$y <- runmean(cc$y,sbw,alg="fast")



What's happening and how to solve it?





You've failed to supply your R code for the run_spp.R script - we aren't able to tell you exactly why if we can't see what you are attempting to run.
– zacdav
Aug 6 at 9:09


run_spp.R





Add library(caTools) in front of your code to activate your package.
– jaySf
Aug 6 at 9:09


library(caTools)





I only added the part with runmean cause the Rscript is too big, it exceeds the limit of words to post
– salamandra
Aug 6 at 9:32





don't know how can I add library(caTools) from the commandline? Or are you suggesting to add in the script?
– salamandra
Aug 6 at 9:32






Sure, add it into the script, the code needs activated library in order to run.
– jaySf
Aug 6 at 13:35









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