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pathologic error: linux-vdso.so.1: No such file or directory

asked 2020-05-30 17:20:36 -0600

jsbowman gravatar image

When I updated to v24 I started receiving this error in the pathologic log file: linux-vdso.so.1: No such file or directory

Googling the error isn't much help, seems that a kernel level library isn't loading? There were no indications of a problem during installation. System is Ubuntu 18.04.4 LTS.

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Hi, Thank you for waiting. I don't have an answer for this, but could you provide the details from the pathologic log file with the error - what was pathologic doing, where there any stack trace or other details from the error.

pmidford gravatar imagepmidford ( 2020-06-03 13:33:57 -0600 )edit

Here's the tail end of the log file, there's no way for me to post or attach the whole thing. The line prior to what's pasted here exceeds the allowed characters. There are no further error messages given, in the terminal the command would appear to complete successfully. 109555040 bytes have been tenured, next gc will be global. See the documentation for variable EXCL:*GLOBAL-GC-BEHAVIOR* for more information. 20 40 linux-vdso.so.1: No such file or directory

jsbowman gravatar imagejsbowman ( 2020-06-04 09:22:15 -0600 )edit

Note that previous comment is standard output/error. I forgot that pathologic creates a separate log file. The output there is quite verbose, evaluation stack points to: ->(TPL::ZOOM-COMMAND :FROM-READ-EVAL-PRINT-LOOP NIL ...) There are then many lines like this: (READ-BROKEN-SEQUENCE 1305806 4 ...) (READ-GENE-SEQUENCE 1305806 4 ...) Which to me suggests a problem with the input files, but I can't find any issue with how they're formatted (worked fine with previous versions of pathway-tools).

jsbowman gravatar imagejsbowman ( 2020-06-04 09:55:31 -0600 )edit

Hi, Could you please send that other file to ptools support. Also, we are looking into this. Apparently linux-vdso.so.1 is not a regular library, but a virtual library generated by the linux kernel (https://unix.stackexchange.com/questions/396987/is-the-vdso-shared-library-linux-vdso-so-the-library-that-contains-the-kernel). Could you also try running blast and see if that's operating correctly.

pmidford gravatar imagepmidford ( 2020-06-04 13:27:30 -0600 )edit

Many thanks, I actually preemptively sent both log files to ptools support after my initial post. Let me know if not easily found and I'll resend. I've confirmed that eutils works (via a call from within Biopython) and blast is functional.

jsbowman gravatar imagejsbowman ( 2020-06-05 18:30:59 -0600 )edit

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answered 2020-06-14 22:49:09 -0600

jsbowman gravatar image

After further digging it seems that the original linux-vdso.so.1: No such file or directory error is fairly generic. In this case the problem seems to stem from an issue reaching eutils through the proxy server.

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Asked: 2020-05-30 17:20:36 -0600

Seen: 177 times

Last updated: Jun 14