# HG changeset patch
# User lecorguille
# Date 1556532921 14400
# Node ID 00be6777edc5b34237c2b134b9c41a166c2cd318
# Parent  1d2cc6c87acf925d79aecd4cece73d190db24b99
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01

diff -r 1d2cc6c87acf -r 00be6777edc5 README.rst
--- a/README.rst	Fri Feb 08 10:04:57 2019 -0500
+++ b/README.rst	Mon Apr 29 06:15:21 2019 -0400
@@ -2,9 +2,11 @@
 Changelog/News
 --------------
 
-**Version 3.4.3.0 - 08/02/2019**
+.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
-- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3
+**Version 3.4.4.0 - 08/02/2019**
+
+- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
 
 **Version 3.0.0.0 - 14/02/2018**
 
diff -r 1d2cc6c87acf -r 00be6777edc5 abims_xcms_summary.xml
--- a/abims_xcms_summary.xml	Fri Feb 08 10:04:57 2019 -0500
+++ b/abims_xcms_summary.xml	Mon Apr 29 06:15:21 2019 -0400
@@ -8,8 +8,7 @@
     </macros>
 
     <requirements>
-        <requirement type="package" version="3.0.0">bioconductor-xcms</requirement>
-        <requirement type="package" version="1.32.0">bioconductor-camera</requirement>
+        <requirement type="package" version="1.38.1">bioconductor-camera</requirement>
         <requirement type="package" version="1.1_4">r-batch</requirement>
     </requirements>
 
@@ -87,9 +86,11 @@
 Changelog/News
 --------------
 
-**Version 3.4.3.0 - 08/02/2019**
+.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
-- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3
+**Version 3.4.4.0 - 08/02/2019**
+
+- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
 
 **Version 3.0.0.0 - 14/02/2018**
 
diff -r 1d2cc6c87acf -r 00be6777edc5 lib.r
--- a/lib.r	Fri Feb 08 10:04:57 2019 -0500
+++ b/lib.r	Mon Apr 29 06:15:21 2019 -0400
@@ -69,7 +69,7 @@
             chromBPI_adjusted_merged <- chromBPI_adjusted
         } else {
             if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
-            else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
+            else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata)
             else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
 
             singlefile_merged <- c(singlefile_merged,singlefile)
@@ -333,7 +333,7 @@
     files[exists] <- sub("//","/",files[exists])
 
     # WHAT IS ON THE FILESYSTEM
-    filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
+    filesystem_filepaths <- system(paste0("find \"",getwd(),"/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
     filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
 
     # COMPARISON
diff -r 1d2cc6c87acf -r 00be6777edc5 macros_xcms.xml
--- a/macros_xcms.xml	Fri Feb 08 10:04:57 2019 -0500
+++ b/macros_xcms.xml	Mon Apr 29 06:15:21 2019 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
 
-    <token name="@WRAPPER_VERSION@">3.4.3</token>
+    <token name="@WRAPPER_VERSION@">3.4.4</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement>
diff -r 1d2cc6c87acf -r 00be6777edc5 test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html
--- a/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html	Fri Feb 08 10:04:57 2019 -0500
+++ b/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html	Mon Apr 29 06:15:21 2019 -0400
@@ -84,7 +84,7 @@
 <h2>Informations about the XCMSnExp object:</h2>
 <div><pre>
 MSn experiment data ("XCMSnExp")
-Object size in memory: 1.36 Mb
+Object size in memory: 1.41 Mb
 - - - Spectra data - - -
  MS level(s): 1 
  Number of spectra: 5112 
@@ -136,7 +136,7 @@
 Profile settings: method = bin
                   step = 0.1
 
-Memory usage: 2.98 MB
+Memory usage: 3.11 MB
 </pre></div>
 <h2>Citations:</h2>
 <div><ul>