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SeuratObject install fails with segfault #51

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TDCasasent opened this issue Sep 6, 2022 · 0 comments
Open

SeuratObject install fails with segfault #51

TDCasasent opened this issue Sep 6, 2022 · 0 comments

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@TDCasasent
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SeuratObject 4.1.1, 4.1.0, and 4.0.4 installs (did not test earlier than that) all fail with a segfault.

Have 4.0.4 currently installed.
R version 4.1.3 (newest version available from RHEL repos)
RHEL 8

gcc -m64 -I"/usr/include/R" -DNDEBUG -I'/home/MYUSER/R/x86_64-redhat-linux-gnu-library/4.1/Rcpp/include' -I'/home/MYUSER/R/x86_64-redhat-linux-gnu-library/4.1/RcppEigen/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c valid_pointer.c -o valid_pointer.o
g++ -m64 -std=gnu++14 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o SeuratObject.so RcppExports.o data_manipulation.o valid_pointer.o -L/usr/lib64/R/lib -lR
installing to /home/MYUSER/R/x86_64-redhat-linux-gnu-library/4.1/00LOCK-SeuratObject/00new/SeuratObject/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
sh: line 1: 1719819 Segmentation fault (core dumped) R_TESTS= '/usr/lib64/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/RtmpwB0npY/file1a3df21daa0c36'

*** caught segfault ***
address 0xffffffffffffffff, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
ERROR: lazy loading failed for package 'SeuratObject'

  • removing '/home/dqs_tcga_service/R/x86_64-redhat-linux-gnu-library/4.1/SeuratObject'
  • restoring previous '/home/dqs_tcga_service/R/x86_64-redhat-linux-gnu-library/4.1/SeuratObject'
    Warning in install.packages :
    installation of package 'SeuratObject' had non-zero exit status
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