Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4459
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
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 1387/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.53.0  (landing page)
Mike Jiang
Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024)
git_url: https://git.bioconductor.org/packages/ncdfFlow
git_branch: devel
git_last_commit: b6e8c04
git_last_commit_date: 2024-10-29 09:39:19 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows 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

BUILD BIN results for ncdfFlow on lconway

To the developers/maintainers of the ncdfFlow package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ncdfFlow.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: ncdfFlow
Version: 2.53.0
Command: rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ncdfFlow_2.53.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ncdfFlow.buildbin-libdir
StartedAt: 2024-11-28 04:13:31 -0500 (Thu, 28 Nov 2024)
EndedAt: 2024-11-28 04:14:00 -0500 (Thu, 28 Nov 2024)
EllapsedTime: 28.7 seconds
RetCode: 0
Status:   OK  
PackageFile: ncdfFlow_2.53.0.tgz
PackageFileSize: 2.041 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ncdfFlow_2.53.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ncdfFlow.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ncdfFlow.buildbin-libdir ncdfFlow_2.53.0.tar.gz'
>>>>>>> 

* installing *source* package ‘ncdfFlow’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c cpp11.cpp -o cpp11.o
In file included from cpp11.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cpp11/include/cpp11/declarations.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cpp11/include/cpp11.hpp:3:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
        ^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c hdfFlow.cpp -o hdfFlow.o
In file included from hdfFlow.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cpp11/include/cpp11.hpp:3:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
        ^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
hdfFlow.cpp:493:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
        herr_t      status;
                    ^
2 warnings generated.
mkdir -p "/Users/biocbuild/bbs-3.21-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib"
ar rs "/Users/biocbuild/bbs-3.21-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/libncdfFlow.a" cpp11.o hdfFlow.o
ar: creating archive /Users/biocbuild/bbs-3.21-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/libncdfFlow.a
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ncdfFlow.so cpp11.o hdfFlow.o /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/libs
** R
** 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 (ncdfFlow)


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

>>>>>>> Paths before fix:
ncdfFlow.buildbin-libdir/ncdfFlow/libs/ncdfFlow.so:
	ncdfFlow.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)

>>>>>>> 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" "ncdfFlow.buildbin-libdir/ncdfFlow/libs/ncdfFlow.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" "ncdfFlow.buildbin-libdir/ncdfFlow/libs/ncdfFlow.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" "ncdfFlow.buildbin-libdir/ncdfFlow/libs/ncdfFlow.so"

>>>>>>> Paths after fix:
ncdfFlow.buildbin-libdir/ncdfFlow/libs/ncdfFlow.so:
	ncdfFlow.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)