downloading reverse dependencies ... downloading GhostKnockoff_0.1.0.tar.gz ... ok downloading knockoff_0.3.6.tar.gz ... ok downloading OptimaRegion_1.2.tar.gz ... ok installing dependencies ‘DepthProc’, ‘Rdsdp’, ‘RPtests’, ‘seqminer’ begin installing package ‘Rdsdp’ begin installing package ‘seqminer’ begin installing package ‘RPtests’ begin installing package ‘DepthProc’ * installing *source* package ‘RPtests’ ... ** this is package ‘RPtests’ version ‘0.1.5’ ** package ‘RPtests’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpSKr5vr/R.INSTALL3d986157f65883/RPtests/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/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 Aux_functions.cpp -o Aux_functions.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/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 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o RPtests.so Aux_functions.o RcppExports.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpSKr5vr/R.INSTALL3d986157f65883/RPtests/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RPtests/00new/RPtests/libs ** R ** 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 (RPtests) * installing *source* package ‘Rdsdp’ ... ** this is package ‘Rdsdp’ version ‘1.0.6’ ** using staged installation ./configure: line 2303: -z: command not found Using bundled DSDP checking for gcc... gcc-14 -std=gnu23 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 -std=gnu23 accepts -g... yes checking for gcc-14 -std=gnu23 option to enable C11 features... none needed checking how to run the C preprocessor... gcc-14 -std=gnu23 -E R_INCLUDE_DIR=/home/hornik/tmp/R-d-gcc-14/include configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Idsdp/include -DUSING_R -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rdsdp.c -o Rdsdp.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Idsdp/include -DUSING_R -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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 -std=gnu23" CFLAGS="-g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include " AR="ar" RANLIB="ranlib") && \ touch dsdp.ts) make[2]: Entering directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp' ========================================== Compiling DSDP5 For help with installation problems, please send EVERYTHING printed out below to the developers ========================================== On Sun Jun 8 18:08:08 CEST 2025 on anduin2 Machine characteristics: Linux anduin2 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) x86_64 GNU/Linux ----------------------------------------- Using C compiler: gcc-14 -std=gnu23 Using compiler options: -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include ----------------------------------------- Current Directory: /home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp Using DSDP directory: ../../ ========================================== cd src; make all make[3]: Entering directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src' cd solver; make dsdplib; make[4]: Entering directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/solver' gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dualalg.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dualimpl.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dsdpcops.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dsdpcg.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dsdpconverge.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dsdpsetup.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dsdpcone.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dsdpsetdata.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dsdprescone.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dsdpobjcone.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dsdpprintout.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -c dsdpschurmatadd.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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/RtmphdHWIF/R.INSTALL3d985b4dd6252e/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/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/solver' make[4]: Leaving directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/solver' cd sdp; make dsdplib; make[4]: Entering directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/sdp' gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -c printsdpa.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -c sdpconevec.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c identity.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c spds.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c zeromat.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c onemat.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c diag.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c rmmat.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c cholmat.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c cholmat2.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c dtrsm2.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpmatx.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpnfac.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdporder.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpalloc.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpsymb.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpxlist.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -I../solver -I../sdp -c sdpdvct.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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/RtmphdHWIF/R.INSTALL3d985b4dd6252e/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/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/vecmat' make[4]: Leaving directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/vecmat' cd sys; make dsdplib; make[4]: Entering directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/sys' gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -DDSDP_TIME -c dsdperror.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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:118:15: warning: variable ‘urank’ set but not used [-Wunused-but-set-variable] 118 | int urank; | ^~~~~ gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -fpic -DNOSHORTS -I../../include -DDSDP_TIME -c dsdplog.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/sys' rm -f dsdperror.o dsdploginfo.o dsdplog.o dsdptime.o make[5]: Leaving directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/sys' make[4]: Leaving directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/sys' cd bounds; make dsdplib; make[4]: Entering directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/bounds' gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DNOSHORTS -I/home/hornik/tmp/R-d-gcc-14/include -DUSING_R -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/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/bounds' rm -f dbounds.o allbounds.o make[5]: Leaving directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/bounds' make[4]: Leaving directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src/bounds' make[3]: Leaving directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp/src' make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src/dsdp' gcc-14 -std=gnu23 -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/RtmphdHWIF/R.INSTALL3d985b4dd6252e/Rdsdp/src' installing to /home/hornik/tmp/CRAN_recheck/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) * installing *source* package ‘seqminer’ ... ** this is package ‘seqminer’ version ‘9.7’ ** package ‘seqminer’ successfully unpacked and MD5 sums checked ** using staged installation configure: CC = gcc-14 -std=gnu23 configure: CFLAGS = -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native configure: CXX = g++-14 -std=gnu++11 configure: CXXFLAGS = -g -O2 -Wall -pedantic -mtune=native 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 g++-14 -std=gnu++11 accepts -g... yes checking how to run the C++ preprocessor... g++-14 -std=gnu++11 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for BZ2_bzDecompressInit in -lbz2... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes configure: Will use system-wide bzip2 library checking for ZSTD_compress in -lzstd... yes checking zstd.h usability... yes checking zstd.h presence... yes checking for zstd.h... yes configure: Will use system-wide zstd library checking for sqlite3_open in -lsqlite3... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes configure: Will use system-wide sqlite library checking for regcomp in -lc... yes checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for working REG_STARTEND... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/config.h ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ using C++17 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpH9OSmJ/R.INSTALL3d985f28a139ec/seqminer/src' have SQLite have bzip2 g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BCFReader.cpp -o BCFReader.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BGenFile.cpp -o BGenFile.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BGenIndex.cpp -o BGenIndex.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BGenVariant.cpp -o BGenVariant.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Exception.cpp -o Exception.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c FileIO.cpp -o FileIO.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c GeneLoader.cpp -o GeneLoader.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MmapFile.cpp -o MmapFile.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PatternMatch.cpp -o PatternMatch.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PeopleSet.cpp -o PeopleSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PlinkInputFile.cpp -o PlinkInputFile.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PlinkOutputFile.cpp -o PlinkOutputFile.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Profiler.cpp -o Profiler.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c R_CPP_interface.cpp -o R_CPP_interface.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RangeList.cpp -o RangeList.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Rannotation.cpp -o Rannotation.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SimpleMatrix.cpp -o SimpleMatrix.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SingleChromosomeBCFIndex.cpp -o SingleChromosomeBCFIndex.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SingleChromosomeVCFIndex.cpp -o SingleChromosomeVCFIndex.o SingleChromosomeVCFIndex.cpp: In member function ‘int SingleChromosomeVCFIndex::createIndex()’: SingleChromosomeVCFIndex.cpp:69:15: warning: unused variable ‘fn’ [-Wunused-variable] 69 | const char* fn = vcfFile_.c_str(); | ^~ SingleChromosomeVCFIndex.cpp: In member function ‘int SingleChromosomeVCFIndex::mapIndex()’: SingleChromosomeVCFIndex.cpp:201:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 201 | if (Nrecord != d[1]) { | ~~~~~~~~^~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TypeConversion.cpp -o TypeConversion.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Utils.cpp -o Utils.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFHeader.cpp -o VCFHeader.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFIndividual.cpp -o VCFIndividual.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFInfo.cpp -o VCFInfo.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFInputFile.cpp -o VCFInputFile.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFUtil.cpp -o VCFUtil.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bcf.c -o bcf.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bcf_index.c -o bcf_index.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bcfutils.c -o bcfutils.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bedidx.c -o bedidx.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bgen2genoLoader.cpp -o bgen2genoLoader.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bgzf.c -o bgzf.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c knetfile.c -o knetfile.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c kstring.c -o kstring.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c plink2genoLoader.cpp -o plink2genoLoader.o plink2genoLoader.cpp: In function ‘int readBedToMatrixByIndex(const std::string&, int, int, const std::vector&, const std::vector&, SEXP)’: plink2genoLoader.cpp:126:3: warning: ‘snpMajorMode’ may be used uninitialized [-Wmaybe-uninitialized] 126 | if (snpMajorMode) { | ^~ plink2genoLoader.cpp:78:8: note: ‘snpMajorMode’ was declared here 78 | bool snpMajorMode; | ^~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rvMetaLoader.cpp -o rvMetaLoader.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scbcf2genoLoader.cpp -o scbcf2genoLoader.o scbcf2genoLoader.cpp: In function ‘int parseBCFVariant(const BCFHeader&, uint32_t, uint32_t, std::vector, std::vector*, std::vector >*)’: scbcf2genoLoader.cpp:287:10: warning: unused variable ‘format_type’ [-Wunused-variable] 287 | int8_t format_type = *pIndv; | ^~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scvcf2genoLoader.cpp -o scvcf2genoLoader.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seqForStat.c -o seqForStat.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seqminer.c -o seqminer.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seqminer_init.c -o seqminer_init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tabixLoader.cpp -o tabixLoader.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tabix_index.c -o tabix_index.o tabix_index.c:19:14: warning: ‘currentTime’ defined but not used [-Wunused-function] 19 | static char* currentTime(void) { | ^~~~~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcf.c -o vcf.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c vcf2genoLoader.cpp -o vcf2genoLoader.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o seqminer.so BCFReader.o BGenFile.o BGenIndex.o BGenVariant.o Exception.o FileIO.o GeneLoader.o MmapFile.o PatternMatch.o PeopleSet.o PlinkInputFile.o PlinkOutputFile.o Profiler.o R_CPP_interface.o RangeList.o Rannotation.o SimpleMatrix.o SingleChromosomeBCFIndex.o SingleChromosomeVCFIndex.o TypeConversion.o Utils.o VCFHeader.o VCFIndividual.o VCFInfo.o VCFInputFile.o VCFUtil.o bcf.o bcf_index.o bcfutils.o bedidx.o bgen2genoLoader.o bgzf.o knetfile.o kstring.o plink2genoLoader.o rvMetaLoader.o scbcf2genoLoader.o scvcf2genoLoader.o seqForStat.o seqminer.o seqminer_init.o tabixLoader.o tabix_index.o vcf.o vcf2genoLoader.o -lz -lm -lbz2 -lzstd -lsqlite3 -lzstd -lsqlite3 -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpH9OSmJ/R.INSTALL3d985f28a139ec/seqminer/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-seqminer/00new/seqminer/libs ** R ** 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 (seqminer) * installing *source* package ‘DepthProc’ ... ** this is package ‘DepthProc’ version ‘2.1.5’ ** package ‘DepthProc’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzJmOzc/R.INSTALL3d985e52f62035/DepthProc/src' g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Depth.cpp -o Depth.o Depth.cpp: In function ‘arma::vec Depth::LPDepth(const arma::mat&, const arma::mat&, const double&, const double&, const double&, int)’: Depth.cpp:22:14: warning: unused variable ‘i’ [-Wunused-variable] 22 | size_t k,i; | ^ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c LocationEstimators.cpp -o LocationEstimators.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c LocationScaleDepth.cpp -o LocationScaleDepth.o LocationScaleDepth.cpp: In function ‘arma::vec LSD::sampleMaxLocScaleDepth(arma::vec, size_t, double, double)’: LocationScaleDepth.cpp:128:12: warning: variable ‘difb’ set but not used [-Wunused-but-set-variable] 128 | double difb = res[3]; //difbound; | ^~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RobCovLib.cpp -o RobCovLib.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c TukeyDepth.cpp -o TukeyDepth.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Utils.cpp -o Utils.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c UtilsCPP.cpp -o UtilsCPP.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c covFunCPP.cpp -o covFunCPP.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c depthFunCPP.cpp -o depthFunCPP.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c depthcpp.cpp -o depthcpp.o g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o DepthProc.so Depth.o LocationEstimators.o LocationScaleDepth.o LocationScaleDepthCPP.o RcppExports.o RobCovLib.o TukeyDepth.o Utils.o UtilsCPP.o covFunCPP.o depthFunCPP.o depthcpp.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -I"/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include" -fopenmp -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzJmOzc/R.INSTALL3d985e52f62035/DepthProc/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘as.matrix’ in package ‘DepthProc’ Creating a generic function for ‘abline’ from package ‘graphics’ in package ‘DepthProc’ ** help *** installing help indices *** copying figures ** 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 (DepthProc) checking Rdsdp_1.0.6.tar.gz ... checking GhostKnockoff_0.1.0.tar.gz ... checking knockoff_0.3.6.tar.gz ... checking OptimaRegion_1.2.tar.gz ... Depends: Package: Rdsdp Imports: utils, methods Timings: user system elapsed Rdsdp 30.372 4.944 37.558 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 1 2 Check results summary: Rdsdp ... OK rdepends_GhostKnockoff ... OK rdepends_knockoff ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_OptimaRegion ... OK Check results changes: Package: GhostKnockoff Check: CRAN incoming feasibility Old result: NOTE Package: OptimaRegion Check: CRAN incoming feasibility Old result: NOTE