* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘microseq’ ...
** this is package ‘microseq’ version ‘2.1.6’
** package ‘microseq’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpKjkyEW/R.INSTALL2ef4db7f6aaf9f/microseq/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ORF_index.cpp -o ORF_index.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c extractSeq.cpp -o extractSeq.o
gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c revComp.cpp -o revComp.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c translate.cpp -o translate.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o microseq.so ORF_index.o RcppExports.o extractSeq.o init.o revComp.o translate.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpKjkyEW/R.INSTALL2ef4db7f6aaf9f/microseq/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpKjkyEW/R.INSTALL2ef4db7f6aaf9f/microseq/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpKjkyEW/R.INSTALL2ef4db7f6aaf9f/microseq/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-microseq/00new/microseq/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘microseq’
    finding HTML links ... done
    backTranslate                           html  
    findGenes                               html  
    findOrfs                                html  
Rd warning: findOrfs.Rd:19: missing link ‘tibble’
    findrRNA                                html  
    gff2fasta                               html  
Rd warning: gff2fasta.Rd:24: missing link ‘tibble’
    gregexpr                                html  
    iupac2regex                             html  
    lorfs                                   html  
Rd warning: lorfs.Rd:13: missing link ‘tibble’
    microseq-package                        html  
    msa2mat                                 html  
    msaTrim                                 html  
    msalign                                 html  
Rd warning: msalign.Rd:15: missing link ‘tibble’
    muscle                                  html  
    orfLength                               html  
    orfSignature                            html  
    readFasta                               html  
Rd warning: readFasta.Rd:14: missing link ‘tibble’
Rd warning: readFasta.Rd:36: missing link ‘tibble’
Rd warning: readFasta.Rd:21: missing link ‘tibble’
    readFastq                               html  
Rd warning: readFastq.Rd:35: missing link ‘tibble’
Rd warning: readFastq.Rd:19: missing link ‘tibble’
    readGFF                                 html  
Rd warning: readGFF.Rd:27: missing link ‘tibble’
    reverseComplement                       html  
    translate                               html  
** 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 (microseq)