Hi Jonathon, Have you considered depending on Rhtslib? See https://bioconductor.org/packages/Rhtslib
Rsamtools itself is implemented on top of Rhtslib. Note that other Bioconductor packages (e.g. DiffBind, deepSNV, BitSeq, qrqc, QuasR, seqbias, TransView, etc...) use Rhtslib internally to implement features not implemented in Rsamtools. H. On 8/23/19 11:05, Jonathon Hill wrote: > Hi, > > I am working through the process of submitting a new package (MMAPPR2). We > are having a problem with the build failing, because our package requires > Samtools installed. We cannot use Rsamtools, as we depend on features not > implemented in the package. How do we resolve the issue? What is the policy > for system dependencies? We have samtools listed in the DESCRIPTION and > installation instructions in our README, but I am sure that is not enough to > get it installed on the Build and Check servers. > > Thanks, > > Jonathon Hill > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AEKZKMjjFTbu5U_zn0bacvzv69lx_S5s7Yb6dSOXbJs&s=s5EMLCdAbnqgXWs3_-Sxm52Zuc3pqFirWz7z3ymBruU&e= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
