##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Rigraphlib.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Rigraphlib_0.99.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘Rigraphlib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rigraphlib’ version ‘0.99.4’
* package encoding: UTF-8
* 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 ‘Rigraphlib’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/f2c/arithchk.c:114:30: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/f2c/backspac.c:47:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/f2c/signal_.c:17:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/npp/npp6.c:853:17: warning: ‘__builtin_memset’ writing between 256 and 17179869176 bytes into a region of size 248 overflows the destination [-Wstringop-overflow=]
  /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:107:5: warning: ‘igraph_array3_resize’ is deprecated [-Wdeprecated-declarations]
  /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:107:5: warning: ‘igraph_array3_int_resize’ is deprecated [-Wdeprecated-declarations]
  /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:107:5: warning: ‘igraph_array3_char_resize’ is deprecated [-Wdeprecated-declarations]
  /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:107:5: warning: ‘igraph_array3_bool_resize’ is deprecated [-Wdeprecated-declarations]
  /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/matrix.c:234:13: warning: ‘igraph_vector_e_tol’ is deprecated [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is 19.4Mb
  sub-directories of 1Mb or more:
    lib  18.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
'LinkingTo' field is unused: package has no 'src' directory
* checking top-level files ... OK
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Rigraphlib
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Rigraphlib’ ...
** this is package ‘Rigraphlib’ version ‘0.99.4’
** using staged installation
-- Version number: 0.10.15
-- The C compiler identification is GNU 13.3.0
-- The CXX compiler identification is GNU 13.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test COMPILER_SUPPORTS_UNKNOWN_WARNING_OPTION_FLAG
-- Performing Test COMPILER_SUPPORTS_UNKNOWN_WARNING_OPTION_FLAG - Failed
-- Performing Test COMPILER_HAS_DEPRECATED_ENUMVAL_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ENUMVAL_ATTR - Success
-- Thread-local storage: supported (__thread)
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Found BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so  
-- Found LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for _stricmp
-- Looking for _stricmp - not found
-- Looking for _strnicmp
-- Looking for _strnicmp - not found
-- Looking for strdup
-- Looking for strdup - found
-- Looking for strndup
-- Looking for strndup - found
-- Looking for include file xlocale.h
-- Looking for include file xlocale.h - not found
-- Looking for uselocale
-- Looking for uselocale - found
-- Looking for _configthreadlocale
-- Looking for _configthreadlocale - not found
-- Performing Test HAVE__UMUL128
-- Performing Test HAVE__UMUL128 - Failed
-- Performing Test HAVE___UMULH
-- Performing Test HAVE___UMULH - Failed
-- Looking for C++ include sys/types.h
-- Looking for C++ include sys/types.h - found
-- Looking for C++ include stdint.h
-- Looking for C++ include stdint.h - found
-- Looking for C++ include stddef.h
-- Looking for C++ include stddef.h - found
-- Check size of __uint128_t
-- Check size of __uint128_t - done
-- Performing Test HAVE__POPCNT64
-- Performing Test HAVE__POPCNT64 - Failed
-- Performing Test HAVE__POPCNT
-- Performing Test HAVE__POPCNT - Failed
-- Performing Test HAVE__BITSCANFORWARD64
-- Performing Test HAVE__BITSCANFORWARD64 - Failed
-- Performing Test HAVE__BITSCANFORWARD
-- Performing Test HAVE__BITSCANFORWARD - Failed
-- Performing Test HAVE__BITSCANREVERSE64
-- Performing Test HAVE__BITSCANREVERSE64 - Failed
-- Performing Test HAVE__BITSCANREVERSE
-- Performing Test HAVE__BITSCANREVERSE - Failed
-- Performing Test HAVE_BUILTIN_OVERFLOW
-- Performing Test HAVE_BUILTIN_OVERFLOW - Success
-- Looking for _LIBCPP_VERSION
-- Looking for _LIBCPP_VERSION - not found
-- Looking for __GLIBCXX__
-- Looking for __GLIBCXX__ - found
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Performing Test HAVE_ENABLE_NEW_DTAGS
-- Performing Test HAVE_ENABLE_NEW_DTAGS - Success
-- Found Python3: /home/biocbuild/.virtualenvs/r-reticulate/bin/python3 (found version "3.12.3") found components: Interpreter 
--  
-- -----[ Build configuration ]----
-- Version:                 0.10.15
-- CMake build type:        Release
-- Library type:             static
-- igraph_integer_t size:   64 bits
--  
-- ----------[ Features ]----------
-- GLPK for optimization:       yes
-- Reading GraphML files:       yes
-- Thread-local storage:        yes
-- Link-time optimization:       no
--  
-- --------[ Dependencies ]--------
-- ARPACK:                 vendored
-- BISON:                        no
-- BLAS:                        yes
-- FLEX:                         no
-- GLPK:                   vendored
-- GMP:                    vendored
-- LAPACK:                      yes
-- LibXml2:                     yes
-- OpenMP:                      yes
-- PLFIT:                  vendored
--  
-- -----------[ Testing ]----------
-- Diff tool:                  diff
-- Sanitizers:                 none
-- Code coverage:                no
-- Verify 'finally' stack:       no
--  
-- --------[ Documentation ]-------
-- HTML:                         no
-- PDF:                          no
-- INFO:                         no
--  
-- igraph configured successfully.
--  
-- Configuring done (5.0s)
-- Generating done (2.1s)
-- Build files have been written to: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/build
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/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/f2c/arithchk.c: In function ‘ccheck’:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/f2c/arithchk.c:114:30: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  114 | const char *const emptyfmt = "";
      |                              ^~
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/f2c/arithchk.c:114:30: warning: zero-length gnu_printf format string [-Wformat-zero-length]
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/f2c/arithchk.c:114:30: warning: zero-length gnu_printf format string [-Wformat-zero-length]
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/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/f2c/backspac.c: In function ‘f_back’:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/f2c/backspac.c:47:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   47 |                 fread((char *)&n,sizeof(uiolen),1,f);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/f2c/signal_.c: In function ‘signal_’:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/f2c/signal_.c:17:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
   17 |         return (ftnint)signal(sig, proc);
      |                ^
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In file included from /usr/include/string.h:548,
                 from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/env/stdc.h:35,
                 from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/env/env.h:25,
                 from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/draft/glpmat.c:22:
In function ‘memset’,
    inlined from ‘_glp_mat_amd_order1’ at /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/draft/glpmat.c:515:7:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: ‘__builtin_memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
   59 |   return __builtin___memset_chk (__dest, __ch, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   60 |                                  __glibc_objsize0 (__dest));
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘memset’,
    inlined from ‘_glp_mat_symamd_ord’ at /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/draft/glpmat.c:557:7:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: ‘__builtin_memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
   59 |   return __builtin___memset_chk (__dest, __ch, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   60 |                                  __glibc_objsize0 (__dest));
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~
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[ 47%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/intopt/spv.c.o
[ 47%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/minisat/minisat.c.o
[ 47%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/avl.c.o
[ 47%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/bignum.c.o
[ 47%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/dimacs.c.o
[ 47%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/dmp.c.o
[ 47%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/ffalg.c.o
[ 47%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/fp2rat.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/fvs.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/gcd.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/hbm.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/jd.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/keller.c.o
In file included from /usr/include/string.h:548,
                 from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/env/stdc.h:35,
                 from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/env/env.h:25,
                 from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/misc/keller.c:23:
In function ‘memset’,
    inlined from ‘_glp_kellerman’ at /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/misc/keller.c:107:7:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: ‘__builtin_memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
   59 |   return __builtin___memset_chk (__dest, __ch, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   60 |                                  __glibc_objsize0 (__dest));
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘memset’,
    inlined from ‘_glp_kellerman’ at /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/misc/keller.c:112:7:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: ‘__builtin_memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
   59 |   return __builtin___memset_chk (__dest, __ch, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   60 |                                  __glibc_objsize0 (__dest));
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/ks.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/mc13d.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/mc21a.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/mt1.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/mygmp.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/okalg.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/qmd.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/relax4.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/rgr.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/rng.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/rng1.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/round2n.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/spm.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/str2int.c.o
[ 50%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/str2num.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/strspx.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/strtrim.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/triang.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/wclique.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/misc/wclique1.c.o
In file included from /usr/include/string.h:548,
                 from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/env/stdc.h:35,
                 from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/env/env.h:25,
                 from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/misc/wclique1.c:22:
In function ‘memset’,
    inlined from ‘_glp_wclique1’ at /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/misc/wclique1.c:111:7:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: ‘__builtin_memset’ specified bound between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
   59 |   return __builtin___memset_chk (__dest, __ch, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   60 |                                  __glibc_objsize0 (__dest));
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘memset’,
    inlined from ‘_glp_wclique1’ at /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/misc/wclique1.c:113:7:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: ‘__builtin_memset’ specified bound between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
   59 |   return __builtin___memset_chk (__dest, __ch, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   60 |                                  __glibc_objsize0 (__dest));
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/mpl/mpl1.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/mpl/mpl2.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/mpl/mpl3.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/mpl/mpl4.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/mpl/mpl5.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/mpl/mpl6.c.o
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[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/npp/npp1.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/npp/npp2.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/npp/npp3.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/npp/npp4.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/npp/npp5.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/npp/npp6.c.o
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/npp/npp6.c: In function ‘_glp_npp_sat_encode_sum_ax’:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/npp/npp6.c:853:17: warning: ‘__builtin_memset’ writing between 256 and 17179869176 bytes into a region of size 248 overflows the destination [-Wstringop-overflow=]
  853 |          set[k] = NULL;
      |                 ^
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/vendor/glpk/npp/npp6.c:836:15: note: at offset 8 into destination object ‘set’ of size 256
  836 |       NPPLSE *set[1+NBIT_MAX], *lse;
      |               ^~~
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/proxy/proxy.c.o
[ 52%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/proxy/proxy1.c.o
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[ 55%] Building C object vendor/glpk/CMakeFiles/glpk_vendored.dir/simplex/spydual.c.o
[ 55%] Built target glpk_vendored
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[ 58%] Built target pcg
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[ 61%] Building C object src/CMakeFiles/igraph.dir/core/array.c.o
In file included from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.c:30:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt: In function ‘igraph_array3_update’:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:107:5: warning: ‘igraph_array3_resize’ is deprecated [-Wdeprecated-declarations]
  107 |     IGRAPH_CHECK(FUNCTION(igraph_array3, resize)(to, from->n1, from->n2, from->n3));
      |     ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.c:29:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:68:25: note: declared here
   68 | igraph_error_t FUNCTION(igraph_array3, resize)(
      |                         ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/include/igraph_pmt.h:24:23: note: in definition of macro ‘CONCAT2x’
   24 | #define CONCAT2x(a,b) a ## _ ## b
      |                       ^
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/include/igraph_pmt.h:169:31: note: in expansion of macro ‘CONCAT2’
  169 |         #define FUNCTION(a,c) CONCAT2(a,c)
      |                               ^~~~~~~
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:68:16: note: in expansion of macro ‘FUNCTION’
   68 | igraph_error_t FUNCTION(igraph_array3, resize)(
      |                ^~~~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.c:36:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt: In function ‘igraph_array3_int_update’:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:107:5: warning: ‘igraph_array3_int_resize’ is deprecated [-Wdeprecated-declarations]
  107 |     IGRAPH_CHECK(FUNCTION(igraph_array3, resize)(to, from->n1, from->n2, from->n3));
      |     ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.c:35:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:68:25: note: declared here
   68 | igraph_error_t FUNCTION(igraph_array3, resize)(
      |                         ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/include/igraph_pmt.h:26:25: note: in definition of macro ‘CONCAT3x’
   26 | #define CONCAT3x(a,b,c) a ## _ ## b ## _ ## c
      |                         ^
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/include/igraph_pmt.h:177:31: note: in expansion of macro ‘CONCAT3’
  177 |         #define FUNCTION(a,c) CONCAT3(a,SHORT,c)
      |                               ^~~~~~~
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:68:16: note: in expansion of macro ‘FUNCTION’
   68 | igraph_error_t FUNCTION(igraph_array3, resize)(
      |                ^~~~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.c:42:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt: In function ‘igraph_array3_char_update’:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:107:5: warning: ‘igraph_array3_char_resize’ is deprecated [-Wdeprecated-declarations]
  107 |     IGRAPH_CHECK(FUNCTION(igraph_array3, resize)(to, from->n1, from->n2, from->n3));
      |     ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.c:41:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:68:25: note: declared here
   68 | igraph_error_t FUNCTION(igraph_array3, resize)(
      |                         ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/include/igraph_pmt.h:26:25: note: in definition of macro ‘CONCAT3x’
   26 | #define CONCAT3x(a,b,c) a ## _ ## b ## _ ## c
      |                         ^
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/include/igraph_pmt.h:177:31: note: in expansion of macro ‘CONCAT3’
  177 |         #define FUNCTION(a,c) CONCAT3(a,SHORT,c)
      |                               ^~~~~~~
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:68:16: note: in expansion of macro ‘FUNCTION’
   68 | igraph_error_t FUNCTION(igraph_array3, resize)(
      |                ^~~~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.c:48:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt: In function ‘igraph_array3_bool_update’:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:107:5: warning: ‘igraph_array3_bool_resize’ is deprecated [-Wdeprecated-declarations]
  107 |     IGRAPH_CHECK(FUNCTION(igraph_array3, resize)(to, from->n1, from->n2, from->n3));
      |     ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.c:47:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:68:25: note: declared here
   68 | igraph_error_t FUNCTION(igraph_array3, resize)(
      |                         ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/include/igraph_pmt.h:26:25: note: in definition of macro ‘CONCAT3x’
   26 | #define CONCAT3x(a,b,c) a ## _ ## b ## _ ## c
      |                         ^
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/array.pmt:68:16: note: in expansion of macro ‘FUNCTION’
   68 | igraph_error_t FUNCTION(igraph_array3, resize)(
      |                ^~~~~~~~
[ 61%] Building C object src/CMakeFiles/igraph.dir/core/bitset.c.o
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/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/matrix.c: In function ‘igraph_matrix_all_e_tol’:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/matrix.c:234:13: warning: ‘igraph_vector_e_tol’ is deprecated [-Wdeprecated-declarations]
  234 |             igraph_vector_e_tol(&lhs->data, &rhs->data, tol);
      |             ^~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/include/igraph_matrix.h:29,
                 from /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/src/core/matrix.c:24:
/home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/_temp/source/include/igraph_vector.h:135:47: note: declared here
  135 | IGRAPH_DEPRECATED IGRAPH_EXPORT igraph_bool_t igraph_vector_e_tol(const igraph_vector_t *lhs,
      |                                               ^~~~~~~~~~~~~~~~~~~
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-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_microscopic_update.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_vector_list.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_visitor.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_conversion.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_cocitation.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_pmt.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_qsort.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_array_pmt.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_interrupt.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_graphlets.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_types.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_attributes.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_constructors.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_centrality.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_bipartite.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_array.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_error.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_heap.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_arpack.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_eulerian.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_iterators.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_matrix.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_cycles.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_components.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_cliques.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_decls.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_operators.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_datatype.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_stack_pmt.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_stack.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_epidemics.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_psumtree.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_structural.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_foreign.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_pmt_off.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_bitset.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_community.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_graphicality.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_bitset_list.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_mixing.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_nongraph.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_neighborhood.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_paths.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_interface.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_matrix_list.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_lapack.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_motifs.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_flow.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_separators.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_lsap.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_hrg.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_cohesive_blocks.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_strvector.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_embedding.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_topology.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_vector_pmt.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_constants.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_vector.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_reachability.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_dqueue.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_statusbar.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_typed_list_pmt.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_graph_list.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_scan.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_layout.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_adjlist.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_matching.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_complex.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_heap_pmt.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_sparsemat.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_games.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_coloring.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_vector_ptr.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_blas.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_random.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_dqueue_pmt.h
-- Up-to-date: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_threading.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_config.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_version.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/include/igraph/igraph_export.h
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/lib/pkgconfig/igraph.pc
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/lib/cmake/igraph/igraph-config.cmake
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/lib/cmake/igraph/igraph-config-version.cmake
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/lib/cmake/igraph/igraph-targets.cmake
-- Installing: /home/biocbuild/bbs-3.21-bioc/meat/Rigraphlib/inst/lib/cmake/igraph/igraph-targets-release.cmake
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rigraphlib)