error installing: CMake Error: Problem with archive_write_finish_entry(): Can't restore time

[sjackman]

I get the following error when installing salmon:

cd /var/tmp/sjackman/salmon20150803-27338-1qoka2g/salmon-0.4.2/external && /gsc/btl/linuxbrew/Cellar/cmake/3.3.0/bin/cmake -P /var/tmp/sjackman/salmon20150803-27338-1qoka2g/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/extract-libcereal.cmake
-- extracting...
     src='/var/tmp/sjackman/salmon20150803-27338-1qoka2g/salmon-0.4.2/external/cereal-v1.0.0.tgz'
     dst='/var/tmp/sjackman/salmon20150803-27338-1qoka2g/salmon-0.4.2/external/cereal-1.0.0'
-- extracting... [tar xfz]
CMake Error: Problem with archive_write_finish_entry(): Can't restore time
CMake Error: Problem extracting tar: /var/tmp/sjackman/salmon20150803-27338-1qoka2g/salmon-0.4.2/external/cereal-v1.0.0.tgz
-- extracting... [error clean up]
CMake Error at /var/tmp/sjackman/salmon20150803-27338-1qoka2g/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/extract-libcereal.cmake:33 (message):
  error: extract of
  '/var/tmp/sjackman/salmon20150803-27338-1qoka2g/salmon-0.4.2/external/cereal-v1.0.0.tgz'
  failed

Is it possible to compile salmon with its external dependencies provided externally rather than vendored into salmon? What is cereal?

[sjackman]

This cmake issue appears to be a bug in Linuxbrew. See Linuxbrew/legacy-linuxbrew#391

[rob-p]

Interesting! cereal is a C++ serialization library. Is the problem related to a specific version of cmake within Linuxbrew?

[sjackman]

My guess, and this is a long shot, is that it's a bug in the tar library of cmake, that's made evident because my system at work has up-to-date Linux headers and glibc but is running an eight-year-old Linux kernel (CentOS 5.10). I can upgrade everything with Linuxbrew except the running kernel. I've seen this situation show bugs before when the software uses compile time kernel feature checks like HAVE_PIPE2 when it should be using a run time check, namely checking whether the call to pipe2 fails with ENOSYS.

[sjackman]

Note that I do (now) have cereal installed, so there is no need for salmon to download and build it. It would be nice if this were an option to use the system-provided cereal library.

[rob-p]

Noted --- I'll add an option to look for it locally first.

[sjackman]

Thanks, Rob!

No smart dashes in GFM? Shame. If you're on a Mac, Option-hyphen and Option-Shift-hyphen produce en- and em- dashes respectively. Option-semicolon produces an ellipsis. I use these three shortcuts all the time. Great for Twitter with limited characters.

[sjackman]

I'm still experiencing this cmake error:

-- extracting... [tar xfz]
CMake Error: Problem with archive_write_finish_entry(): Can't restore time
CMake Error: Problem extracting tar: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/libdivsufsort.zip
-- extracting... [error clean up]
CMake Error at /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libdivsufsort-prefix/src/libdivsufsort-stamp/extract-libdivsufsort.cmake:33 (message):
  error: extract of
  '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/libdivsufsort.zip'
  failed

Here's a gist of the logs:
https://gist.github.com/sjackman/2bbfcf212c555fb20505#file-02-make-L397-L404

[sjackman]

Where does extract-libdivsufsort.cmake live? I don't find it in the salmon repository. Is it generated automatically by cmake? The following patch/hack using unzip works around the cmake -E tar xfz bug for me. It seems to only affect extracting the libdivsufsort.zip, perhaps because it's a .zip. If that is the case, and there's a .tar.gz distribution of libdivsufsort, then there may be a simple fix.

--- libdivsufsort-prefix/src/libdivsufsort-stamp/extract-libdivsufsort.cmake.orig   2016-03-07 22:02:35.000000000 -0800
+++ libdivsufsort-prefix/src/libdivsufsort-stamp/extract-libdivsufsort.cmake    2016-03-07 22:06:49.000000000 -0800
@@ -23,7 +23,7 @@
 # Extract it:
 #
 message(STATUS "extracting... [tar xfz]")
-execute_process(COMMAND ${CMAKE_COMMAND} -E tar xfz ${filename}
+execute_process(COMMAND unzip ${filename}
   WORKING_DIRECTORY ${ut_dir}
   RESULT_VARIABLE rv)

[rob-p]

extract-libdivsufsort.cmake is auto-generated during configuration. However, the zip itself is grabbed as part of RapMap (specifically, it resides here). I can take a look at what would be required to make it a tarball there (or, conversely, if there is a way to force CMake to use unzip rather than cmake -E tar xfz.

[sjackman]

Here's the official tarball release of libdivsufsort:
https://github.com/y-256/libdivsufsort/archive/2.0.1.tar.gz

[rob-p]

I prefer to have it bundled within RapMap (but am willing to hear argument against this). Specifically, this allows that I have control over the availability (i.e. if the official repo disappears, RapMap will continue to build). Of course, the bundled zip was from a slightly updated version of the official libdivsufsort that incorporates a fix into the CMakeLists.txt file where the original failed. It would certainly be easy to just move the bundled version into a tarball rather than a zip without any hassle.

[sjackman]

It's still only a hypothesis that moving to a tarball would fix my issue. I noticed that once I hacked around this one error by using unzip instead, it seems to be working. Still, I think using a tarball rather than zip file is good style anyway.

[sjackman]

The cmake archive_write_finish_entry(): Can't restore time issue affects both .zip files and .tar.gz files.

[sjackman]

I've found a workaround that works for me! cmake -E fails wth Linux 2.6.18 (CentOS 5.11) but succeeds with Linux 2.6.32 (CentOS 6.6). So I'm building Salmon on a newer box, then I can run it on our cluster running ancient OS. Closing.