| Back to Rapid builds (Linux only) of a subset of BioC 3.22 Report updated every 6 hours |
This page was generated on 2025-10-23 10:08 -0400 (Thu, 23 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 926 |
| 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 61/229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| cytolib 2.21.0 (landing page) Mike Jiang
| teran2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
|
To the developers/maintainers of the cytolib package: - 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: 2.21.0 |
| Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:cytolib.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings cytolib_2.21.0.tar.gz |
| StartedAt: 2025-10-23 08:05:47 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 08:05:59 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 12.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cytolib.Rcheck |
| Warnings: 2 |
##############################################################################
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###
### Running command:
###
### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:cytolib.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings cytolib_2.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/cytolib.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘cytolib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cytolib’ version ‘2.21.0’
* 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
installed size is 76.9Mb
sub-directories of 1Mb or more:
include 6.2Mb
lib 70.5Mb
* 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 ... INFO
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, 5 NOTEs
See
‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/cytolib.Rcheck/00check.log’
for details.
cytolib.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL cytolib ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’ * installing *source* package ‘cytolib’ ... ** this is package ‘cytolib’ version ‘2.21.0’ ** 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=2.21.0 configure: creating ./config.status config.status: creating inst/include/cytolib/cytolibConfig.h config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c dummy.cpp -o dummy.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -DROUT -I../inst/include -w 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-Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' 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-I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c GatingSet.cpp -o GatingSet.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c H5CytoFrame.cpp -o H5CytoFrame.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c MemCytoFrame.cpp -o MemCytoFrame.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c POPINDICES.cpp -o POPINDICES.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c calibrationTable.cpp -o calibrationTable.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c compensation.cpp -o compensation.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ellipse2points.cpp -o ellipse2points.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c gate.cpp -o gate.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c global.cpp -o global.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c in_polygon.cpp -o in_polygon.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c nodeProperties.cpp -o nodeProperties.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c spline.cpp -o spline.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c trans_group.cpp -o trans_group.o g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/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'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/RProtoBufLib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c transformation.cpp -o transformation.o mkdir -p "/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/00LOCK-cytolib/00new/cytolib/lib" ar rs "/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/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 /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/00LOCK-cytolib/00new/cytolib/lib/libcytolib.a g++ -std=gnu++11 -shared -L/usr/local/lib -o cytolib.so dummy.o installing to /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/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)