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This page was generated on 2023-11-04 11:37:35 -0400 (Sat, 04 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.2 (2023-10-31) -- "Eye Holes" 4439
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4378
lconwaymacOS 12.6.5 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4407
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 1046/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRISFGM 1.10.0  (landing page)
Yuzhou Chang
Snapshot Date: 2023-11-03 14:05:04 -0400 (Fri, 03 Nov 2023)
git_url: https://git.bioconductor.org/packages/IRISFGM
git_branch: RELEASE_3_18
git_last_commit: 27aef48
git_last_commit_date: 2023-10-24 11:30:04 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

BUILD BIN results for IRISFGM on lconway


To the developers/maintainers of the IRISFGM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IRISFGM.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: IRISFGM
Version: 1.10.0
Command: rm -rf IRISFGM.buildbin-libdir && mkdir IRISFGM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh IRISFGM_1.10.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R IRISFGM.buildbin-libdir
StartedAt: 2023-11-04 00:01:58 -0400 (Sat, 04 Nov 2023)
EndedAt: 2023-11-04 00:04:23 -0400 (Sat, 04 Nov 2023)
EllapsedTime: 145.4 seconds
RetCode: 0
Status:   OK  
PackageFile: IRISFGM_1.10.0.tgz
PackageFileSize: 2.557 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf IRISFGM.buildbin-libdir && mkdir IRISFGM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh IRISFGM_1.10.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R IRISFGM.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=IRISFGM.buildbin-libdir IRISFGM_1.10.0.tar.gz'
>>>>>>> 

* installing *source* package ‘IRISFGM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -DVER=2.08 -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -DVER=2.08 -fPIC  -falign-functions=64 -Wall -g -O2  -c cluster.cpp -o cluster.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -DVER=2.08 -fPIC  -falign-functions=64 -Wall -g -O2  -c expand.cpp -o expand.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -DVER=2.08 -fPIC  -falign-functions=64 -Wall -g -O2  -c get_options.cpp -o get_options.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c getline.c -o getline.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -DVER=2.08 -fPIC  -falign-functions=64 -Wall -g -O2  -c main.cpp -o main.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -DVER=2.08 -fPIC  -falign-functions=64 -Wall -g -O2  -c make_graph.cpp -o make_graph.o
make_graph.cpp:51:5: warning: variable 'i' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
    i++;
    ^
make_graph.cpp:45:29: note: incremented here
  for (int i = 0; i < cols; i++) {
                            ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -DVER=2.08 -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_irisfgm.cpp -o rcpp_irisfgm.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -DVER=2.08 -fPIC  -falign-functions=64 -Wall -g -O2  -c read_array.cpp -o read_array.o
read_array.cpp:882:43: warning: format specifies type 'int' but the argument has type 'std::__vector_base<unsigned long, std::allocator<unsigned long>>::value_type' (aka 'unsigned long') [-Wformat]
        fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
                        ~~                ^~~~~~~~~~~~~
                        %lu
read_array.cpp:1376:43: warning: format specifies type 'int' but the argument has type 'std::__vector_base<unsigned long, std::allocator<unsigned long>>::value_type' (aka 'unsigned long') [-Wformat]
        fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
                        ~~                ^~~~~~~~~~~~~
                        %lu
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -DVER=2.08 -fPIC  -falign-functions=64 -Wall -g -O2  -c struct.cpp -o struct.o
struct.cpp:75:15: warning: variable 'lastTime' set but not used [-Wunused-but-set-variable]
  static long lastTime = 0;
              ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -DVER=2.08 -fPIC  -falign-functions=64 -Wall -g -O2  -c write_block.cpp -o write_block.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o IRISFGM.so RcppExports.o cluster.o expand.o get_options.o getline.o main.o make_graph.o rcpp_irisfgm.o read_array.o struct.o write_block.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc/meat/IRISFGM.buildbin-libdir/00LOCK-IRISFGM/00new/IRISFGM/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘ReadFrom10X_h5’ in package ‘IRISFGM’
Creating a generic function from function ‘ReadFrom10X_folder’ in package ‘IRISFGM’
** 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 (IRISFGM)


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

>>>>>>> Paths before fix:
IRISFGM.buildbin-libdir/IRISFGM/libs/IRISFGM.so:
	IRISFGM.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
	/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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "IRISFGM.buildbin-libdir/IRISFGM/libs/IRISFGM.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "IRISFGM.buildbin-libdir/IRISFGM/libs/IRISFGM.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "IRISFGM.buildbin-libdir/IRISFGM/libs/IRISFGM.so"

>>>>>>> Paths after fix:
IRISFGM.buildbin-libdir/IRISFGM/libs/IRISFGM.so:
	IRISFGM.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
	/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)