installing dependencies ‘cat’, ‘clusterCrit’, ‘clustrd’, ‘diceR’, ‘knockoff’, ‘micemd’, ‘mix’, ‘NPBayesImputeCat’ also installing the dependencies ‘GJRM’, ‘Rdsdp’, ‘RankAggreg’ begin installing package ‘GJRM’ begin installing package ‘Rdsdp’ begin installing package ‘mix’ begin installing package ‘RankAggreg’ begin installing package ‘NPBayesImputeCat’ begin installing package ‘clustrd’ begin installing package ‘cat’ begin installing package ‘clusterCrit’ * installing *source* package ‘RankAggreg’ ... ** package ‘RankAggreg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHl1GEr/R.INSTALL18c569611d6097/RankAggreg/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RankAggreg.c -o RankAggreg.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o RankAggreg.so RankAggreg.o registerDynamicSymbol.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHl1GEr/R.INSTALL18c569611d6097/RankAggreg/src' installing to /home/hornik/tmp/CRAN_special_donttest/Library/00LOCK-RankAggreg/00new/RankAggreg/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 (RankAggreg) begin installing package ‘diceR’ * installing *source* package ‘cat’ ... ** package ‘cat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFGbqX2/R.INSTALL18c5746d90b81b/cat/src' gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c cat.f -o cat.o cat.f:353:1: 353 | 3 continue | 1 Warning: Label 3 at (1) defined but not used [-Wunused-label] cat.f:643:72: 643 | theta(m)=theta(m)*g/sumf | ^ Warning: ‘g’ may be used uninitialized [-Wmaybe-uninitialized] cat.f:605:64: 605 | double precision sumt,sumf,table(ncells),theta(ncells),g | ^ note: ‘g’ was declared here gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o cat.so cat.o init.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFGbqX2/R.INSTALL18c5746d90b81b/cat/src' installing to /home/hornik/tmp/CRAN_special_donttest/Library/00LOCK-cat/00new/cat/libs ** R ** data ** 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 (cat) * installing *source* package ‘mix’ ... ** package ‘mix’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpXax9QJ/R.INSTALL18c57263d0796e/mix/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c mix.f -o mix.o mix.f:1209:60: 1209 | / n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz,l3) | 1 Warning: Unused dummy argument ‘mcz’ at (1) [-Wunused-dummy-argument] mix.f:1209:65: 1209 | / n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz,l3) | 1 Warning: Unused dummy argument ‘nmcz’ at (1) [-Wunused-dummy-argument] mix.f:1057:34: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘c’ at (1) [-Wunused-dummy-argument] mix.f:1057:36: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘d’ at (1) [-Wunused-dummy-argument] mix.f:1057:45: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘dmis’ at (1) [-Wunused-dummy-argument] mix.f:1057:40: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘jmp’ at (1) [-Wunused-dummy-argument] mix.f:1057:27: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘mcw’ at (1) [-Wunused-dummy-argument] mix.f:1057:32: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘nmcw’ at (1) [-Wunused-dummy-argument] mix.f:1057:15: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘t3’ at (1) [-Wunused-dummy-argument] mix.f:1056:60: 1056 | subroutine addstat1(q,psi,npsi,ncells,sigma,mu,theta,t1,t2, | 1 Warning: Unused dummy argument ‘theta’ at (1) [-Wunused-dummy-argument] mix.f:458:56: 458 | subroutine pstepm(q,psi,npsi,ncells,t1,t2,t3,n,p,prior,chf, | 1 Warning: Unused dummy argument ‘p’ at (1) [-Wunused-dummy-argument] mix.f:999:72: 999 | theta(m)=theta(m)*g/sumf | ^ Warning: ‘g’ may be used uninitialized [-Wmaybe-uninitialized] mix.f:961:64: 961 | double precision sumt,sumf,table(ncells),theta(ncells),g | ^ note: ‘g’ was declared here gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o mix.so init.o mix.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpXax9QJ/R.INSTALL18c57263d0796e/mix/src' installing to /home/hornik/tmp/CRAN_special_donttest/Library/00LOCK-mix/00new/mix/libs ** R ** data *** moving datasets to lazyload DB ** 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 (mix) * installing *source* package ‘clusterCrit’ ... ** package ‘clusterCrit’ successfully unpacked and MD5 sums checked ** using staged installation 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-14 accepts -g... yes checking for gcc-14 option to accept ISO C89... none needed checking whether we are using the GNU Fortran compiler... yes checking whether gfortran-14 accepts -g... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp4UnGbU/R.INSTALL18c56e453150c9/clusterCrit/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c criteria.c -o criteria.o criteria.c: In function ‘cluc_errorMsg’: criteria.c:331:17: warning: unused variable ‘msg’ [-Wunused-variable] 331 | char msg[128]; | ^~~ gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c norms.f95 -o norms.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c matrix.f95 -o matrix.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c critUtils.f95 -o critUtils.o critUtils.f95:847:26: 847 | sConc(1) = sConc(1) + ip - 1 | 1 Warning: Possible change of value in conversion from INTEGER(4) to INTEGER(1) at (1) [-Wconversion] critUtils.f95:851:29: 851 | sConc(2) = sConc(2) + (sPNum(1) - iw + 1) | 1 Warning: Possible change of value in conversion from INTEGER(4) to INTEGER(1) at (1) [-Wconversion] critUtils.f95:855:29: 855 | sConc(1) = sConc(1) + 1 | 1 Warning: Possible change of value in conversion from INTEGER(4) to INTEGER(1) at (1) [-Wconversion] gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c indices.f95 -o indices.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c critCalc.f95 -o critCalc.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o clusterCrit.so criteria.o norms.o matrix.o critUtils.o indices.o critCalc.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp4UnGbU/R.INSTALL18c56e453150c9/clusterCrit/src' installing to /home/hornik/tmp/CRAN_special_donttest/Library/00LOCK-clusterCrit/00new/clusterCrit/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 (clusterCrit) * installing *source* package ‘clustrd’ ... ** package ‘clustrd’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (clustrd) * installing *source* package ‘diceR’ ... ** package ‘diceR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjoYJwp/R.INSTALL18cba12554803c/diceR/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c connectivity_matrix.cpp -o connectivity_matrix.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c indicator_matrix.cpp -o indicator_matrix.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o diceR.so RcppExports.o connectivity_matrix.o indicator_matrix.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjoYJwp/R.INSTALL18cba12554803c/diceR/src' installing to /home/hornik/tmp/CRAN_special_donttest/Library/00LOCK-diceR/00new/diceR/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (diceR) * installing *source* package ‘Rdsdp’ ... ** package ‘Rdsdp’ successfully unpacked and MD5 sums checked ** using staged installation Using bundled DSDP checking for gcc... gcc-14 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 the compiler supports GNU C... yes checking whether gcc-14 accepts -g... yes checking for gcc-14 option to enable C11 features... none needed checking how to run the C preprocessor... gcc-14 -E configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Idsdp/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DNOSHORTS -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rdsdp.c -o Rdsdp.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Idsdp/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DNOSHORTS -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rreadsdpa.c -o Rreadsdpa.o Rreadsdpa.c: In function ‘ReadSDPA2’: Rreadsdpa.c:489:9: warning: variable ‘fgets_return_pt’ set but not used [-Wunused-but-set-variable] 489 | char* fgets_return_pt; | ^~~~~~~~~~~~~~~ Rreadsdpa.c:488:7: warning: variable ‘fscanf_return_int’ set but not used [-Wunused-but-set-variable] 488 | int fscanf_return_int; | ^~~~~~~~~~~~~~~~~ Rreadsdpa.c: In function ‘DSDPReadOptions2’: Rreadsdpa.c:1021:9: warning: variable ‘fgets_return_pt’ set but not used [-Wunused-but-set-variable] 1021 | char* fgets_return_pt; | ^~~~~~~~~~~~~~~ (cd dsdp && \ (make dsdplibrary CC="gcc-14 " CFLAGS="-g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include " AR="ar" RANLIB="ranlib") && \ touch dsdp.ts) make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp' ========================================== Compiling DSDP5 For help with installation problems, please send EVERYTHING printed out below to the developers ========================================== On Wed Oct 23 14:00:06 CEST 2024 on anduin2 Machine characteristics: Linux anduin2 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) x86_64 GNU/Linux ----------------------------------------- Using C compiler: gcc-14 Using compiler options: -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include ----------------------------------------- Current Directory: /home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp Using DSDP directory: ../../ ========================================== cd src; make all make[3]: Entering directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src' cd solver; make dsdplib; make[4]: Entering directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/solver' gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dualalg.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dualimpl.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpcops.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpschurmat.c dsdpschurmat.c: In function ‘DSDPSetFixedVariables’: dsdpschurmat.c:696:10: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 696 | int i,info; | ^~~~ gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpcg.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpconverge.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpsetup.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpcone.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpsetoptions.c dsdpsetoptions.c: In function ‘DSDPReadOptions’: dsdpsetoptions.c:152:9: warning: variable ‘fgets_return_pt’ set but not used [-Wunused-but-set-variable] 152 | char* fgets_return_pt; | ^~~~~~~~~~~~~~~ dsdpsetoptions.c:147:9: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 147 | int i,info,line=0; | ^~~~ gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpsetdata.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdprescone.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpobjcone.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpprintout.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpschurmatadd.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -c dsdpx.c dsdpx.c: In function ‘DSDPComputeX’: dsdpx.c:57:76: warning: variable ‘rpobjerr’ set but not used [-Wunused-but-set-variable] 57 | double pobj=0,ppobj2=0,ddobj,tracexs=0,tracexs2=0,rpinfeas=0,rpinfeas2=0,rpobjerr=0; | ^~~~~~~~ ar cr ../..//lib/libdsdp.a dualalg.o dualimpl.o dsdpcops.o dsdpschurmat.o dsdpcg.o dsdpconverge.o dsdpsetup.o dsdpcone.o dsdpsetoptions.o dsdpsetdata.o dsdprescone.o dsdpobjcone.o dsdpprintout.o dsdpschurmatadd.o dsdpx.o ranlib ../..//lib/libdsdp.a make clean make[5]: Entering directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/solver' rm -f dualalg.o dualimpl.o dsdpcops.o dsdpschurmat.o dsdpcg.o dsdpconverge.o dsdpsetup.o dsdpcone.o dsdpsetoptions.o dsdpsetdata.o dsdprescone.o dsdpobjcone.o dsdpprintout.o dsdpschurmatadd.o dsdpx.o make[5]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/solver' make[4]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/solver' cd sdp; make dsdplib; make[4]: Entering directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/sdp' gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -c dsdpstep.c dsdpstep.c: In function ‘ComputeStepROBUST’: dsdpstep.c:283:10: warning: variable ‘LDA’ set but not used [-Wunused-but-set-variable] 283 | int N, LDA, LWORK; | ^~~ gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -c printsdpa.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -c sdpconevec.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -c sdpsss.c sdpsss.c: In function ‘CountNonzeros’: sdpsss.c:59:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 59 | for (j=0;jn; | ^~~ dlpack.c: In function ‘DenseSymPSDNormF2’: dlpack.c:423:7: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 423 | int info; | ^~~~ dlpack.c: In function ‘DSDPXMatPCreateWithData’: dlpack.c:587:10: warning: variable ‘dtmp’ set but not used [-Wunused-but-set-variable] 587 | double dtmp; | ^~~~ dlpack.c: In function ‘DvechmatGetRowAdd’: dlpack.c:717:7: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 717 | int info; | ^~~~ dlpack.c: In function ‘DSDPGetDMat’: dlpack.c:939:10: warning: variable ‘dtmp’ set but not used [-Wunused-but-set-variable] 939 | double dtmp; | ^~~~ gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c dufull.c dufull.c: In function ‘DSDPGetEigs2’: dufull.c:163:23: warning: variable ‘LDZ’ set but not used [-Wunused-but-set-variable] 163 | ffinteger N=n,LDA=n,LDZ=n,LWORK=nd,INFO=0; | ^~~ dufull.c: In function ‘DTRUMatSolve’: dufull.c:255:13: warning: variable ‘ierr’ set but not used [-Wunused-but-set-variable] 255 | ffinteger ierr,INFO=0,NRHS=1,LDA=A->LDA,LDB=A->LDA,N=A->n; | ^~~~ dufull.c: In function ‘DSDPLAPACKSUDualMatCreate2P’: dufull.c:822:7: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 822 | int info; | ^~~~ dufull.c: In function ‘DenseSymPSDNormF2’: dufull.c:855:7: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 855 | int info; | ^~~~ dufull.c: In function ‘DSDPXMatUCreateWithData’: dufull.c:958:10: warning: variable ‘dtmp’ set but not used [-Wunused-but-set-variable] 958 | double dtmp; | ^~~~ dufull.c: In function ‘DvecumatGetRowAdd’: dufull.c:1075:7: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 1075 | int info; | ^~~~ dufull.c: In function ‘DSDPGetDUMat’: dufull.c:1302:10: warning: variable ‘dtmp’ set but not used [-Wunused-but-set-variable] 1302 | double dtmp; | ^~~~ dufull.c: At top level: dufull.c:340:12: warning: ‘DTRUMatView2’ defined but not used [-Wunused-function] 340 | static int DTRUMatView2(void* AA){ | ^~~~~~~~~~~~ gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpvec.c sdpvec.c: In function ‘DSDPVecSetBasis’: sdpvec.c:138:7: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 138 | int info; | ^~~~ sdpvec.c: In function ‘DSDPVecWAXPY’: sdpvec.c:341:7: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 341 | int info; | ^~~~ gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c identity.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c spds.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c zeromat.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c onemat.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c diag.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c rmmat.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c cholmat.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c cholmat2.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c dtrsm2.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpmatx.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpnfac.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdporder.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpalloc.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpsymb.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpxlist.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpdvct.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpexit.c ar cr ../..//lib/libdsdp.a vech.o vechu.o drowcol.o dlpack.o dufull.o sdpvec.o identity.o spds.o zeromat.o onemat.o diag.o rmmat.o cholmat.o cholmat2.o dtrsm2.o sdpmatx.o sdpnfac.o sdporder.o sdpalloc.o sdpsymb.o sdpxlist.o sdpdvct.o sdpexit.o ranlib ../..//lib/libdsdp.a make clean make[5]: Entering directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/vecmat' rm -f vech.o vechu.o drowcol.o dlpack.o dufull.o sdpvec.o identity.o spds.o zeromat.o onemat.o diag.o rmmat.o cholmat.o cholmat2.o dtrsm2.o sdpmatx.o sdpnfac.o sdporder.o sdpalloc.o sdpsymb.o sdpxlist.o sdpdvct.o sdpexit.o make[5]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/vecmat' make[4]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/vecmat' cd sys; make dsdplib; make[4]: Entering directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/sys' gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -DDSDP_TIME -c dsdperror.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -DDSDP_TIME -c dsdploginfo.c dsdploginfo.c: In function ‘DSDPLogInfoAllow’: dsdploginfo.c:70:10: warning: variable ‘ierr’ set but not used [-Wunused-but-set-variable] 70 | char* ierr; | ^~~~ dsdploginfo.c: In function ‘DSDPLogFInfo’: dsdploginfo.c:114:15: warning: variable ‘urank’ set but not used [-Wunused-but-set-variable] 114 | int urank; | ^~~~~ gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -DDSDP_TIME -c dsdplog.c gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -DDSDP_TIME -c dsdptime.c ar cr ../..//lib/libdsdp.a dsdperror.o dsdploginfo.o dsdplog.o dsdptime.o ranlib ../..//lib/libdsdp.a make clean make[5]: Entering directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/sys' rm -f dsdperror.o dsdploginfo.o dsdplog.o dsdptime.o make[5]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/sys' make[4]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/sys' cd bounds; make dsdplib; make[4]: Entering directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/bounds' gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -c dbounds.c dbounds.c: In function ‘BConeComputeS’: dbounds.c:90:12: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 90 | int i,ii,info; | ^~~~ dbounds.c: In function ‘LPANorm2’: dbounds.c:366:12: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 366 | int i,ii,info; | ^~~~ gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -DNOSHORTS -I../../include -I../solver -c allbounds.c allbounds.c: In function ‘LUBoundsHessian’: allbounds.c:100:18: warning: variable ‘asrs’ set but not used [-Wunused-but-set-variable] 100 | double assa,as,asrs=0,sl,su; | ^~~~ ar cr ../..//lib/libdsdp.a dbounds.o allbounds.o ranlib ../..//lib/libdsdp.a make clean make[5]: Entering directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/bounds' rm -f dbounds.o allbounds.o make[5]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/bounds' make[4]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src/bounds' make[3]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp/src' make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src/dsdp' gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o Rdsdp.so Rdsdp.o Rreadsdpa.o -Ldsdp/lib -ldsdp -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -lm -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLKjhm/R.INSTALL18c5701aa97aa4/Rdsdp/src' installing to /home/hornik/tmp/CRAN_special_donttest/Library/00LOCK-Rdsdp/00new/Rdsdp/libs ** R ** 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 (Rdsdp) begin installing package ‘knockoff’ * installing *source* package ‘knockoff’ ... ** package ‘knockoff’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 (knockoff) * installing *source* package ‘NPBayesImputeCat’ ... ** package ‘NPBayesImputeCat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzTeEHZ/R.INSTALL18c56c45c8cf7d/NPBayesImputeCat/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CData.cpp -o CData.o In file included from CData.cpp:26: In static member function ‘static void* CArrayND::flat2arrayND_ln(void*, int, int, int*) [with T = int]’, inlined from ‘static void* CArrayND::flat2arrayND(void*, int, int, ...) [with T = int]’ at CArrayND.h:77:25: CArrayND.h:88:36: warning: ‘lengths’ may be used uninitialized [-Wmaybe-uninitialized] 88 | size[0] = lengths[0]; | ~~~~~~~~~^ CArrayND.h: In static member function ‘static void* CArrayND::flat2arrayND(void*, int, int, ...) [with T = int]’: CArrayND.h:68:21: note: ‘lengths’ declared here 68 | int lengths[20]; | ^~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CEnv.cpp -o CEnv.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CLcm.cpp -o CLcm.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CParam.cpp -o CParam.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CTrace.cpp -o CTrace.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SpecialFunctions.cpp -o SpecialFunctions.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c lczmain.cpp -o lczmain.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c margin_conditions.cpp -o margin_conditions.o In file included from margin_conditions.cpp:23: In static member function ‘static void* CArrayND::flat2arrayND_ln(void*, int, int, int*) [with T = int]’, inlined from ‘static void* CArrayND::flat2arrayND(void*, int, int, ...) [with T = int]’ at CArrayND.h:77:25: CArrayND.h:88:36: warning: ‘lengths’ may be used uninitialized [-Wmaybe-uninitialized] 88 | size[0] = lengths[0]; | ~~~~~~~~~^ CArrayND.h: In static member function ‘static void* CArrayND::flat2arrayND(void*, int, int, ...) [with T = int]’: CArrayND.h:68:21: note: ‘lengths’ declared here 68 | int lengths[20]; | ^~~~~~~ g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o NPBayesImputeCat.so CData.o CEnv.o CLcm.o CParam.o CTrace.o RcppExports.o SpecialFunctions.o lczmain.o margin_conditions.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzTeEHZ/R.INSTALL18c56c45c8cf7d/NPBayesImputeCat/src' installing to /home/hornik/tmp/CRAN_special_donttest/Library/00LOCK-NPBayesImputeCat/00new/NPBayesImputeCat/libs ** R ** data ** demo ** 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 (NPBayesImputeCat) * installing *source* package ‘GJRM’ ... ** package ‘GJRM’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GJRM) begin installing package ‘micemd’ * installing *source* package ‘micemd’ ... ** package ‘micemd’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (micemd) checking clusterMI_1.2.2.tar.gz ... Depends: Package: clusterMI Depends: R (>= 3.5.0) Imports: stats, graphics, parallel, mice, micemd, mclust, mix, fpc, knockoff, withr, glmnet, ClusterR, FactoMineR, diceR, NPBayesImputeCat, e1071, Rfast, cat, utils, ggplot2, gridExtra, reshape2, methods, Rcpp LinkingTo: Rcpp, RcppArmadillo Timings: user system elapsed clusterMI 497.6 14.103 980.382 Results: Check status summary: NOTE Source packages 1 Check results summary: clusterMI ... NOTE * checking examples ... [3m/13m] NOTE * checking re-building of vignette outputs ... [218s/74s] NOTE