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This page was generated on 2026-03-23 11:34 -0400 (Mon, 23 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" 4868
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" 4548
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

Package 226/2368HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.79.5  (landing page)
Hervé Pagès
Snapshot Date: 2026-03-22 13:40 -0400 (Sun, 22 Mar 2026)
git_url: https://git.bioconductor.org/packages/Biostrings
git_branch: devel
git_last_commit: 1006022
git_last_commit_date: 2026-03-06 01:36:30 -0400 (Fri, 06 Mar 2026)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    ERROR  
See other builds for Biostrings in R Universe.

BUILD BIN results for Biostrings on kjohnson3

To the developers/maintainers of the Biostrings package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Biostrings.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: Biostrings
Version: 2.79.5
Command: rm -rf Biostrings.buildbin-libdir && mkdir Biostrings.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Biostrings_2.79.5.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Biostrings.buildbin-libdir
StartedAt: 2026-03-22 22:42:49 -0400 (Sun, 22 Mar 2026)
EndedAt: 2026-03-22 22:43:03 -0400 (Sun, 22 Mar 2026)
EllapsedTime: 14.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf Biostrings.buildbin-libdir && mkdir Biostrings.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Biostrings_2.79.5.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Biostrings.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Biostrings.buildbin-libdir Biostrings_2.79.5.tar.gz'
>>>>>>> 

* installing *source* package ‘Biostrings’ ...
** this is package ‘Biostrings’ version ‘2.79.5’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c BAB_class.c -o BAB_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: unused function 'BitMatrix_print' [-Wunused-function]
  299 | static void BitMatrix_print(BitMatrix *bitmat)
      |             ^~~~~~~~~~~~~~~
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c MIndex_class.c -o MIndex_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_Biostrings.c -o R_init_Biostrings.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RoSeqs_utils.c -o RoSeqs_utils.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XStringSetList_class.c -o XStringSetList_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XStringSet_class.c -o XStringSet_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XString_class.c -o XString_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c find_palindromes.c -o find_palindromes.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gtestsim.c -o gtestsim.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c inject_code.c -o inject_code.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c lcsuffix.c -o lcsuffix.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c letter_frequency.c -o letter_frequency.o
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
  957 |   int x_width, y_width, x_length, *ans_mat, i, x_pos;
      |                                                ^~~~~
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c lowlevel_matching.c -o lowlevel_matching.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c match_PWM.c -o match_PWM.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c match_pattern.c -o match_pattern.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: unused function 'test_match_pattern_indels' [-Wunused-function]
    7 | static void test_match_pattern_indels(const char *p, const char *s,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c match_pdict.c -o match_pdict.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:1031:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
 1031 |         ACnode *node0, *node1, *node2;
      |                 ^
match_pdict_ACtree2.c:1076:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
 1076 |         ACnode *node0, *node1, *node2;
      |                 ^
match_pdict_ACtree2.c:139:13: warning: unused function 'debug_node_counting_functions' [-Wunused-function]
  139 | static void debug_node_counting_functions(int maxdepth)
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
match_pdict_ACtree2.c:602:21: warning: unused function 'a_nice_max_nodeextbuf_nelt' [-Wunused-function]
  602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~
4 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c:653:49: warning: unused variable 'ncol' [-Wunused-variable]
  653 |         int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
      |                                                        ^~~~
match_pdict_utils.c:713:6: warning: unused variable 'nelt' [-Wunused-variable]
  713 |         int nelt, nkey0, nkey1, nkey2, i, key;
      |             ^~~~
match_pdict_utils.c:819:20: warning: unused variable 'ndup' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                           ^~~~
match_pdict_utils.c:819:26: warning: unused variable 'nloci' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                 ^~~~~
match_pdict_utils.c:819:33: warning: unused variable 'NFC' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                        ^~~
match_pdict_utils.c:820:27: warning: unused variable 'total_NFC' [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                  ^~~~~~~~~
match_pdict_utils.c:820:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                                   ^~~~~~~~~~~~
match_pdict_utils.c:261:13: warning: unused function 'match_headtail_by_loc' [-Wunused-function]
  261 | static void match_headtail_by_loc(const HeadTail *headtail,
      |             ^~~~~~~~~~~~~~~~~~~~~
8 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c match_reporting.c -o match_reporting.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_fasta_files.c -o read_fasta_files.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_fastq_files.c -o read_fastq_files.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c replaceAt.c -o replaceAt.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c replace_letter_at.c -o replace_letter_at.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c strutils.c -o strutils.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c translate.c -o translate.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c unstrsplit_methods.c -o unstrsplit_methods.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.c -o utils.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c xscat.c -o xscat.o
clang -arch arm64 -std=gnu23 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o find_palindromes.o gtestsim.o inject_code.o lcsuffix.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/Biostrings.buildbin-libdir/00LOCK-Biostrings/00new/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet”
Creating a new generic function for ‘strsplit’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** 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 (Biostrings)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Biostrings.buildbin-libdir/Biostrings/libs/Biostrings.so
>>>>>>> 

>>>>>>> Paths before fix:
Biostrings.buildbin-libdir/Biostrings/libs/Biostrings.so:
	Biostrings.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)

>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!