Hi

This question may be naive, but I can't figure out why Rsamtools can't find pileup function. 

> library(RNAseqData.HNRNPC.bam.chr14)

> fl<-RNAseqData.HNRNPC.bam.chr14_BAMFILES[1]

> bf<-BamFile(fl)

> chr14_seqinfo<-seqinfo(bf)["chr14"]

> (end_coord<-seqlengths(chr14_seqinfo)/2)

   chr14 

53674770 

> sbp<-ScanBamParam(which=GRanges("chr14",IRanges(1,end_coord)))

> res<-pileup(fl,scanBamParam=sbp)

Error: could not find function "pileup"

> traceback()

No traceback available 

> sessionInfo()

R version 3.3.0 (2016-05-03)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 14.04.5 LTS


locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    

 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       


attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods  

[8] base     


other attached packages:

[1] RNAseqData.HNRNPC.bam.chr14_0.2.0 Rsamtools_1.16.1                 

[3] Biostrings_2.32.1                 XVector_0.4.0                    

[5] GenomicRanges_1.16.4              GenomeInfoDb_1.0.2               

[7] IRanges_1.22.10                   BiocGenerics_0.10.0              


loaded via a namespace (and not attached):

[1] zlibbioc_1.10.0 bitops_1.0-6    stats4_3.3.0   






root@ip-172-31-37-127:~# R --version

R version 3.3.0 (2016-05-03) -- "Supposedly Educational"

Copyright (C) 2016 The R Foundation for Statistical Computing

Platform: x86_64-pc-linux-gnu (64-bit)


R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under the terms of the

GNU General Public License versions 2 or 3.

For more information about these matters see

http://www.gnu.org/licenses/.

You have to load Rsamtools before you can call any functions from that package.

Rsamtools v. 1.16.1 did not contain pileup; your Bioconductor version is (quite!) old. The current version of Rsamtools is 1.24.0, BiocInstaller::biocVersion() 3.4.

When you start R and load the BiocInstaller package, you should see a message that 'BiocInstaller version xx is too old for R version 3.3.0". You could update your version of BiocInstaller by following the instructions at https://bioconductor.org/install/#troubleshoot-biocinstaller

(It's rarely necessary to run R as root).

That fixed the problem. Rsamtools v. 1.16.1 did not contain pileup. It's working now.

Not sure why I had an old version of BioC, since I just installed it. 

Thanks guys, you are great!!!