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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings NetPathMiner_1.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/NetPathMiner.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 ‘NetPathMiner/DESCRIPTION’ ... OK
* this is package ‘NetPathMiner’ version ‘1.37.0’
* 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 ‘NetPathMiner’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* 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 vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘NPMVignette.Rmd’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘NPMVignette.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.170   0.029   0.193 

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

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

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL NetPathMiner
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘NetPathMiner’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... no
Non x86_64 architecture. Using system-wide boost installation!
SBML not found.
libXML2 found
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -c PathRanker.cpp -o PathRanker.o
In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /usr/include/boost/property_map/vector_property_map.hpp:14,
                 from /usr/include/boost/property_map/property_map.hpp:606,
                 from /usr/include/boost/graph/properties.hpp:19,
                 from /usr/include/boost/graph/graph_utility.hpp:22,
                 from PathRanker.cpp:27:
/usr/include/boost/pending/relaxed_heap.hpp:14:1: note: ‘#pragma message: This header is deprecated. Use the standard heap functions instead.’
   14 | BOOST_HEADER_DEPRECATED("the standard heap functions")
      | ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -c handlesegfault.c -o handlesegfault.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -c hme3m.c -o hme3m.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -c kgml_interface.cpp -o kgml_interface.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -c methods.cpp -o methods.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -c pathScope.cpp -o pathScope.o
In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /usr/include/boost/property_map/vector_property_map.hpp:14,
                 from /usr/include/boost/property_map/property_map.hpp:606,
                 from /usr/include/boost/graph/properties.hpp:19,
                 from /usr/include/boost/graph/graph_utility.hpp:22,
                 from pathScope.cpp:34:
/usr/include/boost/pending/relaxed_heap.hpp:14:1: note: ‘#pragma message: This header is deprecated. Use the standard heap functions instead.’
   14 | BOOST_HEADER_DEPRECATED("the standard heap functions")
      | ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -c sbml_interface.cpp -o sbml_interface.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o NetPathMiner.so PathRanker.o handlesegfault.o hme3m.o init.o kgml_interface.o methods.o pathScope.o sbml_interface.o -lxml2 -lxml2 -lz -llzma -lm -L/home/biocbuild/R/R-4.3.0/lib -lRlapack -L/home/biocbuild/R/R-4.3.0/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-NetPathMiner/00new/NetPathMiner/libs
** R
** data
** 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 (NetPathMiner)