Back to Mac ARM64 build report for BioC 3.16
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This page was generated on 2023-04-19 11:01:53 -0400 (Wed, 19 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnsonmacOS 13.0 Venturaarm644.2.2 (2022-10-31) -- "Innocent and Trusting" 4256
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BUILD BIN results for CNEr on kjohnson


To the developers/maintainers of the CNEr package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 361/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
CNEr 1.34.0  (landing page)
Ge Tan
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/CNEr
git_branch: RELEASE_3_16
git_last_commit: 878de98
git_last_commit_date: 2022-11-01 11:09:13 -0400 (Tue, 01 Nov 2022)
kjohnsonmacOS 13.0 Ventura / arm64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CNEr
Version: 1.34.0
Command: rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNEr_1.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNEr.buildbin-libdir
StartedAt: 2023-04-18 14:37:30 -0400 (Tue, 18 Apr 2023)
EndedAt: 2023-04-18 14:39:42 -0400 (Tue, 18 Apr 2023)
EllapsedTime: 131.8 seconds
RetCode: 0
Status:   OK  
PackageFile: CNEr_1.34.0.tgz
PackageFileSize: 10.36 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNEr_1.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNEr.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNEr.buildbin-libdir CNEr_1.34.0.tar.gz'
>>>>>>> 

* installing *source* package ‘CNEr’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_CNEr.c -o R_init_CNEr.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.c -o utils.o
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
  int _binFirstShift = binFirstShift();
      ^
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
  int _binNextShift = binNextShift();
      ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c io.c -o io.o
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
  struct axt *axt=NULL, *curAxt;
                         ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ceScan.c -o ceScan.o
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
  char rest, path[PATH_LEN];
       ^
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
  int i, n;
         ^
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
  struct slCNE *CNE, *nextCNE, *el_CNE;
                ^
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
  struct slThreshold *thresholds, *nextThreshold, *el_threshold;
                      ^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
  int nrCNE[nrThresholds], i;
      ^
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
  int nrCNE[nrThresholds], i;
                           ^
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
  struct slCNE *CNE;
                ^
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
  int nrThresholds = GET_LENGTH(winSize);
      ^
8 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/axt.c -o ucsc/axt.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/base64.c -o ucsc/base64.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/binRange.c -o ucsc/binRange.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/bits.c -o ucsc/bits.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/chain.c -o ucsc/chain.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c:475:16: warning: unused function 'cirTreeOverlaps' [-Wunused-function]
INLINE boolean cirTreeOverlaps(int qChrom, int qStart, int qEnd, 
               ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/common.c -o ucsc/common.o
ucsc/common.c:1982:18: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        if ((*in == '"'))
             ~~~~^~~~~~
ucsc/common.c:1982:18: note: remove extraneous parentheses around the comparison to silence this warning
        if ((*in == '"'))
            ~    ^     ~
ucsc/common.c:1982:18: note: use '=' to turn this equality comparison into an assignment
        if ((*in == '"'))
                 ^~
                 =
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/dlist.c -o ucsc/dlist.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c:942:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
int pastPoly = 0;
    ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/dystring.c -o ucsc/dystring.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/errabort.c -o ucsc/errabort.o
ucsc/errabort.c:30:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
                  ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/hash.c -o ucsc/hash.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/https.c -o ucsc/https.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/intExp.c -o ucsc/intExp.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/kxTok.c -o ucsc/kxTok.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/linefile.c -o ucsc/linefile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/localmem.c -o ucsc/localmem.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/memalloc.c -o ucsc/memalloc.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/obscure.c -o ucsc/obscure.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/options.c -o ucsc/options.o
ucsc/options.c:49:11: warning: variable 'discardMe' set but not used [-Wunused-but-set-variable]
long long discardMe = 0;
          ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/pipeline.c -o ucsc/pipeline.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/sqlList.c -o ucsc/sqlList.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/verbose.c -o ucsc/verbose.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/os.c -o ucsc/os.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include  -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CNEr.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/CNEr.buildbin-libdir/00LOCK-CNEr/00new/CNEr/libs
** R
** data
** 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
** 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 (CNEr)


>>>>>>> 
>>>>>>> FIXING LINKS FOR CNEr.buildbin-libdir/CNEr/libs/CNEr.so
>>>>>>> 

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "CNEr.buildbin-libdir/CNEr/libs/CNEr.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "CNEr.buildbin-libdir/CNEr/libs/CNEr.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "CNEr.buildbin-libdir/CNEr/libs/CNEr.so"