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This page was generated on 2025-01-04 11:43 -0500 (Sat, 04 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4756
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4475
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4435
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4390
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4383
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 488/2275HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 2.19.1  (landing page)
Mike Jiang
Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025)
git_url: https://git.bioconductor.org/packages/CytoML
git_branch: devel
git_last_commit: c84d4bd
git_last_commit_date: 2025-01-01 15:10:21 -0500 (Wed, 01 Jan 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

BUILD BIN results for CytoML on lconway

To the developers/maintainers of the CytoML package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoML.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: CytoML
Version: 2.19.1
Command: rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_2.19.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CytoML.buildbin-libdir
StartedAt: 2025-01-04 00:27:29 -0500 (Sat, 04 Jan 2025)
EndedAt: 2025-01-04 00:28:57 -0500 (Sat, 04 Jan 2025)
EllapsedTime: 88.0 seconds
RetCode: 0
Status:   OK  
PackageFile: CytoML_2.19.1.tgz
PackageFileSize: 9.583 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_2.19.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CytoML.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CytoML.buildbin-libdir CytoML_2.19.1.tar.gz'
>>>>>>> 

* installing *source* package ‘CytoML’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -arch x86_64 -std=gnu++11 accepts -g... yes
checking for gcc... clang -arch x86_64
checking whether we are using the GNU C compiler... yes
checking whether clang -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: setting cytolib-ml commandline tool path...
configure: Using the following compilation and linking flags
configure:    PKG_CPPFLAGS=-I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900
configure:    PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm 
configure:    CYTOLIBML_BIN=/usr/local/bin
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/cytolibml_bin_path.R
** libs
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 -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/flowWorkspace/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c cpp11.cpp -o cpp11.o
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/flowWorkspace/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:5:
In file included from ../inst/include/CytoML/openWorkspace.hpp:11:
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:
In file included from ../inst/include/CytoML/workspace.hpp:10:
In file included from ../inst/include/CytoML/workspace_type.hpp:4:
../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
        Rprintf("%.*s", n, s);
                 ~~^~   ~
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:5:
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/flowWorkspace/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/CytoML/openWorkspace.hpp:11:
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:
In file included from ../inst/include/CytoML/workspace.hpp:10:
In file included from ../inst/include/CytoML/workspace_type.hpp:4:
In file included from ../inst/include/CytoML/wsNode.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/CytoML/openWorkspace.hpp:11:
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:
In file included from ../inst/include/CytoML/workspace.hpp:10:
In file included from ../inst/include/CytoML/workspace_type.hpp:4:
../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
        Rprintf("%.*s", n, s);
                 ~~^~   ~
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
3 warnings generated.
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 CytoML.so cpp11.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/libs
** R
** 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 (CytoML)


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

>>>>>>> Paths before fix:
CytoML.buildbin-libdir/CytoML/libs/CytoML.so:
	CytoML.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
	/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 66.1.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"

>>>>>>> Paths after fix:
CytoML.buildbin-libdir/CytoML/libs/CytoML.so:
	CytoML.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
	/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 66.1.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)