Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 606/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNAcopy 1.82.0  (landing page)
Venkatraman E. Seshan
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/DNAcopy
git_branch: RELEASE_3_21
git_last_commit: 10cfba5
git_last_commit_date: 2025-04-15 09:34:33 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD BIN results for DNAcopy on lconway

To the developers/maintainers of the DNAcopy package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DNAcopy.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: DNAcopy
Version: 1.82.0
Command: rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNAcopy_1.82.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DNAcopy.buildbin-libdir
StartedAt: 2025-04-22 00:43:10 -0400 (Tue, 22 Apr 2025)
EndedAt: 2025-04-22 00:43:23 -0400 (Tue, 22 Apr 2025)
EllapsedTime: 12.8 seconds
RetCode: 0
Status:   OK  
PackageFile: DNAcopy_1.82.0.tgz
PackageFileSize: 498.3 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNAcopy_1.82.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DNAcopy.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DNAcopy.buildbin-libdir DNAcopy_1.82.0.tar.gz'
>>>>>>> 

* installing *source* package ‘DNAcopy’ ...
** this is package ‘DNAcopy’ version ‘1.82.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
using SDK: ‘MacOSX11.3.sdk’
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f:17:16:

   17 |      2     tmaxi, tmaxj, nal0
      |                ^
Warning: 'tmaxi' may be used uninitialized [-Wmaybe-uninitialized]
cbsWtstats.f:17:23:

   17 |      2     tmaxi, tmaxj, nal0
      |                       ^
Warning: 'tmaxj' may be used uninitialized [-Wmaybe-uninitialized]
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c cbststats.f -o cbststats.o
cbststats.f:258:72:

  258 |                      tmaxj = sxmxi + i2j
      |                                                                        ^
Warning: 'sxmxi' may be used uninitialized [-Wmaybe-uninitialized]
cbststats.f:11:63:

   11 |      1     nb2, bi, bj, ilo, ihi, jlo, jhi, alenmax, i2j, sxmxi,
      |                                                               ^
note: 'sxmxi' was declared here
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c changepoints-wtd.f -o changepoints-wtd.o
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c changepoints.f -o changepoints.o
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c esegment.f -o esegment.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c flchoose.c -o flchoose.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fphyper.c -o fphyper.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fpnorm.c -o fpnorm.o
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c getbdry.f -o getbdry.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c prune.f -o prune.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rshared.c -o rshared.o
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c segmentp.f -o segmentp.o
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c smoothCNA.f -o smoothCNA.o
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c tailprobs.f -o tailprobs.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 DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o init.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-bioc/meat/DNAcopy.buildbin-libdir/00LOCK-DNAcopy/00new/DNAcopy/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** 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 (DNAcopy)


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

>>>>>>> Paths before fix:
DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so:
	DNAcopy.so (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so"

>>>>>>> Paths after fix:
DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so:
	DNAcopy.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)