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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:martini.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings martini_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/martini.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘martini/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘martini’ version ‘1.27.0’
* 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 ‘martini’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
  /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/martini.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... OK
* 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 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_GI_network: no visible binding for global variable ‘gene1’
get_GI_network: no visible binding for global variable ‘gene2’
get_GM_network: no visible binding for global variable ‘gene’
group_snps: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . gene gene1 gene2
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'organism_id2name.Rd':
  ‘organism’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/martini/libs/martini.so’:
  Found ‘exit’, possibly from ‘exit’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] 25 - 12 == 13
  ── Failure ('test_scones.cv.R:33:3'): we recover causal SNPs ───────────────────
  sort(names(V(cones))) not equal to sort(grep("[AC]", test_map$snp, value = TRUE)).
  Lengths differ: 25 is not 12
  ── Failure ('test_sigmod.cv.R:32:3'): we recover causal SNPs ───────────────────
  gorder(cones) not equal to sum(grepl("[AC]", test_map$snp)).
  1/1 mismatches
  [1] 25 - 12 == 13
  ── Failure ('test_sigmod.cv.R:33:3'): we recover causal SNPs ───────────────────
  sort(names(V(cones))) not equal to sort(grep("[AC]", test_map$snp, value = TRUE)).
  Lengths differ: 25 is not 12
  
  [ FAIL 4 | WARN 4 | SKIP 4 | PASS 228 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/martini.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL martini
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘martini’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include   -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/RcppEigen.h:25,
                 from ../inst/include/martini_RcppExports.h:7,
                 from ../inst/include/martini.h:7,
                 from RcppExports.cpp:4:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include   -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c mincut.cpp -o mincut.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/RcppEigen.h:25,
                 from mincut.cpp:7:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include   -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c lib/maxflow/maxflow.cpp -o lib/maxflow/maxflow.o
lib/maxflow/maxflow.cpp: In member function ‘void Graph<captype, tcaptype, flowtype>::reallocate_nodes(int) [with captype = int; tcaptype = int; flowtype = int]’:
lib/maxflow/maxflow.cpp:777:91: warning: pointer ‘nodes_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  777 |                         if (i->next) i->next = (node*) ((char*)i->next + (((char*) nodes) - ((char*) nodes_old)));
      |                                                                          ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:765:32: note: call to ‘void* realloc(void*, size_t)’ here
  765 |         nodes = (node*) realloc(nodes_old, node_num_max*sizeof(node));
      |                         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:781:78: warning: pointer ‘nodes_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  781 |                         a->head = (node*) ((char*)a->head + (((char*) nodes) - ((char*) nodes_old)));
      |                                                             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:765:32: note: call to ‘void* realloc(void*, size_t)’ here
  765 |         nodes = (node*) realloc(nodes_old, node_num_max*sizeof(node));
      |                         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp: In member function ‘void Graph<captype, tcaptype, flowtype>::reallocate_arcs() [with captype = int; tcaptype = int; flowtype = int]’:
lib/maxflow/maxflow.cpp:807:143: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  807 |                         if (i->parent && i->parent != ORPHAN && i->parent != TERMINAL) i->parent = (arc*) ((char*)i->parent + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                                                                               ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:806:92: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  806 |                         if (i->first) i->first = (arc*) ((char*)i->first + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:812:80: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  812 |                         a->sister = (arc*) ((char*)a->sister + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:811:89: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  811 |                         if (a->next) a->next = (arc*) ((char*)a->next + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp: In member function ‘void Graph<captype, tcaptype, flowtype>::reallocate_nodes(int) [with captype = short int; tcaptype = int; flowtype = int]’:
lib/maxflow/maxflow.cpp:777:91: warning: pointer ‘nodes_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  777 |                         if (i->next) i->next = (node*) ((char*)i->next + (((char*) nodes) - ((char*) nodes_old)));
      |                                                                          ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:765:32: note: call to ‘void* realloc(void*, size_t)’ here
  765 |         nodes = (node*) realloc(nodes_old, node_num_max*sizeof(node));
      |                         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:781:78: warning: pointer ‘nodes_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  781 |                         a->head = (node*) ((char*)a->head + (((char*) nodes) - ((char*) nodes_old)));
      |                                                             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:765:32: note: call to ‘void* realloc(void*, size_t)’ here
  765 |         nodes = (node*) realloc(nodes_old, node_num_max*sizeof(node));
      |                         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp: In member function ‘void Graph<captype, tcaptype, flowtype>::reallocate_arcs() [with captype = short int; tcaptype = int; flowtype = int]’:
lib/maxflow/maxflow.cpp:807:143: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  807 |                         if (i->parent && i->parent != ORPHAN && i->parent != TERMINAL) i->parent = (arc*) ((char*)i->parent + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                                                                               ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:806:92: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  806 |                         if (i->first) i->first = (arc*) ((char*)i->first + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:812:80: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  812 |                         a->sister = (arc*) ((char*)a->sister + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:811:89: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  811 |                         if (a->next) a->next = (arc*) ((char*)a->next + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp: In member function ‘void Graph<captype, tcaptype, flowtype>::reallocate_nodes(int) [with captype = float; tcaptype = float; flowtype = float]’:
lib/maxflow/maxflow.cpp:777:91: warning: pointer ‘nodes_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  777 |                         if (i->next) i->next = (node*) ((char*)i->next + (((char*) nodes) - ((char*) nodes_old)));
      |                                                                          ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:765:32: note: call to ‘void* realloc(void*, size_t)’ here
  765 |         nodes = (node*) realloc(nodes_old, node_num_max*sizeof(node));
      |                         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:781:78: warning: pointer ‘nodes_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  781 |                         a->head = (node*) ((char*)a->head + (((char*) nodes) - ((char*) nodes_old)));
      |                                                             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:765:32: note: call to ‘void* realloc(void*, size_t)’ here
  765 |         nodes = (node*) realloc(nodes_old, node_num_max*sizeof(node));
      |                         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp: In member function ‘void Graph<captype, tcaptype, flowtype>::reallocate_arcs() [with captype = float; tcaptype = float; flowtype = float]’:
lib/maxflow/maxflow.cpp:807:143: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  807 |                         if (i->parent && i->parent != ORPHAN && i->parent != TERMINAL) i->parent = (arc*) ((char*)i->parent + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                                                                               ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:806:92: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  806 |                         if (i->first) i->first = (arc*) ((char*)i->first + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:812:80: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  812 |                         a->sister = (arc*) ((char*)a->sister + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:811:89: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  811 |                         if (a->next) a->next = (arc*) ((char*)a->next + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp: In member function ‘void Graph<captype, tcaptype, flowtype>::reallocate_nodes(int) [with captype = double; tcaptype = double; flowtype = double]’:
lib/maxflow/maxflow.cpp:777:91: warning: pointer ‘nodes_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  777 |                         if (i->next) i->next = (node*) ((char*)i->next + (((char*) nodes) - ((char*) nodes_old)));
      |                                                                          ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:765:32: note: call to ‘void* realloc(void*, size_t)’ here
  765 |         nodes = (node*) realloc(nodes_old, node_num_max*sizeof(node));
      |                         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:781:78: warning: pointer ‘nodes_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  781 |                         a->head = (node*) ((char*)a->head + (((char*) nodes) - ((char*) nodes_old)));
      |                                                             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:765:32: note: call to ‘void* realloc(void*, size_t)’ here
  765 |         nodes = (node*) realloc(nodes_old, node_num_max*sizeof(node));
      |                         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp: In member function ‘void Graph<captype, tcaptype, flowtype>::reallocate_arcs() [with captype = double; tcaptype = double; flowtype = double]’:
lib/maxflow/maxflow.cpp:807:143: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  807 |                         if (i->parent && i->parent != ORPHAN && i->parent != TERMINAL) i->parent = (arc*) ((char*)i->parent + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                                                                               ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:806:92: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  806 |                         if (i->first) i->first = (arc*) ((char*)i->first + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:812:80: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  812 |                         a->sister = (arc*) ((char*)a->sister + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:811:89: warning: pointer ‘arcs_old’ may be used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free]
  811 |                         if (a->next) a->next = (arc*) ((char*)a->next + (((char*) arcs) - ((char*) arcs_old)));
      |                                                                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lib/maxflow/maxflow.cpp:794:30: note: call to ‘void* realloc(void*, size_t)’ here
  794 |         arcs = (arc*) realloc(arcs_old, arc_num_max*sizeof(arc));
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ar -crus libmaxflow.a lib/maxflow/maxflow.o
cp -r lib/maxflow "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-martini/00new/martini/include"
mkdir -p "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-martini/00new/martini/usrlib"
cp libmaxflow.a "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-martini/00new/martini/usrlib"
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o martini.so RcppExports.o mincut.o -pthread -fopenmp /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-martini/00new/martini/usrlib/libmaxflow.a -fopenmp -pthread -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-martini/00new/martini/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (martini)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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> library(testthat)
> library(martini)
> library(igraph)

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> test_check("martini")
Warning: program compiled against libxml 212 using older 211
trying URL 'https://stringdb-downloads.org/download/protein.links.v11.5/9606.protein.links.v11.5.txt.gz'
Content type 'application/octet-stream' length 72718210 bytes (69.3 MB)
==================================================
downloaded 69.3 MB

[ FAIL 4 | WARN 4 | SKIP 4 | PASS 228 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On Bioconductor (3): 'test_connect_biomart.R:1:1', 'test_get_gxg.R:1:1',
  'test_snp2ensembl.R:1:1'
• empty test (1): 'test_plot_ideogram.R:3:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_scones.cv.R:32:3'): we recover causal SNPs ───────────────────
gorder(cones) not equal to sum(grepl("[AC]", test_map$snp)).
1/1 mismatches
[1] 25 - 12 == 13
── Failure ('test_scones.cv.R:33:3'): we recover causal SNPs ───────────────────
sort(names(V(cones))) not equal to sort(grep("[AC]", test_map$snp, value = TRUE)).
Lengths differ: 25 is not 12
── Failure ('test_sigmod.cv.R:32:3'): we recover causal SNPs ───────────────────
gorder(cones) not equal to sum(grepl("[AC]", test_map$snp)).
1/1 mismatches
[1] 25 - 12 == 13
── Failure ('test_sigmod.cv.R:33:3'): we recover causal SNPs ───────────────────
sort(names(V(cones))) not equal to sort(grep("[AC]", test_map$snp, value = TRUE)).
Lengths differ: 25 is not 12

[ FAIL 4 | WARN 4 | SKIP 4 | PASS 228 ]
Error: Test failures
Execution halted