undefined symbol: _ZNKSt10filesystem7__cxx1118directory_iteratordeEv

[timpeters82]

Hi Aaron,

Not sure if my C++ compilers are out of date (changed the paths in Makeconf from 8.5 to 13.3.1, didn't make a difference) but I keep getting this error when installing on RHEL 8:

R version 4.4.3 (2025-02-28) -- "Trophy Case"
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Platform: x86_64-redhat-linux-gnu

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> BiocManager::install("alabaster.base")
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.3 (2025-02-28)
Installing package(s) 'alabaster.base'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/alabaster.base_1.6.1.tar.gz'
Content type 'application/x-gzip' length 408713 bytes (399 KB)
==================================================
downloaded 399 KB

* installing *source* package ‘alabaster.base’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-24)’
using C++17
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I../inst/include -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rcpp/include' -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rhdf5lib/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 RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I../inst/include -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rcpp/include' -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rhdf5lib/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 check_csv.cpp -o check_csv.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I../inst/include -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rcpp/include' -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rhdf5lib/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 check_list.cpp -o check_list.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I../inst/include -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rcpp/include' -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rhdf5lib/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 choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I../inst/include -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rcpp/include' -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rhdf5lib/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 is_rfc3339.cpp -o is_rfc3339.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I../inst/include -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rcpp/include' -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rhdf5lib/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 load_csv.cpp -o load_csv.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I../inst/include -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rcpp/include' -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rhdf5lib/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 load_list.cpp -o load_list.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I../inst/include -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rcpp/include' -I'/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rhdf5lib/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 validate.cpp -o validate.o
	In file included from ../inst/include/chihaya/validate.hpp:13,
                 from ../inst/include/chihaya/chihaya.hpp:10,
                 from ../inst/include/takane/utils_public.hpp:13,
                 from ../inst/include/takane/_validate.hpp:9,
                 from ../inst/include/takane/takane.hpp:4,
                 from validate.cpp:2:
../inst/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long unsigned int>&, size_t, size_t, bool) [with Index_ = long unsigned int]’:
../inst/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             if (x > start && i <= previous) {
                              ~~^~~~~~~~~~~
../inst/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long unsigned int>&, size_t, size_t, bool) [with Index_ = int]’:
../inst/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             if (x > start && i <= previous) {
                              ~~^~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rhdf5lib/lib/libhdf5_cpp.a /home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -L/usr/lib64/R/lib -lR
installing to /home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/00LOCK-alabaster.base/00new/alabaster.base/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘alabaster.base’
    finding HTML links ... done
    Rfc3339                                 html  
    acquireFile                             html  
    altReadObject                           html  
    altSaveObject                           html  
    anyMissing                              html  
    chooseMissingPlaceholderForHdf5         html  
    createRedirection                       html  
    hdf5                                    html  
    listObjects                             html  
    finding level-2 HTML links ... done

    loadDirectory                           html  
    moveObject                              html  
    quickLoadObject                         html  
    quickReadCsv                            html  
    readAtomicVector                        html  
    readBaseFactor                          html  
    readBaseList                            html  
    readDataFrame                           html  
    readDataFrameFactor                     html  
    readMetadata                            html  
    readObject                              html  
    readObjectFile                          html  
    removeObject                            html  
    saveAtomicVector                        html  
    saveBaseFactor                          html  
    saveBaseList                            html  
    saveDataFrameFactor                     html  
    saveFormats                             html  
    saveMetadata                            html  
    saveObject                              html  
    stageDataFrame                          html  
    transformVectorForHdf5                  html  
    validateDirectory                       html  
    validateObject                          html  
    writeMetadata                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘alabaster.base’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/00LOCK-alabaster.base/00new/alabaster.base/libs/alabaster.base.so':
  /home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/00LOCK-alabaster.base/00new/alabaster.base/libs/alabaster.base.so: undefined symbol: _ZNKSt10filesystem7__cxx1118directory_iteratordeEv
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/timpet/R/x86_64-redhat-linux-gnu-library/4.4/alabaster.base’

Do I need to reinstall gcc from scratch here? (Would rather not...)

Cheers,
Tim

[timpeters82]

SessionInfo...

> sessionInfo()
R version 4.4.3 (2025-02-28)
Platform: x86_64-redhat-linux-gnu
Running under: Red Hat Enterprise Linux 8.10 (Ootpa)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.15.so;  LAPACK version 3.9.0

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       

time zone: Australia/Sydney
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.25 compiler_4.4.3      tools_4.4.3    

[LTLA]

Indeed it seems like your GCC is too old (or specifically, your libstdc++, or whatever the standard library is called). If I had to guess, you're probably using GCC 8, but GCC 9 is the first release with no-longer-experimental support for all C++17 features.

GCC 9 came out more than 5 years ago, so I think it's fair to ask your administrators to make it available on your HPC (which is where I'm assuming this is all happening).

[timpeters82]

Thanks Aaron,

Unfortunately I'm running RHEL 8 on a workstation instead! Not ideal. Was able to change the compiler using gcc-toolkit-<9+> but am now running into annobin.so errors: https://stackoverflow.com/questions/77961171/how-to-avoid-annobin-errors-using-locally-built-gcc-on-rocky-9. No such files (annobin.so nor gcc-annobin.so) are provided with the rpm.

Will keep attempting a workaround - I may even need to deploy a local R build. Fun times.

Cheers,
Tim