Back to Mac ARM64 build report for BioC 3.18
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-03-28 11:32:20 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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 684/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
extraChIPs 1.6.1  (landing page)
Stephen Pederson
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/extraChIPs
git_branch: RELEASE_3_18
git_last_commit: fb27d0b
git_last_commit_date: 2024-02-27 06:23:59 -0400 (Tue, 27 Feb 2024)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for extraChIPs on kjohnson1


To the developers/maintainers of the extraChIPs package:
- 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: extraChIPs
Version: 1.6.1
Command: rm -rf extraChIPs.buildbin-libdir && mkdir extraChIPs.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh extraChIPs_1.6.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R extraChIPs.buildbin-libdir
StartedAt: 2024-03-28 08:04:39 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 08:06:10 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 91.0 seconds
RetCode: 0
Status:   OK  
PackageFile: extraChIPs_1.6.1.tgz
PackageFileSize: 2.71 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf extraChIPs.buildbin-libdir && mkdir extraChIPs.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh extraChIPs_1.6.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R extraChIPs.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=extraChIPs.buildbin-libdir extraChIPs_1.6.1.tar.gz'
>>>>>>> 

* installing *source* package ‘extraChIPs’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FMStable.c -o FMStable.o
FMStable.c:4835:22: warning: unused variable 'sinhalfangle' [-Wunused-variable]
    double sinangle, sinhalfangle;
                     ^
FMStable.c:4924:21: warning: unused variable 'temp' [-Wunused-variable]
    double z,y,dy,t,temp,scale;
                    ^
FMStable.c:227:31: warning: unused variable 'ratio' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
                              ^
FMStable.c:227:37: warning: unused variable 'angle' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
                                    ^
FMStable.c:227:43: warning: unused variable 'C1' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
                                          ^
FMStable.c:227:46: warning: unused variable 'C2' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
                                             ^
FMStable.c:227:49: warning: unused variable 'C3' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
                                                ^
FMStable.c:227:52: warning: unused variable 'C4' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
                                                   ^
FMStable.c:231:35: warning: unused variable 'alphalarge' [-Wunused-variable]
static int distributiontabulated, alphalarge;
                                  ^
9 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o extraChIPs.so FMStable.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/extraChIPs.buildbin-libdir/00LOCK-extraChIPs/00new/extraChIPs/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (extraChIPs)


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

>>>>>>> Paths before fix:
extraChIPs.buildbin-libdir/extraChIPs/libs/extraChIPs.so:
	extraChIPs.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
	/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/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "extraChIPs.buildbin-libdir/extraChIPs/libs/extraChIPs.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "extraChIPs.buildbin-libdir/extraChIPs/libs/extraChIPs.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "extraChIPs.buildbin-libdir/extraChIPs/libs/extraChIPs.so"

>>>>>>> Paths after fix:
extraChIPs.buildbin-libdir/extraChIPs/libs/extraChIPs.so:
	extraChIPs.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
	/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)