Venkatraman E. Seshan
| Snapshot Date: 2025-01-23 13:40 -0500 (Thu, 23 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/DNAcopy |
| git_branch: devel |
| git_last_commit: 8c04c59 |
| git_last_commit_date: 2024-10-29 09:22:58 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-24 11:41 -0500 (Fri, 24 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4609 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4393 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3839 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3835 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 589/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DNAcopy 1.81.0 (landing page) Venkatraman E. Seshan
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: DNAcopy |
| Version: 1.81.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DNAcopy |
| StartedAt: 2025-01-23 15:04:57 -0500 (Thu, 23 Jan 2025) |
| EndedAt: 2025-01-23 15:05:10 -0500 (Thu, 23 Jan 2025) |
| EllapsedTime: 13.2 seconds |
| RetCode: 1 |
| Status: ERROR |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DNAcopy
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘DNAcopy’ ...
** this is package ‘DNAcopy’ version ‘1.81.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using SDK: ‘MacOSX11.3.sdk’
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f:17:23:
17 | 2 tmaxi, tmaxj, nal0
| ^
Warning: ‘tmaxj’ may be used uninitialized [-Wmaybe-uninitialized]
cbsWtstats.f:17:16:
17 | 2 tmaxi, tmaxj, nal0
| ^
Warning: ‘tmaxi’ 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:11:63:
11 | 1 nb2, bi, bj, ilo, ihi, jlo, jhi, alenmax, i2j, sxmxi,
| ^
Warning: ‘sxmxi’ may be used uninitialized [-Wmaybe-uninitialized]
/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 -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0'
ld: library not found for -lemutls_w
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [DNAcopy.so] Error 1
ERROR: compilation failed for package ‘DNAcopy’
* removing ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DNAcopy’