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* clang 13 format #1933 (#1941)Allen Byrne2022-07-281-11/+11
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* Hdf5 1 8 merges from develop and format specifier updates (#670)Allen Byrne2021-05-251-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update supported platforms * Merge PR#3 changes from develop * # WARNING: head commit changed in the meantime Merge gcc 10 diagnostics option from develop Merge CMake changes from develop Merge warnings from develop Merge #318 OSX changes from develop Merge tools changes from develop Merge test macros from develop * Format updates * Fix missing semicolon and format fix * Format update * Correct actions, remove java option * Update autotools build files * Add testfiles * Fix configure issue with make flags * Init fapls to default * Update generated files and fix h5repack id closure * update format * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup whitespace cleanup tools sync * format alignment * initialize vars * revert H5private change * Merge #380 from develop * Split format source and commit changes on repo push * Change windows TS to use older VS. * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * Update unsupported types with precision * Add "option" command for clang options * CMake merges from develop h5cc scripts * Updates from develop and printf formatters * Committing clang-format changes * Issue #669 remove version from pkgcfg filename * remove version from h5cc script Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 8 Merge dev changes for long double and cmake (#548)Allen Byrne2021-04-201-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update supported platforms * Merge PR#3 changes from develop * # WARNING: head commit changed in the meantime Merge gcc 10 diagnostics option from develop Merge CMake changes from develop Merge warnings from develop Merge #318 OSX changes from develop Merge tools changes from develop Merge test macros from develop * Format updates * Fix missing semicolon and format fix * Format update * Correct actions, remove java option * Update autotools build files * Add testfiles * Fix configure issue with make flags * Init fapls to default * Update generated files and fix h5repack id closure * update format * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup whitespace cleanup tools sync * format alignment * initialize vars * revert H5private change * Merge #380 from develop * Split format source and commit changes on repo push * Change windows TS to use older VS. * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * Update unsupported types with precision Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* HDF5 1 8 merge of recent changes and tools (#353)Allen Byrne2021-02-221-33/+131
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update supported platforms * Merge PR#3 changes from develop * # WARNING: head commit changed in the meantime Merge gcc 10 diagnostics option from develop Merge CMake changes from develop Merge warnings from develop Merge #318 OSX changes from develop Merge tools changes from develop Merge test macros from develop * Format updates * Fix missing semicolon and format fix * Format update * Correct actions, remove java option * Update autotools build files * Add testfiles * Fix configure issue with make flags * Init fapls to default * Update generated files and fix h5repack id closure * update format
* Update HDF5 1.8 copyright headers with updated copyright URL (#148)Larry Knox2020-12-041-1/+1
| | | | | | | * Update URL for COPYING file in copyright headers. * Make fortran copyright headers uniformly spaced. * Update url for Copyright file in c++/src/footer.html.
* Source formattedAllen Byrne2020-10-011-599/+603
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* Merge changes from other branchesAllen Byrne2020-02-291-142/+153
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* Merge pull request #2071 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings ↵Kimmy Mu2020-01-101-1/+1
| | | | | | | | | | | | | | | | | | | | | | to develop * commit '0a2bb11b248df6841daabca3970df5d8504adfc7': address problems from comments fix and address comments change according to previous comments add missing piece remove unnecessary check macro fix intel compile warnings Revert "fix warnings from Intel compiler" Revert "fix warnings and some text alignment" Revert "let hdf5 pick up the right compiler in Intel environment" Revert "fix issues from previous PR comments" Revert "using a different MACRO" using a different MACRO fix issues from previous PR comments let hdf5 pick up the right compiler in Intel environment fix warnings and some text alignment fix warnings from Intel compiler
* Merge mostly whitespace changes from 1.10 branchAllen Byrne2019-08-181-8/+11
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* HDFFV-10297 merge from developAllen Byrne2017-10-191-619/+476
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* HDFFV-9774 Add missing error commandsAllen Byrne2017-09-081-168/+115
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* Tools merge from develop-1.10Allen Byrne2017-05-171-96/+123
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* Merge/port changes from develop back to 1.8 for tools and cmakeAllen Byrne2017-03-291-3/+7
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* HDFFV-9994 port changes from develop.Allen Byrne2017-01-181-6/+6
| | | CMake folder changes brought up to standard.
* [svn-r25225] Description:Quincey Koziol2014-05-291-130/+163
| | | | | | | | | | | | | | | | Bring r25215 from trunk to 1.8 branch: Bring changes from Coverity branch back to trunk: r20914: Use HDstrncpy and HDstrncat! --gh r20915: Use HDstrncpy and HDstrncat! --gh Tested on: MacOSX/64 10.9.3 (amazon) w/gcc 4.9, FORTRAN, C++, multi-threads & parallel (h5committested on the trunk)
* [svn-r24810] Description:Quincey Koziol2014-03-171-2/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24803 & r24804 from trunk to 1.8 branch: r24804: Brought changes from Coverity branch back to trunk, and cleaned up misc. other warnings & formatting issues: r20833: Fixed Coverity 667 and 668 with real integer overflow tests this time. r20834: Use HDstrncpy and HDstrncat. --gh r20835: Change to use strncpy - use base_len + 1 for line 156, use HDstrlen(path) + 1 for line 159 r20836: Fixed coverity 585 by casting output of fgetc() to a char. r20837: Changed sprintf calls to snprintf with size 1 less than the allocated buffer to address coverity issue #967. r24803: Rename GCC_DIAG_OFF/ON macros to H5_GCC_DIAG_OFF/ON and move from src/H5private.h to src/H5public.h. Wrap typedef of hsize_t and hssize_t in DIAG_OFF(long-long) macros. Clean up a bunch of "macro '-' is unused" warnings. Tested on: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel (too minor to require h5committest)
* [svn-r24479] Description:Quincey Koziol2013-11-301-41/+0
| | | | | | | | Fix ph5diff worker command handling so it can correctly respond to situations where there's no work to perform. Also, a few minor code cleanups. Tested on: Mac OSX/64 10.9.0 (amazon) w/parallel
* [svn-r24205] Merge HDFFV-8513/8522 from trunk (via cmake branch), h5repack ↵Allen Byrne2013-09-261-8/+7
| | | | | | | | UD plugins. Also warning session fixes. Tested: CMake local linux
* [svn-r23396] Description:Quincey Koziol2013-03-201-17/+17
| | | | | | | | | | | | | | Bring r23395 from trunk to 1.8 branch: Bring Coverity changes from branch to trunk: r20682: fixed coverity: 76, 77, 635, 636, 1164, 1165, 1166, 1121, 1122, 1117, 1343 Tested on: Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN (too minor to require h5committest)
* [svn-r22753] Purpose:Jonathan Kim2012-09-111-0/+22
| | | | | | | | | | | | | HDFFV-5919 - GMQS: h5diff - The number of object difference is not consistent between dataset and group/type when attribute(s) have differences Description: Object differences are not consistent between dataset and group/datatype when their attribute(s) have differences. This is because attribute(s) differences is not accumulated to group or datatype object’s difference, but accumulated to dataset difference. To fix, do not accumulate attribute difference to dataset difference. This is referred to h5diff’s default behavior and also past report from users that users were confused by the accumulated behavior. (also can’t figure out only for dataset difference , also hard to spot dataset difference when it has lots of attributes or differences) This also lead to fix inconsistent format indicating difference between dataset and group/datatype object. Merged from HDF5 trunk r22751. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
* [svn-r22639] HDFFV-8111: Remove special case shortcut and use normal path ↵Allen Byrne2012-08-071-214/+85
| | | | | | for comparing single objects. Merged from trunk
* [svn-r22619] Jonathan Kim2012-08-021-8/+0
| | | | | | | | | | | | | | | Purpose: HDFFV-8003 - ph5diff (parallel h5diff): daily test failure on ember intermittently during non comparable test file comparison HDFFV-7755 - parallel h5diff : hanging on koala intermittently during non comparable test file comparison Description: non-comparable test intermittently hung on koala and ember, but not on jam. it didn't occur until -np reaches 4 or bigger. it occurred once out of many repeated attempts of the same test. There was a incorrectly (mistakenly?) duplicated code in MPI section which caused such hang in a certain condition. The test used more processes than other tests, which increased chance to trigger more undone processes, and such process could enter the incorrect code section and wait for wrong pair of send. it explains why it occurred intermittently according to machine condition and using a certain feature. Removed incorrect code which blocked correct code. Merged from HDF5 trunk r22618. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), some manually repeated test performed in parallel
* [svn-r22320] Purpose:Jonathan Kim2012-04-271-4/+4
| | | | | | | | | | | | | | | Fix for HDFFV-7998-h5diff: incorrect behavior and output for comparing symbolic dangling links without following-symlinks option Description: Fix not to check and display dangling link status without --follow-symlinks option. Berfor the fix, when comparing symbolic link to symbolic link without follow-symlinks option, h5diff followed to check if those links are dangling or not. It caused to display output incorrectly (dangling link instead of symbolic link). The fix also improved performance when comparing lots of symbolic links without the --follow-symlinks option. Test cases were added and tagged with jira#. This merged from HDF5 trunk r22319. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
* [svn-r22188] Purpose:Jonathan Kim2012-03-291-275/+101
| | | | | | | | | | | | | Fix for HDFFV-7644 GMQS: h5diff - incorrect behaviors when comparing HDF5 files with different type of objects (dataset, group, type) as common objects Description: Fixed failure for comparing same named object with different object types in comparing groups. (common object comparison) Prior to the fix, h5diff resulted in error. After the fix, h5diff detects such case as non-comparable and display messages accordingly. Test cases were added and tagged with jira#. Merged from HDF5 trunk 22176. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
* [svn-r22124] Purpose:Jonathan Kim2012-03-221-7/+12
| | | | | | | | | | | | | | | | Fix for HDFFV-7837 - h5diff: incorrect behavior with exclude-path option when unique object exist only in one file Description: If unique objects exists only in one file and try to exclude the unique objects with --exclude-path option, h5diff missed excluding some objects. Fixed to exclude objects correctly in such case. Test cases were added and tagged with jira#. Merged from HDF5 trunk r22114. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
* [svn-r22057] Purpose:Jonathan Kim2012-03-121-20/+31
| | | | | | | | | | | | | | Fix for HDFFV-7835 h5diff: incorrect result for comparing the two same type symlinks as dangling links. Description: When two symbolic dangling links are compared with --follow-symlinks option, the result should be same. It works for comparing two files, but didn't work for comparing two objects. Test cases were added and tagged with jira#. Merged from HDF5 trunk r22038. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
* [svn-r22013] HDFFV-7560:Allen Byrne2012-03-021-40/+40
| | | | | | | | | | Merge 1.8 and h5dump/tools and tests based on tools library from trunk. Reduced warnings. HDFFV-7949: Remove duplicated functions in h5ls Tested: local linux,h5committest
* [svn-r21892] Purpose:Jonathan Kim2012-01-251-11/+13
| | | | | | | | | | | | | | | | Fix for HDFFV-7836 h5diff: displays error stack message for comparing the two dangling symlink with follow-symlinks option Description: While ago, to improve performance, skipping same object checking (h5tools_is_obj_same()) was added. However the checking function doesn't understand about the dangling link and caused the issue. Since handling dangling link code section already implemented, move the checking function after handling dangling-links to address the problem. Test was added and tagged with jira#. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
* [svn-r21404] Purpose:Jonathan Kim2011-09-211-2/+2
| | | | | | | | | | | | | | | | | | | | | | HDFFV-7693 - h5diff produces different behavior between versions: 1.8.3 and 1.8.6 Description: There were two issues on this. One was not displaying all the comparable objects if non-comparable object/attribute exist and compared before comparables ones. This issue occurred after 1.8.4 release. This is the issue from user. The other issue was not displaying all the comparable attributes, if non-comparable object/attribute exist and compared ahead. This issue were exist even before 1.8.4 release. So it's possible some attribute comparison may have not displayed correctly in the past, if non-comparable data were exist in common object. Fixed h5diff to display all the comparable object and attribute regardless of non-comparables. Merged from HDF5 trunk r21396 and r21397. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam, Windows)
* [svn-r20794] Purpose:Jonathan Kim2011-05-101-38/+76
| | | | | | | | | | | | | HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects Description: Merged from HDF5 trunk r20767. Improved performance by eliminating duplicated action for getting object information in half from the previous fixe when comparing group vs group. This is addition to the previous commit r20706. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)
* [svn-r20706] Purpose:Jonathan Kim2011-05-021-0/+66
| | | | | | | | | | | | | | | | | - HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects Description: Merged from HDF5 trunk r20676. Fixed: 1) adding h5tools_is_obj_same() function to check if two given IDs or paths point to the same object. This function can be very useful for other tools and applications. 2) using h5tools_is_obj_same() at h5diff() and diff() in h5diff.c. If two paths point to the same object, there is no need to check the details of the object since we know there is no difference. The fix will increase the performance by skipping the content comparison. It also fixed the problem of reporting difference for some cases of comparing the same file, e.g. empty files or files with incomparable objects the same file. Test update: Updat prvious test cases (171, 172, 530) affected by this fix, so they still perfrom originally intended testing without bypassing. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
* [svn-r20299] Purpose:Jonathan Kim2011-03-231-13/+30
| | | | | | | | | | | | | | | | | Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the different set of attributes (different number and names) Description: Merged from HDF5 trunk r20294 Previously h5diff compared attributes correctly only when two objects have the same number of attributes and attribute names are identical. Also didn't display useful information about attribute difference. This fix covers all other cases. This fixes both issues. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r20286] Purpose:Jonathan Kim2011-03-211-7/+6
| | | | | | | | | | | | | | | | | Fixed Bug 2214 - GMQS: h5diff - memory leak when accessing symbolic links with --follow-symlinks option and the target type is UDLink or some error occurs Description: Merged from HDF5 trunk r20274. Memory leaks occurred when accessing symbolic links with --follow-symlink option. Test cases are in testing script. (400 - 456, 501 - 518) An example test : valgrind --leak-check=full h5diff --follow-symlinks -v h5diff_softlinks.h5 h5diff_softlinks.h5 Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), Cmake - jam
* [svn-r20066] Description:Quincey Koziol2011-02-081-2/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r20065 from trunk to 1.8 branch: Bring changes from Coverity branch to trunk: r19975: Fixed potential mem leak at H5O_attr_open_by_name r19980: Fix coverity issue 792. Free tmp_env_prefix in H5Lexternal.c line 365 if it is not NULL but its contents are 0 when it goes out of scope. r20039: Eliminate warnings about nested extern and implicit declarations of parallel_print and address Coverity defects 712-781 by #including h5tools_utils.h in h5diff_array.c, h5diff_attr.c, h5diff_dset.c and h5diff_util.c. r20046: Purpose: Address TOCTOU warnings in h5jam and h5unjam Description: Coverity is afraid that the state of the input file could change between the call to stat() and the call to open(). This is called a time-of- check time-of-use (TOCTOU) vulnerability. Modified stat calls to fstat which uses an open file pointer so it (hopefully) won't complain any more. r20047: Addressed coverity issues 135-137, 462-464. Local pointers that needed to be freed in case of error were moved out of a switch statement in src/H5Tnative.c, set to NULL, and checked before freeing. Tested on: Mac OS X/32 10.6.6 (amazon) w/debug & production (h5committested on Coverity branch)
* [svn-r19444] Purpose:Jonathan Kim2010-09-201-10/+14
| | | | | | | | | | | Fix for group comparison with exclude-path case. Use relative path. Description: Merge from hdf5 trunk (r19443) Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19407) Tested: jam, amani
* [svn-r19419] On windows, an include bypassed the WIN32_LEAN_AND_MEAN define. ↵Allen Byrne2010-09-171-1/+1
| | | | | | Moved the define up. Moved the h5dif.h to after the h5private include Tested: Windows
* [svn-r19407] Purpose:Jonathan Kim2010-09-161-17/+130
| | | | | | | | | | | | Add --exclude-path option Description: Merged from hdf5 trunk (r19406). Specified path to an object will be excluded from comparing the two files or two groups. If group is specified all the member objects will be excluded. Related to "1890: h5diff excluding object for file comparison via command line" Tested: jam, amani
* [svn-r19401] Purpose:Jonathan Kim2010-09-161-288/+707
| | | | | | | | | | | Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object Description: Merged from hdf5 trunk (r19400). Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly. Tested: jam, amani
* [svn-r19291] Description:Quincey Koziol2010-08-241-8/+8
| | | | | | | | | Avoid getting object information for soft/external links if we aren't going to traverse across the link itself. Tested on: Linux/64 2.6 (chicago) w/debug & production (h5committest coming up)
* [svn-r18874] Purpose:Jonathan Kim2010-05-211-2/+2
| | | | | | | | | | | | Rename '--follow-links' to '--follow-symlinks' Description: The '--follow-links' option is to follow symbolic links (soft and external). Make the name more intuitive and specific to the feature. Merged from hdf5 trunk r18873. Tested: jam
* [svn-r18615] Purpose:Jonathan Kim2010-04-221-145/+0
| | | | | | | | | | | Fix for bug 1817 : h5copy fail to copy dangling link by specifying link path directly Description: Merged from hdf5 trunk r18614. Tested: jam, amani
* [svn-r18279] Purpose:Jonathan Kim2010-02-191-138/+697
| | | | | | | | | | Work for bugzilla 1754: h5diff: support comparing through links. Description: merged from hdf5 trunk (18164, 18165, 18166, 18167, 18170, 18266, 18273) Tested: h5committest (jam, amani and linew)
* [svn-r18198] Description:Quincey Koziol2010-01-301-8/+8
| | | | | | | | | Trim trailing whitespace from source code files, with following command: find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//' Tested on: None - eyeballed only
* [svn-r18135] Purpose:Jonathan Kim2010-01-211-2/+4
| | | | | | | | | | | | Additional fix relted to the fix of bug1672. Description: The fix of bug1672 caused some changes of output which required modifying some test cases. After some discussion, restoring the changes of the test cases was decided. After many experiments for the solution, this fix was made so the code which improved performance can stay. Tested on Jam.
* [svn-r18127] Purpose:Jonathan Kim2010-01-201-12/+2
| | | | | | | | | | | | | Fix for bug1749: Incorrect code in diff() function for links compare Also removed duplicated redundant code, which improves performance. Description: When comparing file1 to file2 and both files contain same soft-links and/or external-links, if file2's target object path name is longer than file1's target object path name, the current code allocates memory buffer incorrectly, so it could end up buffer overflow or wrong result. Tested on Jam.
* [svn-r17921] Purpose:Jonathan Kim2009-11-201-35/+22
| | | | | | | | | | | | | | | | Fix Bug1672 - Display garbage value on LE machine for BE data. Description: Casuing by calling diff_dataset twice when -r or no option was given. Change to call it once which fix the problem. It also improves the performance. (diffing time in half) According further test, it also occurred on BE machine as well and it seems occruing only with the BE data attached to Bugzilla. Don't know how the file was created. Anyway this fix will prevent from diffing with garbage values in similiar potential case. Tested on: linux32 (jam) , linux64 (almani), solaris (linew)
* [svn-r17053] merge 17052 from trunkPedro Vicente Nunes2009-06-151-3/+12
| | | | | | | | | | Add a run to the h5repack shell script to read a family file The file used for input is located in the common source tools for testfiles, in tools/testfiles Modified the h5repack shell script to read files from this location (h5repack reads its input files from a dedicated testfiles location in h5repack/testfiles) Changed the h5diff open file call to use h5tools_fopen, so that it can open all file drivers Tested: linux
* [svn-r16375] merge 16373Pedro Vicente Nunes2009-01-291-10/+10
| | | | | | | replaced some printf statements with parallel_print tested: linux serial (parallel tested in trunk)
* [svn-r16351] merge 16348Pedro Vicente Nunes2009-01-261-2/+4
| | | | | | | | #1368 (E1) h5diff: implement "not comparable" messages. Implemented RFC. The new option is <-c, --compare List objects that are not comparable> added some test cases tested: windows, linux
* [svn-r15967] regarding the return value of h5diff (0, no difference in ↵Pedro Vicente Nunes2008-10-271-4/+18
| | | | | | | | | files, 1 difference ) objects with the same name must be of the same type tested: windows, linux
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