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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1402/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NuPoP 2.8.1  (landing page)
Ji-Ping Wang
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/NuPoP
git_branch: RELEASE_3_17
git_last_commit: 4d0a449
git_last_commit_date: 2023-05-01 20:07:41 -0400 (Mon, 01 May 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for NuPoP on kjohnson2


To the developers/maintainers of the NuPoP 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: NuPoP
Version: 2.8.1
Command: rm -rf NuPoP.buildbin-libdir && mkdir NuPoP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NuPoP_2.8.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R NuPoP.buildbin-libdir
StartedAt: 2023-10-19 15:32:12 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 15:32:53 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 40.5 seconds
RetCode: 0
Status:   OK  
PackageFile: NuPoP_2.8.1.tgz
PackageFileSize: 4.373 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf NuPoP.buildbin-libdir && mkdir NuPoP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NuPoP_2.8.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R NuPoP.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=NuPoP.buildbin-libdir NuPoP_2.8.1.tar.gz'
>>>>>>> 

* installing *source* package ‘NuPoP’ ...
** using staged installation
** libs
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using SDK: ‘MacOSX11.3.sdk’
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c  cvtbfb.f90 -o cvtbfb.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c  cvtbfbNL4.f90 -o cvtbfbNL4.o
cvtbfbNL4.f90:13:51:

   13 |   real*8    freqN4(4,4,4,4),tranN4(5:147,4,4,4,4,4),freqL4(4,4,4,4)
      |                                                   1
Warning: Array ‘trann4’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising]
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c  vtbfb.f90 -o vtbfb.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c  vtbfbNL4.f90 -o vtbfbNL4.o
vtbfbNL4.f90:13:51:

   13 |   real*8    freqN4(4,4,4,4),tranN4(5:147,4,4,4,4,4),freqL4(4,4,4,4)
      |                                                   1
Warning: Array ‘trann4’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising]
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o NuPoP.so cvtbfb.o cvtbfbNL4.o vtbfb.o vtbfbNL4.o -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for _vtbfbnl4_: does not use standard frame
ld: warning: could not create compact unwind for _vtbfb_: does not use standard frame
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
ld: warning: could not create compact unwind for _cvtbfbnl4_: does not use standard frame
ld: warning: could not create compact unwind for _cvtbfb_: does not use standard frame
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/NuPoP.buildbin-libdir/00LOCK-NuPoP/00new/NuPoP/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 (NuPoP)


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

>>>>>>> Paths before fix:
NuPoP.buildbin-libdir/NuPoP/libs/NuPoP.so:
	NuPoP.so (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)
	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)

>>>>>>> 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" "NuPoP.buildbin-libdir/NuPoP/libs/NuPoP.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "NuPoP.buildbin-libdir/NuPoP/libs/NuPoP.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "NuPoP.buildbin-libdir/NuPoP/libs/NuPoP.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "NuPoP.buildbin-libdir/NuPoP/libs/NuPoP.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "NuPoP.buildbin-libdir/NuPoP/libs/NuPoP.so"

>>>>>>> Paths after fix:

NuPoP.buildbin-libdir/NuPoP/libs/NuPoP.so:
	NuPoP.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)
	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)