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This page was generated on 2025-06-19 12:05 -0400 (Thu, 19 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4810
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4548
kjohnson3macOS 13.7.1 Venturaarm644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4528
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4493
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 1454/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.73.0  (landing page)
Benilton Carvalho
Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025)
git_url: https://git.bioconductor.org/packages/oligo
git_branch: devel
git_last_commit: 50bd1ff
git_last_commit_date: 2025-04-15 09:36:44 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  

BUILD BIN results for oligo on kjohnson3

To the developers/maintainers of the oligo package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oligo.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: oligo
Version: 1.73.0
Command: rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.73.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R oligo.buildbin-libdir
StartedAt: 2025-06-18 22:31:24 -0400 (Wed, 18 Jun 2025)
EndedAt: 2025-06-18 22:31:42 -0400 (Wed, 18 Jun 2025)
EllapsedTime: 18.6 seconds
RetCode: 0
Status:   OK  
PackageFile: oligo_1.73.0.tgz
PackageFileSize: 27.83 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.73.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R oligo.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=oligo.buildbin-libdir oligo_1.73.0.tar.gz'
>>>>>>> 

* installing *source* package ‘oligo’ ...
** this is package ‘oligo’ version ‘1.73.0’
** using staged installation
creating cache ./config.cache
checking how to run the C preprocessor... clang -arch arm64 -std=gnu2x -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c DABG.c -o DABG.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c ParserGzXYS.c -o ParserGzXYS.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c ParserXYS.c -o ParserXYS.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c baseProfile.c -o baseProfile.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c basecontent.c -o basecontent.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c chipbackground.c -o chipbackground.o
chipbackground.c:120:58: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1==0)){
                                                         ^  ~~~~~~
chipbackground.c:120:58: note: use '&' for a bitwise operation
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1==0)){
                                                         ^~
                                                         &
chipbackground.c:120:58: note: remove constant to silence this warning
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1==0)){
                                                        ~^~~~~~~~~
chipbackground.c:243:58: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1 ==0)){
                                                         ^  ~~~~~~~
chipbackground.c:243:58: note: use '&' for a bitwise operation
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1 ==0)){
                                                         ^~
                                                         &
chipbackground.c:243:58: note: remove constant to silence this warning
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1 ==0)){
                                                        ~^~~~~~~~~~
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c mas5calls.c -o mas5calls.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma2.c -o rma2.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c trimmed.c -o trimmed.o
trimmed.c:49:13: warning: variable 'n1' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
            ^
trimmed.c:49:17: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
                ^
trimmed.c:49:21: warning: variable 'n3' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
                    ^
3 warnings generated.
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc/meat/oligo.buildbin-libdir/00LOCK-oligo/00new/oligo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Note: in method for ‘pm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition:
subset = "missing", target = "missing"
Note: in method for ‘mm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition:
subset = "missing", target = "missing"
** 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 (oligo)


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

>>>>>>> Paths before fix:
oligo.buildbin-libdir/oligo/libs/oligo.so:
	oligo.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so"

>>>>>>> Paths after fix:
oligo.buildbin-libdir/oligo/libs/oligo.so:
	oligo.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)