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This page was generated on 2023-05-26 06:18:08 -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 flowWorkspace on kunpeng2


To the developers/maintainers of the flowWorkspace package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowWorkspace.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 725/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 4.13.0  (landing page)
Greg Finak , Mike Jiang
Snapshot Date: 2023-05-25 13:29:39 -0000 (Thu, 25 May 2023)
git_url: https://git.bioconductor.org/packages/flowWorkspace
git_branch: devel
git_last_commit: ba22296
git_last_commit_date: 2023-04-25 14:19:50 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

Summary

Package: flowWorkspace
Version: 4.13.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings flowWorkspace_4.13.0.tar.gz
StartedAt: 2023-05-26 04:41:32 -0000 (Fri, 26 May 2023)
EndedAt: 2023-05-26 04:41:43 -0000 (Fri, 26 May 2023)
EllapsedTime: 11.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: flowWorkspace.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings flowWorkspace_4.13.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/flowWorkspace.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 ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘4.13.0’
* 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 ‘flowWorkspace’ can be installed ... OK
* 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 75.3Mb
  sub-directories of 1Mb or more:
    libs  73.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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’
* 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 ...
  ‘HowToMergeGatingSet.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘flowWorkspace-Introduction.Rmd’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘HowToMergeGatingSet.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.155   0.046   0.195 

... incomplete output.  Crash?
when running code in ‘flowWorkspace-Introduction.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.173   0.028   0.196 

... 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
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
* DONE

Status: 2 ERRORs, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.

Installation output

flowWorkspace.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** 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 -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/usr/local/include    -fPIC  -g -O2  -c R_API.cpp -o R_API.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/usr/local/include    -fPIC  -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/usr/local/include    -fPIC  -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/usr/local/include    -fPIC  -g -O2  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/usr/local/include    -fPIC  -g -O2  -c cytoframeAPI.cpp -o cytoframeAPI.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/usr/local/include    -fPIC  -g -O2  -c cytosetAPI.cpp -o cytosetAPI.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/usr/local/include    -fPIC  -g -O2  -c getDescendants.cpp -o getDescendants.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/usr/local/include    -fPIC  -g -O2  -c getPopStats.cpp -o getPopStats.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/usr/local/include    -fPIC  -g -O2  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/usr/local/include    -fPIC  -g -O2  -c h5_error_r_handler.cpp -o h5_error_r_handler.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/usr/local/include    -fPIC  -g -O2  -c setCounts.cpp -o setCounts.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o cpp11.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.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 -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-flowWorkspace/00new/flowWorkspace/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 (flowWorkspace)

Tests output

Example timings