fix

R/RcppExports.R

@@ -181,16 +181,14 @@ tableFormat <- function(vcffile, region, samples, format, ids, qualval, pass, IN
 #' \itemize{ \item Parameter: line - A string for a line in the variant of VCF. Not ended with "newline" }
 #' @field close Close and save the vcf file
 #' @examples
-#' outvcf <- file.path(tempdir(), "test_vcfwriter.vcf.gz")
-#' file.create(outvcf)
+#' outvcf <- file.path(paste0(tempfile(), ".vcf.gz"))
 #' bw <- vcfwriter$new(outvcf, "VCF4.3")
 #' bw$addContig("chr20")
-#' bw$addINFO("AF", "A", "Float", "Estimated allele frequency in the range (0,1)");
 #' bw$addFORMAT("GT", "1", "String", "Genotype");
 #' bw$addSample("NA12878")
 #' bw$addSample("NA12879")
-#' s1 <- "chr20\t2006060\trs146931526\tG\tC\t100\tPASS\tAF=0.04\tGT\t1|0\t1|1"
+#' s1 <- "chr20\t2006060\trs146931526\tG\tC\t100\tPASS\t.\tGT\t1|0\t1|1"
+#' tryCatch((bw$writeline(s1)), error=function(e) e)
 #' bw$close()
-#' file.remove(outvcf)
 NULL
 

src/vcf-writer.cpp

@@ -37,18 +37,15 @@ using namespace std;
 //' \itemize{ \item Parameter: line - A string for a line in the variant of VCF. Not ended with "newline" }
 //' @field close Close and save the vcf file
 //' @examples
-//' outvcf <- file.path(tempdir(), "test_vcfwriter.vcf.gz")
-//' file.create(outvcf)
+//' outvcf <- file.path(paste0(tempfile(), ".vcf.gz"))
 //' bw <- vcfwriter$new(outvcf, "VCF4.3")
 //' bw$addContig("chr20")
-//' bw$addINFO("AF", "A", "Float", "Estimated allele frequency in the range (0,1)");
 //' bw$addFORMAT("GT", "1", "String", "Genotype");
 //' bw$addSample("NA12878")
 //' bw$addSample("NA12879")
-//' s1 <- "chr20\t2006060\trs146931526\tG\tC\t100\tPASS\tAF=0.04\tGT\t1|0\t1|1"
+//' s1 <- "chr20\t2006060\trs146931526\tG\tC\t100\tPASS\t.\tGT\t1|0\t1|1"
 //' tryCatch((bw$writeline(s1)), error=function(e) e)
 //' bw$close()
-//' file.remove(outvcf)
 class vcfwriter {
    public:
     vcfwriter(std::string vcffile, std::string version) : bw(vcffile, version) {}

tests/testthat/test-vcf-writer.R

@@ -1,17 +1,14 @@
 library(testthat)
 
 test_that("vcfwriter: writing variant works", {
-  skip_on_os(c("windows"), arch = NULL)
-  outvcf <- file.path(tempdir(), "test_vcfwriter.vcf.gz")
-  file.create(outvcf)
+  ## skip_on_os(c("windows"), arch = NULL)
+  outvcf <- file.path(paste0(tempfile(), ".vcf.gz"))
   bw <- vcfwriter$new(outvcf, "VCF4.3")
   bw$addLine('##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">')
   bw$addContig("chr20")
   bw$addFILTER("PASS", "All filters passed")
   bw$addINFO("AF", "A", "Float", "Estimated allele frequency in the range (0,1)");
-  bw$addFORMAT("GT", "1", "String", "Genotype");
-  bw$addSample("NA12878")
-  s1 <- "chr20\t2006060\trs146931526\tG\tC\t100\tPASS\tAF=0.000998403\tGT\t1|0"
+  s1 <- "chr20\t2006060\trs146931526\tG\tC\t100\tPASS\t."
   bw$writeline(s1)
   bw$close()
   ## tests