Update Description file

.travis.yml

@@ -1,35 +1,27 @@
-# Sample .travis.yml for R projects.
-#
-# See README.md for instructions, or for more configuration options,
-# see the wiki:
-#   https://github.com/craigcitro/r-travis/wiki
-
-language: c
-sudo: required
-
+language: r
+cache: packages
+r: 3.6.1
+warnings_are_errors: false
+r_check_args: "--no-build-vignettes --no-manual --as-cran --no-examples"
+bioc_packages:
+- GenomicRanges
+- rtracklayer
+- GenomicAlignments
+- Biostrings
+- GenomeInfoDb
 before_install:
   - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
   - chmod 755 ./travis-tool.sh
   - ./travis-tool.sh bootstrap
-
-install:
-  - ./travis-tool.sh install_bioc_deps
-  - ./travis-tool.sh install_bioc BSgenome.Hsapiens.UCSC.hg19
-  - ./travis-tool.sh install_deps
-  - ./travis-tool.sh install_github r-lib/covr
-  - ./travis-tool.sh install_github mskilab/gUtils
-  - ./travis-tool.sh install_github mskilab/bamUtils
-  - ./travis-tool.sh install_github mskilab/gTrack
-
-script: ./travis-tool.sh run_tests
-
+  - export R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE
+script: "./travis-tool.sh run_tests"
 after_failure:
-  - ./travis-tool.sh dump_logs
-
+  - "./travis-tool.sh dump_logs"
 after_success:
-  - Rscript -e 'covr::codecov()'
-
-notifications:
-  email:
-    on_success: change
-    on_failure: change
+- travis_wait Rscript -e 'covr::codecov()'
+env:
+  global:
+  - R_CHECK_ARGS="--no-build-vignettes --no-manual --as-cran --no-examples"
+  - _R_CHECK_TESTS_NLINES_=0
+  - R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE
+  - _R_CHECK_FORCE_SUGGESTS_=false

DESCRIPTION

@@ -7,7 +7,15 @@ Authors@R: c(person(given = "Jeremiah", family = "Wala", role = c("aut"), email
     family = "Imielinski", role = c("aut", "cre"), email =
     "[email protected]"))
 Description: R package providing additional capabilities and speed for GenomicRanges operations.
-biocViews:
+Remotes: 
+  github::mskilab/gUtils,
+  github::mskilab/gTrack,
+  github::mskilab/bamUtils,
+  bioc::3.10/GenomicRanges,
+  bioc::3.10/rtracklayer,
+  bioc::3.10/GenomicAlignments,
+  bioc::3.10/Biostrings,
+  bioc::3.10/GenomeInfoDb
 Depends:
     R (>= 3.1.0),
     GenomicRanges (>= 1.18),
@@ -22,8 +30,9 @@ Imports:
     gTrack
 Suggests:
     BSgenome.Hsapiens.UCSC.hg19,
-    testthat,
+    covr,
+    testthat
 License: GPL-2
-BugReports: http://github.com/mskilab/gUtils/issues
+BugReports: http://github.com/mskilab/gChain/issues
 LazyData: true
 RoxygenNote: 7.1.0

R/gChain.R

@@ -3077,3 +3077,4 @@ gr.tostring = function(gr, places = 2, interval = 1e6, unit = 'MB', prefix = 'ch
 
 
 
+

tests/testthat/test_gChain.R

@@ -5,7 +5,7 @@ library(gUtils)
 library(gTrack)
 
 
-Sys.setenv(DEFAULT_BSGENOME = "BSgenome.Hsapiens.UCSC.hg19::Hsapiens")
+#Sys.setenv(DEFAULT_BSGENOME = "BSgenome.Hsapiens.UCSC.hg19::Hsapiens")
 
 
 gr = GRanges(1, IRanges(c(3,7,13), c(5,9,16)), strand=c('+','-','-'), seqinfo=Seqinfo("1", 25), name=c("A","B","C"))