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This page was generated on 2023-05-26 06:18:06 -0000 (Fri, 26 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4254
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CHECK results for CytoML on kunpeng2


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 477/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 2.13.1  (landing page)
Mike Jiang
Snapshot Date: 2023-05-25 13:29:39 -0000 (Thu, 25 May 2023)
git_url: https://git.bioconductor.org/packages/CytoML
git_branch: devel
git_last_commit: c0cb055
git_last_commit_date: 2023-05-01 04:04:39 -0000 (Mon, 01 May 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

Summary

Package: CytoML
Version: 2.13.1
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CytoML_2.13.1.tar.gz
StartedAt: 2023-05-26 04:38:08 -0000 (Fri, 26 May 2023)
EndedAt: 2023-05-26 04:38:20 -0000 (Fri, 26 May 2023)
EllapsedTime: 12.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: CytoML.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CytoML_2.13.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CytoML.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘CytoML/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CytoML’ version ‘2.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
 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 ‘CytoML’ can be installed ... WARNING
Found the following significant warnings:
  ../inst/include/CytoML/workspace_type.hpp:67:124: warning: ‘boost::filesystem::recursive_directory_iterator::recursive_directory_iterator(const boost::filesystem::path&, boost::filesystem::symlink_option)’ is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.18-bioc/meat/CytoML.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 68.5Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs     62.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘jsonlite’ ‘methods’
A package should be listed in only one of these fields.
* 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 R 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 ... OK
* checking Rd files ... OK
* 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 ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
  apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
  apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars.in’
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘HowToExportGatingSet.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘cytobank2GatingSet.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘flowjo_to_gatingset.Rmd’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘HowToExportGatingSet.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.172   0.035   0.202 

... incomplete output.  Crash?
when running code in ‘cytobank2GatingSet.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.176   0.032   0.203 

... incomplete output.  Crash?
when running code in ‘flowjo_to_gatingset.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.173   0.028   0.195 

... incomplete output.  Crash?

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
.Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
.Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
* DONE

Status: 2 ERRORs, 2 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/CytoML.Rcheck/00check.log’
for details.

Installation output

CytoML.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL CytoML
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 g++ -std=gnu++11 accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc 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/usr/include/libxml2
configure:    PKG_LIBS=-lxml2 -lz -llzma -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: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/R/R-4.3.0/library/cpp11/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/flowWorkspace/include' -I/usr/local/include    -fPIC  -g -O2  -c cpp11.cpp -o cpp11.o
In file included from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from CytoML_types.h:5,
                 from cpp11.cpp:4:
../inst/include/CytoML/workspace_type.hpp: In function ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > CytoML::list_files(const string&, const string&)’:
../inst/include/CytoML/workspace_type.hpp:67:124: warning: ‘boost::filesystem::recursive_directory_iterator::recursive_directory_iterator(const boost::filesystem::path&, boost::filesystem::symlink_option)’ is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
   67 |         for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
      |                                                                                                                            ^
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/filesystem.hpp:18,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/CytoVFS.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/global.hpp:21,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/compensation.hpp:19,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from /home/biocbuild/R/R-4.3.0/site-library/flowWorkspace/include/flowWorkspace.h:5,
                 from CytoML_types.h:4,
                 from cpp11.cpp:4:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/filesystem/directory.hpp:577:5: note: declared here
  577 |     recursive_directory_iterator(path const& dir_path, BOOST_SCOPED_ENUM_NATIVE(symlink_option) opts)
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/R/R-4.3.0/library/cpp11/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/flowWorkspace/include' -I/usr/local/include    -fPIC  -g -O2  -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
../inst/include/CytoML/workspace_type.hpp: In function ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > CytoML::list_files(const string&, const string&)’:
../inst/include/CytoML/workspace_type.hpp:67:124: warning: ‘boost::filesystem::recursive_directory_iterator::recursive_directory_iterator(const boost::filesystem::path&, boost::filesystem::symlink_option)’ is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
   67 |         for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
      |                                                                                                                            ^
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/filesystem.hpp:18,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/CytoVFS.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/global.hpp:21,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/compensation.hpp:19,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/R/R-4.3.0/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/filesystem/directory.hpp:577:5: note: declared here
  577 |     recursive_directory_iterator(path const& dir_path, BOOST_SCOPED_ENUM_NATIVE(symlink_option) opts)
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o CytoML.so cpp11.o parseFlowJoWorkspace.o /home/biocbuild/R/R-4.3.0/site-library/cytolib/lib/libcytolib.a /home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R-4.3.0/lib -lRlapack -L/home/biocbuild/R/R-4.3.0/lib -lRblas -lxml2 -lz -llzma -lm -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/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)

Tests output

Example timings