diff --git a/MD5 b/MD5 index afc4752..a2d3769 100644 --- a/MD5 +++ b/MD5 @@ -4,12 +4,12 @@ dc74f3941cd7eb5d5d2820a78e855291 *NEWS 0090c3e305006e38f8ec8cef5616a3e2 *R/bayes.R 1c95cfc1a6597466e42c386b0c6a6196 *R/extract.R c37085ee8b851dfd42eea66341904e82 *R/fit.R -06b55a573555d6e0315478fb47fd48c0 *R/gcstats.R +594c9ccd9c0816666791fb018756c2b2 *R/gcstats.R 3ad97d0891d98e23cd5be6b4417067c5 *R/graphics.R 79624c9cf668bfb2b05e8a339e98f393 *R/misc.R 4b7f3320bad5b252cc0727ba9e019ab8 *R/model.R 8ab48098af7628c6d2f155b8f9f24b74 *R/mutations.R -1415cb2b3e892624fb7ea4ff76a2c46f *R/read.R +574485fa2da5de558b74b117512a84a7 *R/read.R bfe91a98d0c94dab8ae8bcb554eb5acd *R/results.R f763a946f45e700642201c486263b969 *R/segments.R 0359f75dbcc67975a0a8654cc04e32a3 *R/solutions.R diff --git a/R/gcstats.R b/R/gcstats.R index 9c7b0fa..c6a5e1b 100644 --- a/R/gcstats.R +++ b/R/gcstats.R @@ -22,7 +22,7 @@ gc.sample.stats <- function(file, col_types = "c--dd----d----", message("Collecting GC information ", appendLF = FALSE) } res <- chunk.apply(input = con, FUN = parse_chunck, col_types = col_types, - CH.MAX.SIZE = buffer, parallel = parallel) + CH.MAX.SIZE = buffer, CH.PARALLEL = parallel) close(con) if (verbose){ message(" done\n") diff --git a/R/read.R b/R/read.R index 6de1968..11e120a 100644 --- a/R/read.R +++ b/R/read.R @@ -43,7 +43,7 @@ read.seqz.chr <- function(file, chr_name, col_names, } res <- chunk.apply(input = con, FUN = parse_chunck, chr_name = chr_name, col_names = col_names, col_types = col_types, CH.MAX.SIZE = buffer, - parallel = parallel) + CH.PARALLEL = parallel) close(con) res } diff --git a/README.md b/README.md new file mode 100644 index 0000000..afd1914 --- /dev/null +++ b/README.md @@ -0,0 +1,11 @@ +Solve the following issues: +
+Collecting GC information Error in (function (x, col_types) : unused argument (parallel = 1) +
+Calls: main ... preprocess.seqz -> sequenza.extract -> gc.sample.stats -> chunk.apply +
+Execution halted + +The reason: +
+The "chunk.apply" function from R iotools package with new version does not have "parallel" parameter which has been changed to "CH.PARALLEL"