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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 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 328/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 3.58.0  (landing page)
Thomas Girke
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/ChemmineR
git_branch: RELEASE_3_20
git_last_commit: 1654f13
git_last_commit_date: 2024-10-29 09:30:11 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

BUILD BIN results for ChemmineR on lconway

To the developers/maintainers of the ChemmineR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChemmineR.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: ChemmineR
Version: 3.58.0
Command: rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_3.58.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ChemmineR.buildbin-libdir
StartedAt: 2024-11-20 04:18:43 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 04:19:26 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 42.4 seconds
RetCode: 0
Status:   OK  
PackageFile: ChemmineR_3.58.0.tgz
PackageFileSize: 2.61 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_3.58.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ChemmineR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ChemmineR.buildbin-libdir ChemmineR_3.58.0.tar.gz'
>>>>>>> 

* installing *source* package ‘ChemmineR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c DisjointSets.cpp -o DisjointSets.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c cluster.cc -o cluster.o
cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
            ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c cstrsplit.cc -o cstrsplit.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c desc.cc -o desc.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c fingerprints.cc -o fingerprints.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c formats.cc -o formats.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c molecule.cc -o molecule.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c r_wrap.cc -o r_wrap.o
r_wrap.cc:758:10: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
# define R_NO_REMAP
         ^
<command line>:5:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
r_wrap.cc:761:10: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined]
# define STRICT_R_HEADERS
         ^
<command line>:4:9: note: previous definition is here
#define STRICT_R_HEADERS 1
        ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c script.cc -o script.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c similarity.cc -o similarity.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/ChemmineR.buildbin-libdir/00LOCK-ChemmineR/00new/ChemmineR/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 (ChemmineR)


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

>>>>>>> Paths before fix:
ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.so:
	ChemmineR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/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/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.so"

>>>>>>> Paths after fix:
ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.so:
	ChemmineR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)