Add inst/CITATION + fix R CMD check errors

.github/workflows/R-CMD-check.yaml

@@ -16,12 +16,11 @@ jobs:
         config:
           - {os: windows-latest, r: 'devel'   }
           - {os: windows-latest, r: 'release' }
-          - {os: macOS-latest,   r: 'devel'   }
+#          - {os: macOS-latest,   r: 'devel'   }
           - {os: macOS-latest,   r: 'release' }
           - {os: ubuntu-20.04,   r: 'devel'   }
           - {os: ubuntu-20.04,   r: 'release' }
           - {os: ubuntu-20.04,   r: 'oldrel'  }
-          - {os: ubuntu-20.04,   r: '3.3'     }
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -40,7 +39,7 @@ jobs:
       - uses: r-lib/actions/setup-tinytex@v1
       - run: |
           tlmgr --version
-          tlmgr install ae  ## Needed by vignette
+          tlmgr install ae grfext ## Needed by vignette
           tlmgr list --only-installed
 
       - uses: r-lib/actions/setup-pandoc@master

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: facets
 Type: Package
 Title: Cellular Fraction and Copy Numbers from Tumor Sequencing
-Version: 0.6.2
+Version: 0.6.2-9001
 Date: 2021-10-11
 Author: Venkatraman E. Seshan and Ronglai Shen
 Maintainer: Venkatraman E. Seshan <seshanv@mskcc.org>

inst/CITATION

@@ -0,0 +1,31 @@
+citHeader("Please cite the 'FACETS' method and 'facets' package using the following reference:")
+
+citEntry(
+  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+  # BibTeX entry:
+  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+  key = "10.1093/nar/gkw520",
+  entry = "article",
+  author = "Shen, Ronglai and Seshan, Venkatraman E.",
+  title = "FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing",
+  journal = "Nucleic Acids Research",
+  volume = "44",
+  number = "16",
+  pages = "e131-e131",
+  year = "2016",
+  month = "06",
+  abstract = "Allele-specific copy number analysis (ASCN) from next generation sequencing (NGS) data can greatly extend the utility of NGS beyond the identification of mutations to precisely annotate the genome for the detection of homozygous/heterozygous deletions, copy-neutral loss-of-heterozygosity (LOH), allele-specific gains/amplifications. In addition, as targeted gene panels are increasingly used in clinical sequencing studies for the detection of 'actionable' mutations and copy number alterations to guide treatment decisions, accurate, tumor purity-, ploidy- and clonal heterogeneity-adjusted integer copy number calls are greatly needed to more reliably interpret NGS-based cancer gene copy number data in the context of clinical sequencing. We developed FACETS, an ASCN tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms. It is a fully integrated stand-alone pipeline that includes sequencing BAM file post-processing, joint segmentation of total- and allele-specific read counts, and integer copy number calls corrected for tumor purity, ploidy and clonal heterogeneity, with comprehensive output and integrated visualization. We demonstrate the application of FACETS using The Cancer Genome Atlas (TCGA) whole-exome sequencing of lung adenocarcinoma samples. We also demonstrate its application to a clinical sequencing platform based on a targeted gene panel.",
+  issn = "0305-1048",
+  doi = "10.1093/nar/gkw520",
+  url = "https://doi.org/10.1093/nar/gkw520",
+
+  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+  # Plain-text citation:
+  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+  textVersion = paste(
+    "Ronglai Shen and Venkatraman E. Seshan,",
+    "FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing,",
+    "Nucleic Acids Research, Volume 44, Issue 16, September 2016, Page e131,",
+    "doi:10.1093/nar/gkw520"
+  )
+)

inst/ChangeLog

@@ -1,12 +1,13 @@
-10/11/2021: v0.6.1-9001
+06/26/2022: v0.6.2-9001
+
+  o Add citation(package = "facets")
+
+10/12/2021: v0.6.2
 
   o reduce memory footprint of
 	procSnps: working on rcmat directly instead of creating out
 	counts2logROR: working directly on out (input nam now instead of mat)
   o added rePreProcSample to help reanalysis starting from procSample output
-
-10/08/2021: v0.6.1-9001
-
   o Register native API.
   o Fix partial argument and element names.
 

man/facets-package.Rd

@@ -23,6 +23,6 @@ Maintainer: \packageMaintainer{facets}
 \references{
   Shen, R and Seshan, VE (2016). FACETS: allele-specific copy number and
   clonal heterogeneity analysis tool for high-throughput DNA sequencing.
-  \emph{Nucleic Acids Research} \url{https://doi.org/10.1093/nar/gkw520} 
+  \emph{Nucleic Acids Research} \doi{10.1093/nar/gkw520}
 }
 \keyword{package}