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This page was generated on 2024-05-18 11:37:40 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 387/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.40.0  (landing page)
Ge Tan
Snapshot Date: 2024-05-17 14:00:11 -0400 (Fri, 17 May 2024)
git_url: https://git.bioconductor.org/packages/CNEr
git_branch: RELEASE_3_19
git_last_commit: e967f84
git_last_commit_date: 2024-04-30 10:35:00 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

BUILD BIN results for CNEr on lconway


To the developers/maintainers of the CNEr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNEr.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: CNEr
Version: 1.40.0
Command: rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNEr_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNEr.buildbin-libdir
StartedAt: 2024-05-18 01:08:47 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 01:10:07 -0400 (Sat, 18 May 2024)
EllapsedTime: 79.9 seconds
RetCode: 0
Status:   OK  
PackageFile: CNEr_1.40.0.tgz
PackageFileSize: 10.49 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNEr_1.40.0.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_1.40.0.tar.gz'
>>>>>>> 

* installing *source* package ‘CNEr’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_CNEr.c -o R_init_CNEr.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
  struct slThreshold *thresholds, *nextThreshold, *el_threshold;
                      ^
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
  struct slCNE *CNE, *nextCNE, *el_CNE;
                ^
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
  int nrCNE[nrThresholds], i;
                           ^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/axt.c -o ucsc/axt.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/base64.c -o ucsc/base64.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/binRange.c -o ucsc/binRange.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/bits.c -o ucsc/bits.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/chain.c -o ucsc/chain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/dlist.c -o ucsc/dlist.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/dystring.c -o ucsc/dystring.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/hash.c -o ucsc/hash.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/https.c -o ucsc/https.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/intExp.c -o ucsc/intExp.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/kxTok.c -o ucsc/kxTok.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/linefile.c -o ucsc/linefile.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/localmem.c -o ucsc/localmem.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/memalloc.c -o ucsc/memalloc.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/obscure.c -o ucsc/obscure.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/pipeline.c -o ucsc/pipeline.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/sqlList.c -o ucsc/sqlList.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/verbose.c -o ucsc/verbose.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/os.c -o ucsc/os.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include   -g -fPIC  -falign-functions=64 -Wall -g -O2  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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
installing to /Users/biocbuild/bbs-3.19-bioc/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 PATHS TO DYNAMIC LIBRARIES FOR CNEr.buildbin-libdir/CNEr/libs/CNEr.so
>>>>>>> 

>>>>>>> Paths before fix:
CNEr.buildbin-libdir/CNEr/libs/CNEr.so:
	CNEr.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "CNEr.buildbin-libdir/CNEr/libs/CNEr.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "CNEr.buildbin-libdir/CNEr/libs/CNEr.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "CNEr.buildbin-libdir/CNEr/libs/CNEr.so"

>>>>>>> Paths after fix:
CNEr.buildbin-libdir/CNEr/libs/CNEr.so:
	CNEr.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)