**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)? Salmon
I was aware of such problem - the problem may happen in customized Linux. OS, reported pinbin relocation error, the reason is file /etc/ld.so.preload was present in system. That file only contained one line “libachk.so” it changed the order of library loading to cause Inspector break. I obtain: 'ln: relocation error: /lib64/tls/libc.so.6: symbol rtldglobalro, version GLIBCPRIVATE not defined in file ld-linux-x86-64.so.2.
Describe the bug
I downloaded salmon-0.11.3-linux_x86_64.tar.gz file and extracted it. There is no makefile or install.sh files, just the bin. lib, sample_data. Therefore no any installation steps. The bin and lib were put in environment paths PATH and LD_LIBRARY_PATH.
When I run trinity command i get following error:
I downloaded salmon-0.11.3-linux_x86_64.tar.gz file and extracted it. There is no makefile or install.sh files, just the bin. lib, sample_data. Therefore no any installation steps. The bin and lib were put in environment paths PATH and LD_LIBRARY_PATH.
When I run trinity command i get following error:
Trinity version: Trinity-v2.6.6
-ERROR: couldn't run the network check to confirm latest Trinity software version.
-ERROR: couldn't run the network check to confirm latest Trinity software version.
Tuesday, September 11, 2018: 14:29:38 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /path/to/trinity/2.6.6/x86_64/util/support_scripts/ExitTester.jar 0
Error: dl failure on line 893
Error: failed /path/to/java/8u131/x86_64/jre/lib/amd64/server/libjvm.so, because /path/to/bin/salmon/0.11.3/x86_64/lib/libm.so.6: symbol __get_cpu_features, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
Error, cmd: java -Xmx64m -XX:ParallelGCThreads=2 -jar /path/to/trinity/2.6.6/x86_64/util/support_scripts/ExitTester.jar 0 died with ret 1536 at /path/to/bin/core/../..//trinity/2.6.6/x86_64/bin/Trinity line 2581.
main::process_cmd('java -Xmx64m -XX:ParallelGCThreads=2 -jar /path/to...') called at /path/to/bin/core/../..//trinity/2.6.6/x86_64/bin/Trinity line 2666
eval {...} called at /path/to/bin/core/../..//trinity/2.6.6/x86_64/bin/Trinity line 2665
main::test_java_failure_capture() called at /path/to/bin/core/../..//trinity/2.6.6/x86_64/bin/Trinity line 1159
Error: dl failure on line 893
Error: failed /path/to/java/8u131/x86_64/jre/lib/amd64/server/libjvm.so, because /path/to/bin/salmon/0.11.3/x86_64/lib/libm.so.6: symbol __get_cpu_features, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
Error, cmd: java -Xmx64m -XX:ParallelGCThreads=2 -jar /path/to/trinity/2.6.6/x86_64/util/support_scripts/ExitTester.jar 0 died with ret 1536 at /path/to/bin/core/../..//trinity/2.6.6/x86_64/bin/Trinity line 2581.
main::process_cmd('java -Xmx64m -XX:ParallelGCThreads=2 -jar /path/to...') called at /path/to/bin/core/../..//trinity/2.6.6/x86_64/bin/Trinity line 2666
eval {...} called at /path/to/bin/core/../..//trinity/2.6.6/x86_64/bin/Trinity line 2665
main::test_java_failure_capture() called at /path/to/bin/core/../..//trinity/2.6.6/x86_64/bin/Trinity line 1159
I get similar error while just checking for java version
$ java -version
$ java -version
Error: dl failure on line 893
Error: failed /tsl/software/testing/java/8u131/x86_64/jre/lib/amd64/server/libjvm.so, because /tsl/software/testing/bin/core/../..//salmon/0.11.3/x86_64/lib/libm.so.6: symbol __get_cpu_features, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
Error: failed /tsl/software/testing/java/8u131/x86_64/jre/lib/amd64/server/libjvm.so, because /tsl/software/testing/bin/core/../..//salmon/0.11.3/x86_64/lib/libm.so.6: symbol __get_cpu_features, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
To Reproduce
Steps and data to reproduce the behavior:
Steps and data to reproduce the behavior:
Specifically, please provide at least the following information:
- Which version of salmon was used? 0.11.3
- How was salmon installed (compiled, downloaded executable, through bioconda)? downloaded executables
- Which reference (e.g. transcriptome) was used? no reference
- Which read files were used? fastq
- Which program options were used? Trinity options
Expected behavior
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A clear and concise description of what you expected to happen.
Screenshots
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Desktop (please complete the following information):
- OS: [e.g. Ubuntu Linux, OSX] CentOS
- Version [ If you are on OSX, the output of
sw_vers
. If you are on linux the output ofuname -a
andlsb_release -a
]
![Version Glibc_private Not Defined In File Version Glibc_private Not Defined In File](/uploads/1/2/5/8/125850606/825925647.png)
Additional context
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