Running ‘testthat.R’ [60s/119s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > # library("testthat")
  > # library("inDAGO")
  > 
  > testthat::test_check("inDAGO")
  Loading required package: inDAGO
  The following packages are not installed: ShortRead.
  To enable all the features of inDAGO, install with:
    if (!requireNamespace('BiocManager', quietly=TRUE))
      install.packages('BiocManager')
    BiocManager::install(c("ShortRead"))
  
  'getOption("repos")' replaces Bioconductor standard repositories, see
  'help("repositories", package = "BiocManager")' for details.
  Replacement repositories:
      CRAN: file:///data/gannet/ripley/R
  Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
    (2026-03-03 r89531)
  Installing package(s) 'BiocVersion', 'ShortRead'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BiocVersion_3.23.1.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/ShortRead_1.69.2.tar.gz'
  * installing *source* package ‘BiocVersion’ ...
  ** this is package ‘BiocVersion’ version ‘3.23.1’
  ** using staged installation
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded from temporary location
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
  * DONE (BiocVersion)
  * installing *source* package ‘ShortRead’ ...
  ** this is package ‘ShortRead’ version ‘1.69.2’
  ** using staged installation
  checking for gcc... clang-22 -std=gnu23
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables... 
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether we are using the GNU C compiler... yes
  checking whether clang-22 -std=gnu23 accepts -g... yes
  checking for clang-22 -std=gnu23 option to accept ISO C89... unsupported
  checking for gzeof in -lz... yes
  checking how to run the C preprocessor... clang-22 -std=gnu23 -E
  checking for grep that handles long lines and -e... /usr/bin/grep
  checking for egrep... /usr/bin/grep -E
  checking for ANSI C header files... yes
  checking for sys/types.h... yes
  checking for sys/stat.h... yes
  checking for stdlib.h... yes
  checking for string.h... yes
  checking for memory.h... yes
  checking for strings.h... yes
  checking for inttypes.h... yes
  checking for stdint.h... yes
  checking for unistd.h... yes
  checking size of unsigned long... 8
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  using C compiler: ‘clang version 22.1.0 (https://github.com/llvm/llvm-project 4434dabb69916856b824f68a64b029c67175e532)’
  using C++ compiler: ‘clang version 22.1.0 (https://github.com/llvm/llvm-project 4434dabb69916856b824f68a64b029c67175e532)’
  make[1]: Entering directory '/tmp/RtmpcfOaIP/working_dir/Rtmp6cL7cm/R.INSTALL2a322289819d1/ShortRead/src'
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Biostrings_stubs.c -o Biostrings_stubs.o
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c IRanges_stubs.c -o IRanges_stubs.o
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c R_init_ShortRead.c -o R_init_ShortRead.o
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c XVector_stubs.c -o XVector_stubs.o
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c alphabet.c -o alphabet.o
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c count.c -o count.o
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c io.c -o io.o
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c io_bowtie.c -o io_bowtie.o
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c io_soap.c -o io_soap.o
  clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c readBfaToc.cc -o readBfaToc.o
  clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c read_maq_map.cc -o read_maq_map.o
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c sampler.c -o sampler.o
  io.c:49:11: error: use of undeclared identifier 'IS_S4_OBJECT'; did you mean 'SET_OBJECT'?
     49 |     if (!(IS_S4_OBJECT(id) && strcmp(get_classname(id), "BStringSet") == 0))
        |           ^~~~~~~~~~~~
        |           SET_OBJECT
  /data/gannet/ripley/R/R-clang/include/Rinternals.h:1215:7: note: 'SET_OBJECT' declared here
   1215 | void (SET_OBJECT)(SEXP x, int v); // used by Rcpp (not?), Matrix and more
        |       ^
  io.c:49:26: error: too few arguments to function call, expected 2, have 1
     49 |     if (!(IS_S4_OBJECT(id) && strcmp(get_classname(id), "BStringSet") == 0))
        |           ~~~~~~~~~~~~   ^
  /data/gannet/ripley/R/R-clang/include/Rinternals.h:1215:7: note: 'SET_OBJECT' declared here
   1215 | void (SET_OBJECT)(SEXP x, int v); // used by Rcpp (not?), Matrix and more
        |       ^           ~~~~~~~~~~~~~
  io_soap.c:82:5: error: use of undeclared identifier 'SET_TYPEOF'
     82 |     NEW_CALL(s, t, qtype, nmspc, 2);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ./call.h:10:5: note: expanded from macro 'NEW_CALL'
     10 |     SET_TYPEOF((T), LANGSXP);                                   \
        |     ^~~~~~~~~~
  io_bowtie.c:73:5: error: use of undeclared identifier 'SET_TYPEOF'
     73 |     NEW_CALL(s, t, qtype, nmspc, 2);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ./call.h:10:5: note: expanded from macro 'NEW_CALL'
     10 |     SET_TYPEOF((T), LANGSXP);                                   \
        |     ^~~~~~~~~~
  io.c:51:11: error: use of undeclared identifier 'IS_S4_OBJECT'; did you mean 'SET_OBJECT'?
     51 |     if (!(IS_S4_OBJECT(sread) &&
        |           ^~~~~~~~~~~~
        |           SET_OBJECT
  /data/gannet/ripley/R/R-clang/include/Rinternals.h:1215:7: note: 'SET_OBJECT' declared here
   1215 | void (SET_OBJECT)(SEXP x, int v); // used by Rcpp (not?), Matrix and more
        |       ^
  io_soap.c:88:5: error: use of undeclared identifier 'SET_TYPEOF'
     88 |     NEW_CALL(s, t, ".SOAP_AlignedDataFrame", nmspc, 6);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ./call.h:10:5: note: expanded from macro 'NEW_CALL'
     10 |     SET_TYPEOF((T), LANGSXP);         io_bowtie.c : 79 : 5 :   error:  use of undeclared identifier 'SET_TYPEOF' 
                   79  |     \ 
         N| E    ^~~~~~~~~~W
  _CALL(s, t, ".Bowtie_AlignedDataFrame", nmspc, 3);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ./call.h:10:5: note: expanded from macro 'NEW_CALL'
     10 |     SET_TYPEOF((T), LANGSXP);                                   \
        |     ^~~~~~~~~~
  io.c:51:29: error: too few arguments to function call, expected 2, have 1
     51 |     if (!(IS_S4_OBJECT(sread) &&
        |           ~~~~~~~~~~~~      ^
  /data/gannet/ripley/R/R-clang/include/Rinternals.h:1215:7: note: 'SET_OBJECT' declared here
   1215 | void (SET_OBJECT)(SEXP x, int v); // used by Rcpp (not?), Matrix and more
        |       ^           ~~~~~~~~~~~~~
  io_bowtie.cio_soap.c::8698::55::  error: error: use of undeclared identifier 'SET_TYPEOF'use of undeclared identifier 'SET_TYPEOF'
  
        9886 |  |         NNEEWW__CCAALLLL((ss,,  tt,,  ""AAlliiggnneeddRReeaadd"",,  nnmmssppcc,,  88));;
  
              | |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  ./call.h./call.h::1010::55::  note: note: expanded from macro 'NEW_CALL'expanded from macro 'NEW_CALL'
  
        1010 |  |         SSEETT__TTYYPPEEOOFF((((TT)),,  LLAANNGGSSXXPP));;                                                                      \\
  
              | |     ^~~~~~~~~~    ^~~~~~~~~~
  
  3 errors generated.
  io.c:227:43: warning: format specifies type 'double' but the argument has type 'const char *' [-Wformat]
    227 |         error("could not read file '%f'", translateChar(STRING_ELT(fname, 0)));
        |                                     ~~    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        |                                     %s
  /data/gannet/ripley/R/R-clang/include/Rinternals.h:1021:24: note: expanded from macro 'translateChar'
   1021 | #define translateChar           Rf_translateChar
        |                                 ^
  3 errors generated.
  make[1]: *** [/data/gannet/ripley/R/R-clang/etc/Makeconf:190: io_bowtie.o] Error 1
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c trim.c -o trim.o
  make[1]: *** [/data/gannet/ripley/R/R-clang/etc/Makeconf:190: io_soap.o] Error 1
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c util.c -o util.o
  clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/S4Vectors/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/IRanges/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/XVector/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Biostrings/include' -I'/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c xsnap.c -o xsnap.o
  io.c:510:5: error: use of undeclared identifier 'SET_TYPEOF'
    510 |     NEW_CALL(s, t, "SFastqQuality", nmspc, 2);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ./call.h:10:5: note: expanded from macro 'NEW_CALL'
     10 |     SET_TYPEOF((T), LANGSXP);                                   \
        |     ^~~~~~~~~~
  io.c:516:5: error: use of undeclared identifier 'SET_TYPEOF'
    516 |     NEW_CALL(s, t, "NumericQuality", nmspc, 2);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ./call.h:10:5: note: expanded from macro 'NEW_CALL'
     10 |     SET_TYPEOF((T), LANGSXP);                                   \
        |     ^~~~~~~~~~
  io.c:525:5: error: use of undeclared identifier 'SET_TYPEOF'
    525 |     NEW_CALL(s, t, "factor", nmspc, 2);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ./call.h:10:5: note: expanded from macro 'NEW_CALL'
     10 |     SET_TYPEOF((T), LANGSXP);                                   \
        |     ^~~~~~~~~~
  io.c:531:5: error: use of undeclared identifier 'SET_TYPEOF'
    531 |     NEW_CALL(s, t, "data.frame", nmspc,
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    532 |              8 + withMultiplexIndex + withPairedReadNumber);
        |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ./call.h:10:5: note: expanded from macro 'NEW_CALL'
     10 |     SET_TYPEOF((T), LANGSXP);                                   \
        |     ^~~~~~~~~~
  io.c:550:5: error: use of undeclared identifier 'SET_TYPEOF'
    550 |     NEW_CALL(s, t, ".SolexaExport_AlignedDataFrame", nmspc, 2);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ./call.h:10:5: note: expanded from macro 'NEW_CALL'
     10 |     SET_TYPEOF((T), LANGSXP);                                   \
        |     ^~~~~~~~~~
  io.c:556:5: error: use of undeclared identifier 'SET_TYPEOF'
    556 |     NEW_CALL(s, t, "AlignedRead", nmspc, 8 + withIds);
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ./call.h:10:5: note: expanded from macro 'NEW_CALL'
     10 |     SET_TYPEOF((T), LANGSXP);                                   \
        |     ^~~~~~~~~~
  io.c:659:23: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
    658 |                 error("invalid 'strand' field '%s', %s:%d",
        |                                                ~~
        |                                                %c
    659 |                       *elt[13], fname, lineno);
        |                       ^~~~~~~~
  io.c:677:19: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
    676 |             error("invalid 'filtering' field '%s', %s:%d",
        |                                               ~~
        |                                               %c
    677 |                   *elt[21], fname, lineno);
        |                   ^~~~~~~~
  3 warnings and 10 errors generated.
  make[1]: *** [/data/gannet/ripley/R/R-clang/etc/Makeconf:190: io.o] Error 1
  make[1]: Target 'all' not remade because of errors.
  make[1]: Leaving directory '/tmp/RtmpcfOaIP/working_dir/Rtmp6cL7cm/R.INSTALL2a322289819d1/ShortRead/src'
  ERROR: compilation failed for package ‘ShortRead’
  * removing ‘/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/ShortRead’
  * restoring previous ‘/tmp/RtmpcfOaIP/RLIBS_27ec3c52ccd02a/ShortRead’
  
  The downloaded source packages are in
  	'/tmp/RtmpcfOaIP/working_dir/RtmpmB6jXG/downloaded_packages'
  Old packages: 'Biobase', 'BiocGenerics', 'BiocIO', 'BiocParallel',
    'Biostrings', 'DESeq2', 'DelayedArray', 'GenomicAlignments', 'GenomicRanges',
    'HTSFilter', 'IRanges', 'MatrixGenerics', 'Rhtslib', 'Rsamtools', 'Rsubread',
    'S4Arrays', 'S4Vectors', 'Seqinfo', 'ShortRead', 'SparseArray',
    'SummarizedExperiment', 'XVector', 'cigarillo', 'edgeR', 'limma', 'pwalign',
    'rtracklayer'
  Saving _problems/test-inDAGO_shiny-26.R
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-inDAGO_shiny.R:26:3'): Shiny app is generated ──────────────────
  Error in `inDAGO()`: The following packages are not installed: ShortRead.
  To enable all the features of inDAGO install with:
    if (!requireNamespace('BiocManager', quietly=TRUE))
      install.packages('BiocManager')
    BiocManager::install(c("ShortRead"))
  
  Backtrace:
      ▆
   1. ├─testthat::expect_s3_class(inDAGO(), "shiny.appobj") at test-inDAGO_shiny.R:26:3
   2. │ └─testthat::quasi_label(enquo(object))
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─inDAGO::inDAGO()
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted