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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 487/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 2.19.0  (landing page)
Mike Jiang
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/CytoML
git_branch: devel
git_last_commit: 57e3e6e
git_last_commit_date: 2024-10-29 10:12:05 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped


INSTALL results for CytoML on kjohnson3

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: 2.19.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoML
StartedAt: 2024-12-23 15:06:18 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 15:06:23 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 5.2 seconds
RetCode: 1
Status:   ERROR  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoML
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* 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 arm64 -std=gnu++11 accepts -g... yes
checking for gcc... clang -arch arm64
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 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 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -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-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/flowWorkspace/include' -I/opt/R/arm64/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-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.5-arm64/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-arm64/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: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:
../inst/include/CytoML/workspace_type.hpp:67:101: error: no member named 'symlink_option' in namespace 'boost::filesystem'
        for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
                                                                                                ~~~~^
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 and 1 error generated.
make: *** [cpp11.o] Error 1
ERROR: compilation failed for package ‘CytoML’
* removing ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/CytoML’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/CytoML’