Eleni Adam
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/hummingbird |
| git_branch: RELEASE_3_19 |
| git_last_commit: a78fbf8 |
| git_last_commit_date: 2024-04-30 11:25:54 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 993/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hummingbird 1.14.0 (landing page) Eleni Adam
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the hummingbird package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hummingbird.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: hummingbird |
| Version: 1.14.0 |
| Command: rm -rf hummingbird.buildbin-libdir && mkdir hummingbird.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh hummingbird_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R hummingbird.buildbin-libdir |
| StartedAt: 2024-06-10 00:22:36 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 00:23:13 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 36.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: hummingbird_1.14.0.tgz |
| PackageFileSize: 476.5 KiB |
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### Running command:
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### rm -rf hummingbird.buildbin-libdir && mkdir hummingbird.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh hummingbird_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R hummingbird.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=hummingbird.buildbin-libdir hummingbird_1.14.0.tar.gz'
>>>>>>>
* installing *source* package ‘hummingbird’ ...
** 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 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c em.cpp -o em.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.cpp -o init.o
init.cpp:11:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
NULL
^~~~
{ }
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/stddef.h:84:18: note: expanded from macro 'NULL'
# define NULL __null
^~~~~~
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c postAdjustment.cpp -o postAdjustment.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o hummingbird.so RcppExports.o em.o init.o postAdjustment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc/meat/hummingbird.buildbin-libdir/00LOCK-hummingbird/00new/hummingbird/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (hummingbird)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR hummingbird.buildbin-libdir/hummingbird/libs/hummingbird.so
>>>>>>>
>>>>>>> Paths before fix:
hummingbird.buildbin-libdir/hummingbird/libs/hummingbird.so:
hummingbird.so (compatibility version 0.0.0, current version 0.0.0)
/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/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/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/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "hummingbird.buildbin-libdir/hummingbird/libs/hummingbird.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" "hummingbird.buildbin-libdir/hummingbird/libs/hummingbird.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" "hummingbird.buildbin-libdir/hummingbird/libs/hummingbird.so"
>>>>>>> Paths after fix:
hummingbird.buildbin-libdir/hummingbird/libs/hummingbird.so:
hummingbird.so (compatibility version 0.0.0, current version 0.0.0)
/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/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)