v1.2.6.2

qzhang503 · Jun 1, 2023 · 2bb14b5 · 2bb14b5
1 parent 55711a5
commit 2bb14b5
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Showing 22 changed files with 388 additions and 226 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: mzion
 Type: Package
 Title: Database Searches of Proteomic Mass-spectrometrirc Data
-Version: 1.2.6.1
+Version: 1.2.6.2
 Authors@R: 
     person(given = "Qiang",
            family = "Zhang",

diff --git a/R/mgfs.R b/R/mgfs.R
@@ -97,7 +97,7 @@ load_mgfs <- function (out_path, mgf_path, min_mass = 200L, max_mass = 4500L,
 
   delete_files(
     out_path, 
-    ignores = c("\\.[Rr]$", "\\.(mgf|MGF)$", "\\.xlsx$", 
+    ignores = c("\\.[Rr]$", "\\.(mgf|MGF)$", "\\.mzML$", "\\.xlsx$", 
                 "\\.xls$", "\\.csv$", "\\.txt$", "\\.tsv$", 
                 "^mgf$", "^mgfs$", "Calls", 
                 # in case of reprocessing after proteoQ
@@ -1339,8 +1339,8 @@ readmzML <- function (filepath = NULL, filelist = NULL,
   # parallel here
   files <- file.path(filepath, filelist)
   sizes <- max(unlist(lapply(files, file.size)))/1024^3
-  # n_cores <- min(detect_cores(16L), floor((max_ram <- 32)/(sizes * 8)), len)
-  n_cores <- min(detect_cores(32L), floor((find_free_mem()/1024)/(sizes * 8)), len)
+  # n_cores <- min(detect_cores(32L), floor((find_free_mem()/1024)/(sizes * 8)), len)
+  n_cores <- min(detect_cores(32L), floor((find_free_mem()/1024)/(sizes * 8)) + 1L, len)
   n_cores <- max(1L, n_cores)
 
   if (n_cores == 1L) {