Thanks for taking time to post the question! https://bioconductor.org/packages/3.5/BiocViews.html#___BSgenome lists BSgenomes that can be directly used as input to CRISPRseek .
For detailed information on how to use the package, please read the user guide at http://bioconductor.org/packages/devel/bioc/vignettes/CRISPRseek/inst/doc/CRISPRseek.pdf and the supplementary file in the following publication
Zhu LJ, Holmes BR, Aronin N and Brodsky MH (2014). “CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems.” PLoS one, 9(9). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172692/.
To design guides without available BSgenome, please refer to this post at CRISPRseek with genome not available in BSgenome. It also talks about analyzing data for novel genome using compare2Sequences function https://github.com/Bioconductor-mirror/CRISPRseek/blob/master/man/compare2Sequences.Rd.