Multiple platform build/check report for BioC 3.20 - BUILD BIN results for seqTools on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (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*

BUILD BIN results for seqTools on kjohnson1

To the developers/maintainers of the seqTools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqTools.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: seqTools

Version: 1.40.0

Command: rm -rf seqTools.buildbin-libdir && mkdir seqTools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqTools_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R seqTools.buildbin-libdir

StartedAt: 2024-12-21 16:40:11 -0500 (Sat, 21 Dec 2024)

EndedAt: 2024-12-21 16:40:20 -0500 (Sat, 21 Dec 2024)

EllapsedTime: 8.9 seconds

RetCode: 0

Status: OK

PackageFile: seqTools_1.40.0.tgz

PackageFileSize: 816.1 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf seqTools.buildbin-libdir && mkdir seqTools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqTools_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R seqTools.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=seqTools.buildbin-libdir seqTools_1.40.0.tar.gz'
>>>>>>> 

* installing *source* package ‘seqTools’ ...
** 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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c seqTools.c -o seqTools.o
seqTools.c:851:65: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
                                error("[count_genome_Kmers] character mismatch at position %u!");
                                                                                           ~^
seqTools.c:3296:71: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
                error("[scale_kmer_matrix] scale[%i]=%i must be >1!", column_index, scale);
                                                     ~~                             ^~~~~
                                                     %f
seqTools.c:3306:75: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
                                error("[scale_kmer_matrix] scale[%i] = %i must be >1!", column_index, scale);
                                                                       ~~                             ^~~~~
                                                                       %f
3 warnings generated.
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 seqTools.so seqTools.o -lm -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/seqTools.buildbin-libdir/00LOCK-seqTools/00new/seqTools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
In fun(libname, pkgname) :
  Package 'zlibbioc' is deprecated and will be removed from Bioconductor
  version 3.22
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'zlibbioc' is deprecated and will be removed from Bioconductor
  version 3.22
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'zlibbioc' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (seqTools)


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

>>>>>>> Paths before fix:
seqTools.buildbin-libdir/seqTools/libs/seqTools.so:
	seqTools.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/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)

>>>>>>> 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" "seqTools.buildbin-libdir/seqTools/libs/seqTools.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "seqTools.buildbin-libdir/seqTools/libs/seqTools.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "seqTools.buildbin-libdir/seqTools/libs/seqTools.so"

>>>>>>> Paths after fix:
seqTools.buildbin-libdir/seqTools/libs/seqTools.so:
	seqTools.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/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)