Question

edgeR package fails to load after install

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jenny.russ • 0

@jennyruss-18107

Last seen 5.5 years ago

Hi,

I have problems installing edgeR on R-3.5.1. I get the following error at the end of the install:

** testing if installed package can be loaded
Error: package or namespace load failed for ‘edgeR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/opt/R-3.5.1/library/edgeR/libs/edgeR.so':
/opt/R-3.5.1/library/edgeR/libs/edgeR.so: undefined symbol: _ZNSt13runtime_errorC1EPKc
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/opt/R-3.5.1/library/edgeR’

Do you have an idea what the problem is and how I can solve this. I cannot install the package 'scater' without edgeR.

Thanks, Jenny

edger install error • 3.2k views

ADD COMMENT • link updated 5.5 years ago by Aaron Lun ★ 28k • written 5.5 years ago by jenny.russ • 0

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Hi, I met the same error. Do you find any good solution to this?

Thanks

ADD REPLY • link 5.5 years ago hongbo919 • 0

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It would probably help to include the full transcript of the attempt to install edgeR, and to include the output of sessionInfo().

ADD REPLY • link 5.5 years ago Martin Morgan 25k

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Hi, Thanks. Following is the code and error information.

R CMD INSTALL edgeR_3.24.0.tar.gz

Error: package or namespace load failed for ‘edgeR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/R/R_3_5_1/lib64/R/library/edgeR/libs/edgeR.so':
/home/R/R_3_5_1/lib64/R/library/edgeR/libs/edgeR.so: undefined symbol: _ZNSt13runtime_errorC1EPKc
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/R/R_3_5_1/lib64/R/library/edgeR’

> sessionInfo()

R version 3.5.1 (2018-07-02)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

Matrix products: default

BLAS: /home/R/R_3_5_1/lib64/R/lib/libRblas.so

LAPACK: /home/R/R_3_5_1/lib64/R/lib/libRlapack.so

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8

[7] LC_PAPER=en_US.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] BiocInstaller_1.32.1

loaded via a namespace (and not attached):

[1] BiocManager_1.30.2 compiler_3.5.1 tools_3.5.1

ADD REPLY • link 5.5 years ago hongbo919 • 0

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I realize there is a character limit, but it is the compile and link rather than load part of the installation that is likely to be useful. For me I have

$ bioc-3.8 CMD INSTALL edgeR_3.24.0.tar.gz
* installing to library ‘/Users/ma38727/Library/R/3.5/Bioc/3.8’
* installing *source* package ‘edgeR’ ...
** libs
g++ -std=gnu++11 -I"/Users/ma38727/bin/R-3-5-branch/include" -DNDEBUG  -I"/Users/ma38727/Library/R/3.5/Bioc/3.8/Rcpp/include" -I/usr/local/include   -fPIC  -g -O0 -c R_add_prior_count.cpp -o R_add_prior_count.o
g++ -std=gnu++11 -I"/Users/ma38727/bin/R-3-5-branch/include" -DNDEBUG  -I"/Users/ma38727/Library/R/3.5/Bioc/3.8/Rcpp/include" -I/usr/local/include   -fPIC  -g -O0 -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o
...
g++ -std=gnu++11 -I"/Users/ma38727/bin/R-3-5-branch/include" -DNDEBUG  -I"/Users/ma38727/Library/R/3.5/Bioc/3.8/Rcpp/include" -I/usr/local/include   -fPIC  -g -O0 -c objects.cpp -o objects.o
g++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o -L/Users/ma38727/bin/R-3-5-branch/lib -lRlapack -L/Users/ma38727/bin/R-3-5-branch/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -Wl,-framework -Wl,CoreFoundation
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
installing to /Users/ma38727/Library/R/3.5/Bioc/3.8/edgeR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edgeR)

ADD REPLY • link 5.5 years ago Martin Morgan 25k

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Hi Martin, Thanks very much! However, the command "R CMD INSTALL edgeR_3.24.0.tar.gz" still report error in my end.

ADD REPLY • link 5.5 years ago hongbo919 • 0

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I know, but it reports an error after printing out a bunch of stuff...it does not fail after printing only the line that you show... or does it?

I think it would also be valuable to indicate how you retrieved the .tar.gz file.

ADD REPLY • link 5.5 years ago Martin Morgan 25k

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It seems like your C++ standard library is... out of date? Perhaps missing altogether? Your linker is not able to find the std::runtime_error constructor, and that's been in the C++ standard since 2003 (at least). This probably represents an issue with your build environment - I would guess that there's some ABI incompatibilities between the system's C++ library and whatever GCC you're using. Probably worth talking to your sysadmin about this.

ADD REPLY • link 5.5 years ago Aaron Lun ★ 28k

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Hi Aaron, Thank you. I will contact sysadmin about this.

ADD REPLY • link 5.5 years ago hongbo919 • 0

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Hi Aaron. I have checked the version of C++ standard library as showing in following:

strings /usr/lib64/libstdc++.so.6 | grep LIBCXX

GLIBCXX_3.4

GLIBCXX_3.4.1

GLIBCXX_3.4.2

GLIBCXX_3.4.3

GLIBCXX_3.4.4

GLIBCXX_3.4.5

GLIBCXX_3.4.6

GLIBCXX_3.4.7

GLIBCXX_3.4.8

GLIBCXX_3.4.9

GLIBCXX_3.4.10

GLIBCXX_3.4.11

GLIBCXX_3.4.12

GLIBCXX_3.4.13

GLIBCXX_FORCE_NEW

GLIBCXX_DEBUG_MESSAGE_LENGTH

GCC version is 6.2.1. I am not sure where is the incompatibilities between them.

ADD REPLY • link 5.5 years ago hongbo919 • 0

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This page lists the symbol versions corresponding to the GCC version. The numbers you're showing correspond to GCC version 4.4.2 or earlier - quite old. This is probably the cause of ABI incompatibilities with object files created with GCC version 5.1.0 or later, read this.

ADD REPLY • link 5.5 years ago Aaron Lun ★ 28k

score 1 · Answer 1 · 2018-10-30

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Aaron Lun ★ 28k

@alun

Last seen 6 hours ago

The city by the bay

This is a very unusual error that I have not seen before. I would say that there is a problem with your GCC set-up - maybe because it's not linking to the correct C++ standard library? - so you'll have to talk to your sysadmin or whoever set up your build system.

ADD COMMENT • link 5.5 years ago Aaron Lun ★ 28k