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re-apply clang compile fix after pwiz upgrade, closes #263

Steffen Neumann authored on 14/03/2022 10:47:04
Showing3 changed files

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@@ -2,7 +2,7 @@ Package: mzR
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 Type: Package
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 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
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        (mass spectrometry data)
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-Version: 2.29.3
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+Version: 2.29.4
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 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
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 Authors@R: c(
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     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
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@@ -12,10 +12,7 @@ Authors@R: c(
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     )
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 Description: mzR provides a unified API to the common file formats and
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         parsers available for mass spectrometry data. It comes with a
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-        wrapper for the ISB random access parser for mass spectrometry
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-        mzXML, mzData and mzML files. The package contains the
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-        original code written by the ISB, and a subset of the
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-        proteowizard library for mzML and mzIdentML. The netCDF
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+        subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF
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         reading code has previously been used in XCMS.
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 License: Artistic-2.0
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 LazyLoad: yes
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@@ -1,3 +1,8 @@
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+CHANGES IN VERSION 2.29.4
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+-------------------------
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+ o Re-apply fix for compile error on clang by Kurt Hornik, closes #263
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+ o Remove text in DESCRIPTION hinting at the RAMP wrapper for mzData removed in 2.29.3
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+
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 CHANGES IN VERSION 2.29.3
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 -------------------------
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  o Update to Proteowizard 3_0_21263
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@@ -6,7 +11,7 @@ CHANGES IN VERSION 2.29.3
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 CHANGES IN VERSION 2.29.2
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 -------------------------
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- o Cleanup in build files 
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+ o Cleanup in build files
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 CHANGES IN VERSION 2.29.1
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 -------------------------
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@@ -6,16 +6,16 @@
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 //
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 // Copyright 2009 Vanderbilt University - Nashville, TN 37232
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 //
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-// Licensed under the Apache License, Version 2.0 (the "License"); 
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-// you may not use this file except in compliance with the License. 
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-// You may obtain a copy of the License at 
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+// Licensed under the Apache License, Version 2.0 (the "License");
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+// you may not use this file except in compliance with the License.
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+// You may obtain a copy of the License at
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 //
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 // http://www.apache.org/licenses/LICENSE-2.0
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 //
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-// Unless required by applicable law or agreed to in writing, software 
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-// distributed under the License is distributed on an "AS IS" BASIS, 
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-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
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-// See the License for the specific language governing permissions and 
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+// Unless required by applicable law or agreed to in writing, software
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+// distributed under the License is distributed on an "AS IS" BASIS,
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+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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+// See the License for the specific language governing permissions and
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 // limitations under the License.
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 //
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@@ -154,7 +154,7 @@ class stream_vector_const_iterator
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             return (that.end_ - that.begin_) / that.value_size_;
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 	}
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-	reference operator[](difference_type _Off) const
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+	reference operator[](difference_type _Off)
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 	{
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         next_ = _Off * value_size_;
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 		return (**this);
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@@ -370,7 +370,7 @@ class BinaryIndexStream::Impl
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         EntryPtr entryPtr(new Entry); entryPtr->id = id;
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         const stream_offset indexBegin = indexedMetadataHeaderSize_ + sizeof(streamLength_) + sizeof(maxIdLength_) + entrySize_ * size_;
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         const stream_offset indexEnd = indexedMetadataHeaderSize_ + streamLength_;
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-      
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+
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         {
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             boost::mutex::scoped_lock io_lock(io_mutex);
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             isPtr_->clear();