Multiple platform build/check report for BioC 3.23 - INSTALL results for ShortRead on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"	4453
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-02-28 r89501) -- "Unsuffered Consequences"	3376
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
INSTALL results for ShortRead on nebbiolo1

To the developers/maintainers of the ShortRead package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ShortRead.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: ShortRead
Version: 1.69.2
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ShortRead
StartedAt: 2026-03-06 17:31:46 -0500 (Fri, 06 Mar 2026)
EndedAt: 2026-03-06 17:32:23 -0500 (Fri, 06 Mar 2026)
EllapsedTime: 37.1 seconds
RetCode: 1
Status: ERROR
Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ShortRead
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘ShortRead’ ...
** this is package ‘ShortRead’ version ‘1.69.2’
** using staged installation
checking for gcc... gcc -std=gnu2x
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 gcc -std=gnu2x accepts -g... yes
checking for gcc -std=gnu2x option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -std=gnu2x -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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c alphabet.c -o alphabet.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c count.c -o count.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c io.c -o io.o
io.c: In function ‘write_fastq’:
io.c:49:11: warning: implicit declaration of function ‘IS_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
   49 |     if (!(IS_S4_OBJECT(id) && strcmp(get_classname(id), "BStringSet") == 0))
      |           ^~~~~~~~~~~~
      |           SET_OBJECT
io.c: In function ‘read_prb_as_character’:
io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=]
  227 |         error("could not read file '%f'", translateChar(STRING_ELT(fname, 0)));
      |                                     ~^
      |                                      |
      |                                      double
      |                                     %s
In file included from io.c:5:
io.c: In function ‘_AlignedRead_Solexa_make’:
call.h:10:5: warning: implicit declaration of function ‘SET_TYPEOF’; did you mean ‘TYPEOF’? [-Wimplicit-function-declaration]
   10 |     SET_TYPEOF((T), LANGSXP);                                   \
      |     ^~~~~~~~~~
io.c:510:5: note: in expansion of macro ‘NEW_CALL’
  510 |     NEW_CALL(s, t, "SFastqQuality", nmspc, 2);
      |     ^~~~~~~~
io.c: In function ‘_read_solexa_export_file’:
io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  658 |                 error("invalid 'strand' field '%s', %s:%d",
      |                                                ~^
      |                                                 |
      |                                                 char *
      |                                                %d
  659 |                       *elt[13], fname, lineno);
      |                       ~~~~~~~~                   
      |                       |
      |                       int
io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  676 |             error("invalid 'filtering' field '%s', %s:%d",
      |                                               ~^
      |                                                |
      |                                                char *
      |                                               %d
  677 |                   *elt[21], fname, lineno);
      |                   ~~~~~~~~                      
      |                   |
      |                   int
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c io_bowtie.c -o io_bowtie.o
In file included from io_bowtie.c:3:
io_bowtie.c: In function ‘_AlignedRead_Bowtie_make’:
call.h:10:5: warning: implicit declaration of function ‘SET_TYPEOF’; did you mean ‘TYPEOF’? [-Wimplicit-function-declaration]
   10 |     SET_TYPEOF((T), LANGSXP);                                   \
      |     ^~~~~~~~~~
io_bowtie.c:73:5: note: in expansion of macro ‘NEW_CALL’
   73 |     NEW_CALL(s, t, qtype, nmspc, 2);
      |     ^~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c io_soap.c -o io_soap.o
In file included from io_soap.c:3:
io_soap.c: In function ‘_AlignedRead_SOAP_make’:
call.h:10:5: warning: implicit declaration of function ‘SET_TYPEOF’; did you mean ‘TYPEOF’? [-Wimplicit-function-declaration]
   10 |     SET_TYPEOF((T), LANGSXP);                                   \
      |     ^~~~~~~~~~
io_soap.c:82:5: note: in expansion of macro ‘NEW_CALL’
   82 |     NEW_CALL(s, t, qtype, nmspc, 2);
      |     ^~~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/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  -g -O2  -Wall -Werror=format-security  -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’:
readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   35 |       (void) fread( seq_name, sizeof(char), name_len, fp );
      |              ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   36 |       (void) fread( &seq_ori_len, sizeof(int), 1, fp );
      |              ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   37 |       (void) fread( &seq_len, sizeof(int), 1, fp );
      |              ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/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  -g -O2  -Wall -Werror=format-security  -c read_maq_map.cc -o read_maq_map.o
In file included from read_maq_map.cc:13:
maqmap_m.h: In function ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 128]’:
maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free]
  102 |             Rf_error("MAQ format '%d' not supported", mm->format);
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]’,
    inlined from ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]’ at maqmap_m.h:74:35,
    inlined from ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 128]’ at maqmap_m.h:101:30:
maqmap_m.h:84:14: note: call to ‘void free(void*)’ here
   84 |     std::free(mm);
      |     ~~~~~~~~~^~~~
maqmap_m.h: In function ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 64]’:
maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free]
  102 |             Rf_error("MAQ format '%d' not supported", mm->format);
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]’,
    inlined from ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]’ at maqmap_m.h:74:35,
    inlined from ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 64]’ at maqmap_m.h:101:30:
maqmap_m.h:84:14: note: call to ‘void free(void*)’ here
   84 |     std::free(mm);
      |     ~~~~~~~~~^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c sampler.c -o sampler.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c trim.c -o trim.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c util.c -o util.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c xsnap.c -o xsnap.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-ShortRead/00new/ShortRead/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 from temporary location
Error: package or namespace load failed for ‘ShortRead’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-ShortRead/00new/ShortRead/libs/ShortRead.so':
  /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-ShortRead/00new/ShortRead/libs/ShortRead.so: undefined symbol: IS_S4_OBJECT
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/ShortRead’