Back to Multiple platform build/check report for BioC 3.20:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 387/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNAnorm 1.52.0  (landing page)
Stefano Berri
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/CNAnorm
git_branch: RELEASE_3_20
git_last_commit: 37e5455
git_last_commit_date: 2024-10-29 09:38:43 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for CNAnorm on kjohnson1

To the developers/maintainers of the CNAnorm package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNAnorm.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: CNAnorm
Version: 1.52.0
Command: rm -rf CNAnorm.buildbin-libdir && mkdir CNAnorm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNAnorm_1.52.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNAnorm.buildbin-libdir
StartedAt: 2024-12-21 14:20:09 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 14:20:19 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 10.1 seconds
RetCode: 0
Status:   OK  
PackageFile: CNAnorm_1.52.0.tgz
PackageFileSize: 1.842 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNAnorm.buildbin-libdir && mkdir CNAnorm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNAnorm_1.52.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNAnorm.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNAnorm.buildbin-libdir CNAnorm_1.52.0.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]
f951: Warning: Nonconforming tab character in column 1 of line 45 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 46 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 47 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 48 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 50 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 51 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 52 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 53 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 54 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 55 [-Wtabs]
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]
f951: Warning: Nonconforming tab character in column 1 of line 59 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 60 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 61 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 62 [-Wtabs]
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]
f951: Warning: Nonconforming tab character in column 1 of line 66 [-Wtabs]
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]
f951: Warning: Nonconforming tab character in column 1 of line 85 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 87 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 88 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 89 [-Wtabs]
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 -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
installing to /Users/biocbuild/bbs-3.20-bioc/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/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/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)