.writeImzMlDocument doesn't pass the 'processed' argument to .addIbdOffsets

[SvenSondhauss]

In the .writeImzMlDocument function, .addIbdOffsets gets called without the processed argument, leading to .addIbdOffsets using always the default (=TRUE). Subsequently, a wrong imzml file is created,
which makes the exported data unusable.
Original function:

.writeImzMlDocument <- function(x, file,
                                id=.withoutFileExtension(basename(file)),
                                processed=TRUE, uuid=.uuid(),
                                coordinates=MALDIquant::coordinates(x),
                                pixelSize=c(metaData(x[[1L]])$imaging$pixelSize,
                                            100, 100)[1L:2L], ...) {

...

  .writeMzMlDocument(x=.addIbdOffsets(x), file=file, id=id,
                     imsArgs=list(uuid=uuid, sha1=sha1, processed=processed),
                     ...)
}

Suggested fix:

.writeImzMlDocument <- function(x, file,
                                id=.withoutFileExtension(basename(file)),
                                processed=TRUE, uuid=.uuid(),
                                coordinates=MALDIquant::coordinates(x),
                                pixelSize=c(metaData(x[[1L]])$imaging$pixelSize,
                                            100, 100)[1L:2L], ...) {

...

  .writeMzMlDocument(x=.addIbdOffsets(x, processed=processed), file=file, id=id,
                     imsArgs=list(uuid=uuid, sha1=sha1, processed=processed),
                     ...)
}

[sgibb]

@SvenSondhauss thanks for reporting and fixing this. I applied your suggested fix. Unfortunately CRAN doesn't accept to frequent updates. So could you please install the most recent version of MALDIquantForeign from github via devtools::install_github("sgibb/MALDIquantForeign")?

[sgibb]

@SvenSondhauss just want to inform you that MALDIquantForeign 0.11.1 is on CRAN now. So no need to use install_github anymore.