* installing *source* package ‘qcluster’ ...
** package ‘qcluster’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/qcluster/src'
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Rsample_from.c -o Rsample_from.o
Rsample_from.c:46:9: warning: variable 'totiter' set but not used [-Wunused-but-set-variable]
46 | int totiter = 0;
| ^
1 warning generated.
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c alloc_utils.c -o alloc_utils.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c cluster_to_triplets.c -o cluster_to_triplets.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c ecm.c -o ecm.o
ecm.c:67:9: warning: variable 'iter' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
67 | if (sumtau) {
| ^~~~~~
ecm.c:617:16: note: uninitialized use occurs here
617 | res.iter = iter;
| ^~~~
ecm.c:67:5: note: remove the 'if' if its condition is always true
67 | if (sumtau) {
| ^~~~~~~~~~~
68 | alloctable_add(&head, sumtau, 1, 'A');
69 | first_head = head;
70 | } else {
| ~~~~~~
71 | warning
| ~~~~~~~
72 | ("ecm.c (ERR_MALLOC): not able to allocate sumtau (%d)-vector",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | K);
| ~~~
74 | info = -100;
| ~~~~~~~~~~~~
75 | goto output;
| ~~~~~~~~~~~~
76 | }
| ~
ecm.c:90:5: note: variable 'iter' is declared here
90 | int iter = 0;
| ^
1 warning generated.
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c ecm_winit.c -o ecm_winit.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c gss.c -o gss.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c helper_score_smd.c -o helper_score_smd.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c init.c -o init.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c kmedians.c -o kmedians.o
kmedians.c:78:9: warning: variable 'assigned_cluster' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
78 | if (cluster_marginal)
| ^~~~~~~~~~~~~~~~
kmedians.c:137:10: note: uninitialized use occurs here
137 | free(assigned_cluster);
| ^~~~~~~~~~~~~~~~
kmedians.c:78:5: note: remove the 'if' if its condition is always true
78 | if (cluster_marginal)
| ^~~~~~~~~~~~~~~~~~~~~
79 | alloctable_add(&head, cluster_marginal, 0, 'C');
| ~
80 | else {
| ~~~~~~
81 | warning
| ~~~~~~~
82 | ("kmedians.c (ERR_MALLOC): not able to allocate cluster_marginal (%d)-array",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
83 | N);
| ~~~
84 | success = 0;
| ~~~~~~~~~~~~
85 | goto output;
| ~~~~~~~~~~~~
86 | }
| ~
kmedians.c:66:9: warning: variable 'assigned_cluster' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
66 | if (l1_dist)
| ^~~~~~~
kmedians.c:137:10: note: uninitialized use occurs here
137 | free(assigned_cluster);
| ^~~~~~~~~~~~~~~~
kmedians.c:66:5: note: remove the 'if' if its condition is always true
66 | if (l1_dist)
| ^~~~~~~~~~~~
67 | alloctable_add(&head, l1_dist, 0, 'B');
| ~
68 | else {
| ~~~~~~
69 | warning
| ~~~~~~~
70 | ("kmedians.c (ERR_MALLOC): not able to allocate l1_dist (%d, %d)-array",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | N, K);
| ~~~~~~
72 | success = 0;
| ~~~~~~~~~~~~
73 | goto output;
| ~~~~~~~~~~~~
74 | }
| ~
kmedians.c:51:9: warning: variable 'assigned_cluster' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
51 | if (MM)
| ^~
kmedians.c:137:10: note: uninitialized use occurs here
137 | free(assigned_cluster);
| ^~~~~~~~~~~~~~~~
kmedians.c:51:5: note: remove the 'if' if its condition is always true
51 | if (MM)
| ^~~~~~~
52 | alloctable_add(&head, MM, 1, 'A');
| ~
53 | else {
| ~~~~~~
54 | warning
| ~~~~~~~
55 | ("kmedians.c (ERR_MALLOC): not able to allocate MM (%d, %d)-array",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | K, P);
| ~~~~~~
57 | success = 0;
| ~~~~~~~~~~~~
58 | goto output;
| ~~~~~~~~~~~~
59 | }
| ~
kmedians.c:90:5: note: variable 'assigned_cluster' is declared here
90 | int *assigned_cluster = malloc(N * sizeof(int)); /* Store cluster memberships */
| ^
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c quickselect.c -o quickselect.o
3 warnings generated.
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c score_hard.c -o score_hard.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c score_hard_cluster.c -o score_hard_cluster.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c score_smooth.c -o score_smooth.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c score_smooth_cluster.c -o score_smooth_cluster.o
/usr/local/clang19/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o qcluster.so Rsample_from.o alloc_utils.o cluster_to_triplets.o ecm.o ecm_winit.o gss.o helper_score_smd.o init.o kmedians.o quickselect.o score_hard.o score_hard_cluster.o score_smooth.o score_smooth_cluster.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/qcluster/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/qcluster/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/qcluster/src'
installing to /data/gannet/ripley/R/packages/tests-clang/qcluster.Rcheck/00LOCK-qcluster/00new/qcluster/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (qcluster)