##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:XNAString.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings XNAString_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/XNAString.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘XNAString/DESCRIPTION’ ... OK
* this is package ‘XNAString’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘XNAString’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘XNAString_vignette.Rmd’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘XNAString_vignette.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.156   0.044   0.195 

... incomplete output.  Crash?

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/XNAString.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL XNAString
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘XNAString’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/utils/higher_order_functions.c -o ViennaRNA/utils/higher_order_functions.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/utils/string_utils.c -o ViennaRNA/utils/string_utils.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/utils/utils.c -o ViennaRNA/utils/utils.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/constraints/SHAPE.c -o ViennaRNA/constraints/SHAPE.o
ViennaRNA/constraints/SHAPE.c: In function ‘vrna_constraints_add_SHAPE’:
ViennaRNA/constraints/SHAPE.c:202:10: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  202 |   method = shape_method;
      |          ^
ViennaRNA/constraints/SHAPE.c:206:51: warning: comparison between pointer and integer
  206 |   vrna_file_SHAPE_read(shape_file, length, method == 'W' ? 0 : -1, sequence, values);
      |                                                   ^~
ViennaRNA/constraints/SHAPE.c:208:14: warning: comparison between pointer and integer
  208 |   if (method == 'D') {
      |              ^~
ViennaRNA/constraints/SHAPE.c:210:21: warning: comparison between pointer and integer
  210 |   } else if (method == 'Z') {
      |                     ^~
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/constraints/hard.c -o ViennaRNA/constraints/hard.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/datastructures/char_stream.c -o ViennaRNA/datastructures/char_stream.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/datastructures/heap.c -o ViennaRNA/datastructures/heap.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/datastructures/stream_output.c -o ViennaRNA/datastructures/stream_output.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/io/file_formats.c -o ViennaRNA/io/file_formats.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/landscape/findpath.c -o ViennaRNA/landscape/findpath.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/landscape/move.c -o ViennaRNA/landscape/move.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/landscape/neighbor.c -o ViennaRNA/landscape/neighbor.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/io/io_utils.c -o ViennaRNA/io/io_utils.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/external.c -o ViennaRNA/loops/external.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/internal.c -o ViennaRNA/loops/internal.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/external_bt.c -o ViennaRNA/loops/external_bt.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/hairpin_pf.c -o ViennaRNA/loops/hairpin_pf.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/internal_bt.c -o ViennaRNA/loops/internal_bt.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/multibranch_pf.c -o ViennaRNA/loops/multibranch_pf.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/hairpin.c -o ViennaRNA/loops/hairpin.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/multibranch.c -o ViennaRNA/loops/multibranch.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/external_pf.c -o ViennaRNA/loops/external_pf.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/hairpin_bt.c -o ViennaRNA/loops/hairpin_bt.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/internal_pf.c -o ViennaRNA/loops/internal_pf.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/loops/multibranch_bt.c -o ViennaRNA/loops/multibranch_bt.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/params/default.c -o ViennaRNA/params/default.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/params/io.c -o ViennaRNA/params/io.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/params/params.c -o ViennaRNA/params/params.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/search/BoyerMoore.c -o ViennaRNA/search/BoyerMoore.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/2Dfold.c -o ViennaRNA/2Dfold.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/concentrations.c -o ViennaRNA/concentrations.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/gquad.c -o ViennaRNA/gquad.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/part_func.c -o ViennaRNA/part_func.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/snofold.c -o ViennaRNA/snofold.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/2Dpfold.c -o ViennaRNA/2Dpfold.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/alphabet.c -o ViennaRNA/alphabet.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/grammar.c -o ViennaRNA/grammar.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/boltzmann_sampling.c -o ViennaRNA/boltzmann_sampling.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/dist_vars.c -o ViennaRNA/dist_vars.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/part_func_up.c -o ViennaRNA/part_func_up.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/special_const.c -o ViennaRNA/special_const.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/Lfold.c -o ViennaRNA/Lfold.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/bs_wrappers.c -o ViennaRNA/bs_wrappers.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/dp_matrices.c -o ViennaRNA/dp_matrices.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/mfe.c -o ViennaRNA/mfe.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/MEA.c -o ViennaRNA/MEA.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/c_plex.c -o ViennaRNA/c_plex.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/duplex.c -o ViennaRNA/duplex.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/mfe_window.c -o ViennaRNA/mfe_window.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/perturbation_fold.c -o ViennaRNA/perturbation_fold.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/subopt.c -o ViennaRNA/subopt.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/ProfileAln.c -o ViennaRNA/ProfileAln.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/centroid.c -o ViennaRNA/centroid.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/equilibrium_probs.c -o ViennaRNA/equilibrium_probs.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/mfe_window_wrappers.c -o ViennaRNA/mfe_window_wrappers.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/pf_fold.c -o ViennaRNA/pf_fold.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/cofold.c -o ViennaRNA/cofold.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/eval.c -o ViennaRNA/eval.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/mfe_wrappers.c -o ViennaRNA/mfe_wrappers.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/plex.c -o ViennaRNA/plex.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/RNAstruct.c -o ViennaRNA/RNAstruct.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/eval_wrappers.c -o ViennaRNA/eval_wrappers.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/mm.c -o ViennaRNA/mm.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/plex_functions.c -o ViennaRNA/plex_functions.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/units.c -o ViennaRNA/units.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/ali_plex.c -o ViennaRNA/ali_plex.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/combinatorics.c -o ViennaRNA/combinatorics.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/fold.c -o ViennaRNA/fold.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/model.c -o ViennaRNA/model.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/ribo.c -o ViennaRNA/ribo.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/commands.c -o ViennaRNA/commands.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/fold_compound.c -o ViennaRNA/fold_compound.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/sequence.c -o ViennaRNA/sequence.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c ViennaRNA/unstructured_domains.c -o ViennaRNA/unstructured_domains.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c predict_mfe.cpp -o predict_mfe.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o XNAString.so ./ViennaRNA/utils/cpu.o ./ViennaRNA/utils/msa_utils.o ./ViennaRNA/utils/structure_tree.o ./ViennaRNA/utils/higher_order_functions.o ./ViennaRNA/utils/string_utils.o ./ViennaRNA/utils/structure_utils.o ./ViennaRNA/utils/utils.o ./ViennaRNA/constraints/SHAPE.o ./ViennaRNA/constraints/constraints.o ./ViennaRNA/constraints/soft.o ./ViennaRNA/constraints/hard.o ./ViennaRNA/constraints/ligand.o ./ViennaRNA/datastructures/basic_datastructures.o ./ViennaRNA/datastructures/lists.o ./ViennaRNA/datastructures/char_stream.o ./ViennaRNA/datastructures/heap.o ./ViennaRNA/datastructures/stream_output.o ./ViennaRNA/io/file_formats.o ./ViennaRNA/landscape/findpath.o ./ViennaRNA/landscape/move.o ./ViennaRNA/landscape/neighbor.o ./ViennaRNA/io/io_utils.o ./ViennaRNA/loops/external.o ./ViennaRNA/loops/internal.o ./ViennaRNA/loops/external_bt.o ./ViennaRNA/loops/hairpin_pf.o ./ViennaRNA/loops/internal_bt.o ./ViennaRNA/loops/multibranch_pf.o ./ViennaRNA/loops/hairpin.o ./ViennaRNA/loops/multibranch.o ./ViennaRNA/loops/external_pf.o ./ViennaRNA/loops/hairpin_bt.o ./ViennaRNA/loops/internal_pf.o ./ViennaRNA/loops/multibranch_bt.o ./ViennaRNA/params/default.o ./ViennaRNA/params/io.o ./ViennaRNA/params/params.o ./ViennaRNA/search/BoyerMoore.o ./ViennaRNA/2Dfold.o ./ViennaRNA/concentrations.o ./ViennaRNA/gquad.o ./ViennaRNA/part_func.o ./ViennaRNA/snofold.o ./ViennaRNA/2Dpfold.o ./ViennaRNA/alphabet.o ./ViennaRNA/grammar.o ./ViennaRNA/boltzmann_sampling.o ./ViennaRNA/dist_vars.o ./ViennaRNA/part_func_up.o ./ViennaRNA/special_const.o ./ViennaRNA/Lfold.o ./ViennaRNA/bs_wrappers.o ./ViennaRNA/dp_matrices.o ./ViennaRNA/mfe.o ./ViennaRNA/MEA.o ./ViennaRNA/c_plex.o ./ViennaRNA/duplex.o ./ViennaRNA/mfe_window.o ./ViennaRNA/perturbation_fold.o ./ViennaRNA/subopt.o ./ViennaRNA/ProfileAln.o ./ViennaRNA/centroid.o ./ViennaRNA/equilibrium_probs.o ./ViennaRNA/mfe_window_wrappers.o ./ViennaRNA/pf_fold.o ./ViennaRNA/cofold.o ./ViennaRNA/eval.o ./ViennaRNA/mfe_wrappers.o ./ViennaRNA/plex.o ./ViennaRNA/RNAstruct.o ./ViennaRNA/eval_wrappers.o ./ViennaRNA/mm.o ./ViennaRNA/plex_functions.o ./ViennaRNA/units.o ./ViennaRNA/ali_plex.o ./ViennaRNA/combinatorics.o ./ViennaRNA/fold.o ./ViennaRNA/model.o ./ViennaRNA/ribo.o ./ViennaRNA/commands.o ./ViennaRNA/fold_compound.o ./ViennaRNA/sequence.o ./ViennaRNA/unstructured_domains.o predict_mfe.o RcppExports.o -L../src -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-XNAString/00new/XNAString/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
in method for ‘name’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘name<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘base’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘base<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘sugar’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘sugar<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘backbone’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘backbone<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘target’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘target<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘conjugate5’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘conjugate5<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘conjugate3’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘conjugate3<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘dictionary’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘dictionary<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘secondary_structure’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘secondary_structure<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘compl_dictionary’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘compl_dictionary<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘duplex_structure’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘duplex_structure<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘default_sugar’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘default_sugar<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘default_backbone’ with signature ‘"XNAString"’: no definition for class “XNAString”
in method for ‘default_backbone<-’ with signature ‘"XNAString"’: no definition for class “XNAString”
Creating a new generic function for ‘objects’ in package ‘XNAString’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (XNAString)