@@ -103,9 +103,9 @@

             ## issue #151: CV param ?? is not valid.

             ## if (length(z) == 2)

             ##     z <- c(z, "MS:-1")

-            if (length(z) < 2)

+            if (length(z) < 3)

                 stop("Each element in 'software_processing' has to be of ",

-                     "length >= 2")

+                     "length >= 3")

             z

         }

         x <- lapply(x, check_element)

@@ -178,7 +178,7 @@ copyWriteMSData <- function(object, file, original_file, header,

     ## Check software_processing:

     software_processing <- .check_software_processing(software_processing)

     ## Add mzR processing:

-    mzR <- c("mzR", paste(packageVersion("mzR"), collapse = "."))

+    mzR <- c("mzR", paste(packageVersion("mzR"), collapse = "."), "MS:-1")

     if (outformat == "mzml")

         mzR <- c(mzR, "MS:1000544")

     if (outformat == "mzxml")

@@ -48,8 +48,9 @@ test_validSpectrumList <- function() {

 test_check_software_processing <- function() {

     checkException(mzR:::.check_software_processing("a"))

-    res <- mzR:::.check_software_processing(c("mzR", "1.0.0"))

+    res <- mzR:::.check_software_processing(c("mzR", "1.0.0", "MS:-1"))

     checkEquals(class(res), "list")

-    checkEquals(res, list(c("mzR", "1.0.0")))

+    checkEquals(res, list(c("mzR", "1.0.0", "MS:-1")))

+    checkException(mzR:::.check_software_processing(c("mzR", "1.0.0")))

     checkException(mzR:::.check_software_processing(c(3, 5)))

 }

@@ -40,9 +40,9 @@ test_mzML <- function() {

     checkTrue(any(colnames(hdr) == "spectrumId"))

     checkTrue(all(hdr$centroided))

     checkEquals(hdr$spectrumId, paste0("spectrum=", hdr$acquisitionNum))

-    hdr <- header(mzxml,1)

+    hdr <- header(mzml,1)

     checkTrue(is.list(hdr))

-    hdr <- header(mzxml, 2:3)

+    hdr <- header(mzml, 2:3)

     checkTrue(is.data.frame(hdr))

     checkTrue(nrow(hdr) == 2)

@@ -250,7 +250,7 @@ test_copyWriteMSData <- function() {

     out_file <- paste0(test_folder, "test_copyWrite.mzML")

     mzR::copyWriteMSData(file = out_file, original_file = test_file,

                          header = hdr, object = pks,

-                         software_processing = c("MSnbase", "2.3.8"))

+                         software_processing = c("MSnbase", "2.3.8", "MS:-1"))

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -264,7 +264,7 @@ test_copyWriteMSData <- function() {

     out_file <- paste0(test_folder, "test_copyWrite.mzXML")

     mzR::copyWriteMSData(file = out_file, original_file = test_file,

                          header = hdr, object = pks, outformat = "mzXML",

-                         software_processing = c("MSnbase", "2.3.8"))

+                         software_processing = c("MSnbase", "2.3.8", "MS:-1"))

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -543,7 +543,8 @@ void RcppPwiz::writeSpectrumList(const string& file, const string& format,

  * o soft_proc: is supposed to be a character vector of length >= 2:

  *   soft_proc[0]: The software name (required).

  *   soft_proc[1]: The software version (required).

- *   soft_proc[2]: The CV ID of the software. Use "-1" if not known.

+ *   soft_proc[2]: The CV ID of the software. Use "MS:-1" if not known, in 

+ *                 which case we are NOT writing the corresponding CV element.

  *   soft_proc[3-length]: CV IDs of the processing steps (optional). 

  */

 void RcppPwiz::addDataProcessing(MSData& msd, Rcpp::StringVector soft_proc) {

@@ -552,8 +553,10 @@ void RcppPwiz::addDataProcessing(MSData& msd, Rcpp::StringVector soft_proc) {

   new_soft->version = soft_proc(1);

   int soft_proc_size = soft_proc.size();

   if (soft_proc_size > 2) {

-    CVTermInfo cv_term = cvTermInfo(soft_proc(2));

-    new_soft->set(cv_term.cvid);

+    if (soft_proc(2) != "MS:-1") {

+      CVTermInfo cv_term = cvTermInfo(soft_proc(2));

+      new_soft->set(cv_term.cvid);

+    }

   }

   // Order: get the number of already present dataProcessingPtrs and

   // increment