[英]Segmentation fault when looping through directories with bash script
I understand this is usually to do with recursion, except I am pretty sure I am not doing this. 我知道这通常与递归有关,除非我很确定自己没有这样做。 On each time round the loop it gives a segmentation error pointing to the for loop's line.
在循环的每次循环中,它都会给出指向for循环行的分段错误。
for file in $DATAFOLDER*; do
echo $file;
filename=$(basename $file);
echo $filename;
echo "$DESTFOLDER$SUBFOLDER${filename%%.*}"
pwd
# move data to cppapplication folder
cp -R "$file" "$DESTFOLDER";
sleep 1
# create subdirectory
mkdir "$SUBFOLDER";
# create new folder for extracted data
mkdir "$DESTFOLDER$SUBFOLDER${filename%%.*}";
# copy MassLynx header file into new folder (get the description info)
cp "$file/_HEADER.TXT" "$DESTFOLDER$SUBFOLDER${filename%%.*}";
# run the cppapplication
# <program> <project file> <MassSpectrum> <Mobilogram> <bins in Da> <extract m/z ranges>
./cppapplication.exe "$filename" 0 1 1 0 ;
# fix last character comma bug
sed -i '$ s/,$//g' MassMobility.txt
# move the created files into the new folder
mv Mobilogram.txt "$DESTFOLDER$SUBFOLDER${filename%%.*}";
mv MassMobility.txt "$DESTFOLDER$SUBFOLDER${filename%%.*}";
mv MassMobilityXaxis.txt "$DESTFOLDER$SUBFOLDER${filename%%.*}";
mv MassMobilityYaxis.txt "$DESTFOLDER$SUBFOLDER${filename%%.*}";
# get driftscope quicklook image
sleep 3
python "C:\Users\ganesh\Dropbox\PhD\03_Amphitrite\CppApplication\quicklook_driftscope.py" "$DESTFOLDERWINDOWS$SUBFOLDERWINDOWS" "${filename%%.*}" "$DESTFOLDERWINDOWS$SUBFOLDERWINDOWS${filename%%.*}";
# remove MassLynx Project
rm -r "$filename";
done
Aside from the copying of the file, I don't think the loop has any contact with the original folder being looped through. 除了复制文件之外,我认为循环与循环通过的原始文件夹没有任何联系。
This is the error: 这是错误:
./extract_all_projects.sh: line 26: 7500 Segmentation fault (core dumped)
I have no idea what the problem is as "cppapplication.exe" works fine on these files if run outside of the bash script. 我不知道这是什么问题,因为如果在bash脚本之外运行,“ cppapplication.exe”在这些文件上可以正常工作。
Your $filename
could be empty or not as expected. 您的
$filename
可能为空或与预期不符。 I'm sure the segfault is the cppapplication.exe
crashing (Why didn't you tell us what line 26 is?) To test this, try 我确定segfault是
cppapplication.exe
崩溃了(为什么不告诉我们第26行是什么?)要对此进行测试,请尝试
./cppapplication.exe "" 0 1 1 0
and see if it segfaults. 看看它是否存在段错误。 If I had to guess: the app tries to open a file but doesn't check the return value and soldiers on with a NULL pointer.
如果我不得不猜测:该应用程序尝试打开文件,但不检查返回值,并使用NULL指针指示士兵是否继续前进。
BTW, all except the first semicolon in your script are useless. 顺便说一句,脚本中除第一个分号外的所有字符都没有用。 The shell is not C :-)
外壳不是C :-)
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