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Update smudgeplot to 0.4.0 #51904

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merged 6 commits into from
Nov 4, 2024
Merged

Update smudgeplot to 0.4.0 #51904

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3fd7df7
Update smudgeplot to 0.4.0
BiocondaBot Nov 4, 2024
d41b9e0
edit install command
mencian Nov 4, 2024
fc506c5
update dependencies
mencian Nov 4, 2024
f7f317e
patch gcc in Makefile
mencian Nov 4, 2024
8a10ffc
edit tests
mencian Nov 4, 2024
d3a7976
add pandas
mencian Nov 4, 2024
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13 changes: 13 additions & 0 deletions recipes/smudgeplot/0001-Makefile.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
diff --git a/Makefile b/Makefile
index ad29043..4dff5ca 100644
--- a/Makefile
+++ b/Makefile
@@ -15,7 +15,7 @@ $(INSTALL_PREFIX)/bin/% : exec/%
install -C $< $(INSTALL_PREFIX)/bin

exec/hetmers: src_ploidyplot/PloidyPlot.c src_ploidyplot/libfastk.c src_ploidyplot/libfastk.h src_ploidyplot/matrix.c src_ploidyplot/matrix.h
- gcc $(CFLAGS) -o $@ src_ploidyplot/PloidyPlot.c src_ploidyplot/libfastk.c src_ploidyplot/matrix.c -lpthread -lm
+ $(CC) $(CFLAGS) -o $@ src_ploidyplot/PloidyPlot.c src_ploidyplot/libfastk.c src_ploidyplot/matrix.c -lpthread -lm


.PHONY : clean
7 changes: 5 additions & 2 deletions recipes/smudgeplot/build.sh
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Original file line number Diff line number Diff line change
@@ -1,10 +1,13 @@
#!/bin/bash

export CPATH="${PREFIX}/include"

mkdir -p $PREFIX/bin

# Install the current codebase as an R package
Rscript install.R
make -s INSTALL_PREFIX="${PREFIX}" CC="${CC}" -j"${CPU_COUNT}"

# Install executables
install -C exec/smudgeplot.py $PREFIX/bin
install -C exec/hetmers $PREFIX/bin
install -C exec/smudgeplot_plot.R $PREFIX/bin
install -C exec/centrality_plot.R $PREFIX/bin
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💡 Codebase verification

Files referenced in install commands do not exist

The files hetmers, smudgeplot_plot.R, and centrality_plot.R that are being installed in the build.sh script do not exist in the repository. The installation commands will fail as the source files are missing from the expected exec/ directory.

  • install -C exec/hetmers $PREFIX/bin will fail
  • install -C exec/smudgeplot_plot.R $PREFIX/bin will fail
  • install -C exec/centrality_plot.R $PREFIX/bin will fail
🔗 Analysis chain

Verify executable permissions for new files.

The new executables hetmers and centrality_plot.R have been added. Please ensure they have the correct executable permissions set.

Let me verify if these files exist in a different location since the exec directory wasn't found.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if the new executables have proper permissions in the source directory

# Test: Check executable permissions
echo "Checking executable permissions:"
ls -l exec/hetmers exec/centrality_plot.R

# Test: Verify if files exist and are executable
for file in "hetmers" "centrality_plot.R"; do
  if [[ -x "exec/$file" ]]; then
    echo "$file is executable"
  else
    echo "WARNING: $file is not executable"
  fi
done

Length of output: 572

Script:

#!/bin/bash
# Search for the files in the repository
echo "Searching for files:"
fd "hetmers|centrality_plot.R|smudgeplot_plot.R" --type f

# If found, check their permissions
find . -type f -name "hetmers" -o -name "centrality_plot.R" -o -name "smudgeplot_plot.R" -exec ls -l {} \;

Length of output: 216

11 changes: 7 additions & 4 deletions recipes/smudgeplot/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,17 +1,19 @@
{% set version = "0.3.0" %}
{% set version = "0.4.0" %}

package:
name: smudgeplot
version: {{ version }}

build:
number: 1
number: 0
run_exports:
- {{ pin_subpackage('smudgeplot', max_pin="x.x") }}

source:
url: https://github.com/KamilSJaron/smudgeplot/archive/v{{ version }}.tar.gz
sha256: b95b61e517de8f33c49910825a5c68e9a0d1e27cc33463939ef4c994e61dda92
sha256: 61ca437e29830a415e6f18f39d5d1fd994d20ea4a9bd46d1ab5fdcc52fa4008d
patches:
- 0001-Makefile.patch

requirements:
build:
Expand All @@ -31,10 +33,11 @@ requirements:
- r-argparse
- numpy
- scipy
- pandas

test:
commands:
- smudgeplot.py --version 2>&1 | grep 'Running'
- "smudgeplot.py --version 2>&1"

about:
home: https://github.com/KamilSJaron/smudgeplot
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