Travis issues

manszamore · Mar 2, 2020 · cbe6ac2 · cbe6ac2
1 parent 08cd215
commit cbe6ac2
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Showing 29 changed files with 244 additions and 86 deletions.
diff --git a/.gitignore b/.gitignore
@@ -12,6 +12,7 @@ R/Rplots.pdf
 *.Rproj
 .RData
 *.old
+*.log
 
 # Folders
 ignore

diff --git a/.travis.yml b/.travis.yml
@@ -1,8 +1,7 @@
 # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
 
 language: R
-r: bioc-release
-sudo: false
+r: bioc-devel
 cache: packages
 apt_packages:
     - libc6 
@@ -12,4 +11,4 @@ apt_packages:
     - libssl-dev
     - libglu1-mesa-dev
     - libudunits2-dev
-
+
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: NormalyzerDE
 Title: Evaluation of normalization methods and calculation of differential expression analysis statistics
-Version: 1.5.1
+Version: 1.5.2
 Author: Jakob Willforss
 Authors@R: c(
     person("Jakob", "Willforss", email="[email protected]", role=c("aut", "cre")),
@@ -41,6 +41,6 @@ biocViews:
     Normalization, MultipleComparison, Visualization, Bayesian, Proteomics, Metabolomics, DifferentialExpression
 License: Artistic-2.0
 Encoding: UTF-8
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 URL: https://github.com/ComputationalProteomics/NormalyzerDE
 Depends: R (>= 3.6)
diff --git a/NEWS b/NEWS
@@ -1,3 +1,9 @@
+CHANGES IN VERSION 1.5.2
+----------------------------------
+
+* Updated to follow Bioconductor release cycle
+* Updated to fix issues in vignette introduced by updated external packages
+
 CHANGES IN VERSION 1.3.4
 ----------------------------------
 

diff --git a/man/NormalyzerDataset.Rd b/man/NormalyzerDataset.Rd
diff --git a/man/calculateContrasts.Rd b/man/calculateContrasts.Rd
diff --git a/man/calculateCorrSum.Rd b/man/calculateCorrSum.Rd
diff --git a/man/calculateSummarizedCorrelationVector.Rd b/man/calculateSummarizedCorrelationVector.Rd
diff --git a/man/detectSingleReplicate.Rd b/man/detectSingleReplicate.Rd
diff --git a/man/detectSingletonSample.Rd b/man/detectSingletonSample.Rd
diff --git a/man/generateStatsReport.Rd b/man/generateStatsReport.Rd
diff --git a/man/getLowCountSampleFiltered.Rd b/man/getLowCountSampleFiltered.Rd
diff --git a/man/getRTNormalizedMatrix.Rd b/man/getRTNormalizedMatrix.Rd
diff --git a/man/getSmoothedRTNormalizedMatrix.Rd b/man/getSmoothedRTNormalizedMatrix.Rd
diff --git a/man/getVerifiedNormalyzerObject.Rd b/man/getVerifiedNormalyzerObject.Rd
diff --git a/man/getWidenedRTRange.Rd b/man/getWidenedRTRange.Rd
diff --git a/man/normMethods.Rd b/man/normMethods.Rd
diff --git a/man/normalyzer.Rd b/man/normalyzer.Rd
diff --git a/man/normalyzerDE.Rd b/man/normalyzerDE.Rd
-Original file line number
+Diff line change
@@ Expand Up / @@ -12,6 +12,7 @@ R/Rplots.pdf @@
     *.Rproj
     .RData
     *.old
+    *.log
     # Folders
     ignore
@@ Expand Down @@