Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:39 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 486/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cytolib 2.17.0 (landing page) Mike Jiang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the cytolib package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cytolib.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. |
Package: cytolib |
Version: 2.17.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cytolib.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cytolib_2.17.0.tar.gz |
StartedAt: 2024-08-26 22:01:41 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 22:01:57 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 16.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: cytolib.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cytolib.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cytolib_2.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/cytolib.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘cytolib/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cytolib’ version ‘2.17.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘cytolib’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 82.9Mb sub-directories of 1Mb or more: include 6.2Mb lib 76.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: AGPL-3.0-only Standardizable: FALSE * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE CxxFlags: no visible global function definition for ‘cytolibCxxFlags’ Undefined global functions or variables: cytolibCxxFlags * checking Rd files ... NOTE checkRd: (-1) cytolib_LdFlags.Rd:12: Lost braces; missing escapes or markup? 12 | PKG_LIBS += $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "cytolib::cytolib_LdFlags()") | ^ checkRd: (-1) cytolib_LdFlags.Rd:12: Lost braces; missing escapes or markup? 12 | PKG_LIBS += $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "cytolib::cytolib_LdFlags()") | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... WARNING Non-portable flags in variable 'PKG_CPPFLAGS': -w -Wfatal-errors * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/cytolib.Rcheck/00check.log’ for details.
cytolib.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL cytolib ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘cytolib’ ... ** using staged installation checking for a sed that does not truncate output... /usr/bin/sed 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 g++ -std=gnu++17 accepts -g... yes checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes configure: Parsing cytolib version info ... configure: CYTOLIB_VERSION=2.17.0 configure: creating ./config.status config.status: creating inst/include/cytolib/cytolibConfig.h config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c dummy.cpp -o dummy.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR 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boost/libs/filesystem/src/portability.cpp -o boost/libs/filesystem/src/portability.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' 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-I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c calibrationTable.cpp -o calibrationTable.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c compensation.cpp -o compensation.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c ellipse2points.cpp -o ellipse2points.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c gate.cpp -o gate.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c global.cpp -o global.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c in_polygon.cpp -o in_polygon.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c nodeProperties.cpp -o nodeProperties.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c spline.cpp -o spline.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c trans_group.cpp -o trans_group.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c transformation.cpp -o transformation.o mkdir -p "/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-cytolib/00new/cytolib/lib" ar rs "/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-cytolib/00new/cytolib/lib/libcytolib.a" CytoFrame.o CytoFrameView.o CytoVFS.o GatingHierarchy.o GatingSet.o H5CytoFrame.o MemCytoFrame.o POPINDICES.o calibrationTable.o compensation.o dummy.o ellipse2points.o gate.o global.o in_polygon.o nodeProperties.o spline.o trans_group.o transformation.o boost/libs/filesystem/src/codecvt_error_category.o boost/libs/filesystem/src/directory.o boost/libs/filesystem/src/exception.o boost/libs/filesystem/src/operations.o boost/libs/filesystem/src/path.o boost/libs/filesystem/src/path_traits.o boost/libs/filesystem/src/portability.o boost/libs/filesystem/src/unique_path.o boost/libs/filesystem/src/utf8_codecvt_facet.o boost/libs/filesystem/src/windows_file_codecvt.o boost/libs/system/src/error_code.o ar: creating /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-cytolib/00new/cytolib/lib/libcytolib.a g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o cytolib.so dummy.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-cytolib/00new/cytolib/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 (cytolib)