Stefano Berri
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/CNAnorm |
| git_branch: RELEASE_3_17 |
| git_last_commit: c5e4453 |
| git_last_commit_date: 2023-05-01 20:03:54 -0400 (Mon, 01 May 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (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 376/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNAnorm 1.46.1 (landing page) Stefano Berri
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the CNAnorm 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. |
| Package: CNAnorm |
| Version: 1.46.1 |
| Command: rm -rf CNAnorm.buildbin-libdir && mkdir CNAnorm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNAnorm_1.46.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNAnorm.buildbin-libdir |
| StartedAt: 2023-10-19 12:12:44 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 12:13:02 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 17.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CNAnorm_1.46.1.tgz |
| PackageFileSize: 1.845 MiB |
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### Running command:
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### rm -rf CNAnorm.buildbin-libdir && mkdir CNAnorm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNAnorm_1.46.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNAnorm.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNAnorm.buildbin-libdir CNAnorm_1.46.1.tar.gz'
>>>>>>>
* installing *source* package ‘CNAnorm’ ...
** 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 daxpy.f -o daxpy.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c ddot.f -o ddot.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c dgbfa.f -o dgbfa.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c dgbsl.f -o dgbsl.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c dscal.f -o dscal.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c dsmooth.f -o dsmooth.o
f951: Warning: Nonconforming tab character in column 1 of line 14 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 15 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 16 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 17 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 18 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 19 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 20 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 21 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 22 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 23 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 24 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 25 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 26 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 27 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 28 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 29 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 30 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 31 [-Wtabs]
f951: Warning: Nonconforming tab character in column 2 of line 32 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 33 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 34 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 35 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 36 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 37 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 38 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 39 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 40 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 41 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 42 [-Wtabs]
f951: Warning: Nonconforming tab character in column 4 of line 43 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 44 [-Wtabs]
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f951: Warning: Nonconforming tab character in column 1 of line 54 [-Wtabs]
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f951: Warning: Nonconforming tab character in column 1 of line 56 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 57 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 58 [-Wtabs]
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f951: Warning: Nonconforming tab character in column 1 of line 60 [-Wtabs]
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f951: Warning: Nonconforming tab character in column 1 of line 63 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 64 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 65 [-Wtabs]
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f951: Warning: Nonconforming tab character in column 3 of line 67 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 68 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 69 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 71 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 72 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 73 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 74 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 75 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 76 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 77 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 78 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 79 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 80 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 81 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 82 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 83 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 84 [-Wtabs]
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f951: Warning: Nonconforming tab character in column 1 of line 90 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 91 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 92 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 93 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 94 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 95 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 96 [-Wtabs]
dsmooth.f:62:21:
62 | do 10 i=1,n-1
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
dsmooth.f:70:8:
70 | & diff(i-1)*diff(i+1) .lt. 0.) isplit(i)=1
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
dsmooth.f:50:6:
50 | function amed3(a,b,c)
| ^
Warning: ‘__result_amed3’ may be used uninitialized [-Wmaybe-uninitialized]
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c idamax.f -o idamax.o
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 CNAnorm.so daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.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 _dgbsl_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _med3r_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _split_: registers 23 and 24 not saved contiguously in frame
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CNAnorm.buildbin-libdir/00LOCK-CNAnorm/00new/CNAnorm/libs
** R
** data
** 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 (CNAnorm)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR CNAnorm.buildbin-libdir/CNAnorm/libs/CNAnorm.so
>>>>>>>
>>>>>>> Paths before fix:
CNAnorm.buildbin-libdir/CNAnorm/libs/CNAnorm.so:
CNAnorm.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)
>>>>>>> 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" "CNAnorm.buildbin-libdir/CNAnorm/libs/CNAnorm.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "CNAnorm.buildbin-libdir/CNAnorm/libs/CNAnorm.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "CNAnorm.buildbin-libdir/CNAnorm/libs/CNAnorm.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" "CNAnorm.buildbin-libdir/CNAnorm/libs/CNAnorm.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" "CNAnorm.buildbin-libdir/CNAnorm/libs/CNAnorm.so"
>>>>>>> Paths after fix:
CNAnorm.buildbin-libdir/CNAnorm/libs/CNAnorm.so:
CNAnorm.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)