downloading reverse dependencies ... downloading adepro_4.2.7.tar.gz ... ok downloading airship_1.4.3.tar.gz ... ok downloading dextergui_1.0.0.tar.gz ... ok downloading FastRWeb_1.2-1.tar.gz ... ok downloading forsearch_6.4.0.tar.gz ... ok downloading ggrastr_1.0.2.tar.gz ... ok downloading iSTATS_1.7.tar.gz ... ok downloading memery_0.6.0.tar.gz ... ok downloading MetaComp_1.1.2.tar.gz ... ok downloading mmaqshiny_1.0.0.tar.gz ... ok downloading rcssci_0.4.0.tar.gz ... ok downloading SGP_2.2-0.0.tar.gz ... ok downloading ultrapolaRplot_0.1.1.tar.gz ... ok downloading valhallr_0.1.0.tar.gz ... ok downloading visStatistics_0.1.7.tar.gz ... ok downloading visvow_1.3.11.tar.gz ... ok downloading aroma.core_3.3.2.tar.gz ... ok downloading BoutrosLab.plotting.general_7.1.2.tar.gz ... ok downloading corclass_0.2.1.tar.gz ... ok downloading cowplot_1.2.0.tar.gz ... ok downloading dexter_1.6.2.tar.gz ... ok downloading dplR_1.7.8.tar.gz ... ok downloading gaawr2_0.0.3.tar.gz ... ok downloading ggmcmc_1.5.1.1.tar.gz ... ok downloading hamlet_0.9.6.tar.gz ... ok downloading hetu_1.1.0.tar.gz ... ok downloading htmltools_0.5.8.1.tar.gz ... ok downloading imager_1.0.5.tar.gz ... ok downloading metaviz_0.3.1.tar.gz ... ok downloading patternplot_1.0.0.tar.gz ... ok downloading plotdap_1.1.0.tar.gz ... ok downloading plotly_4.11.0.tar.gz ... ok downloading QurvE_1.1.1.tar.gz ... ok downloading R.devices_2.17.2.tar.gz ... ok downloading repr_1.1.7.tar.gz ... ok downloading shiny_1.11.1.tar.gz ... ok downloading sorvi_0.8.21.tar.gz ... ok downloading StanMoMo_1.2.0.tar.gz ... ok downloading stars_0.6-8.tar.gz ... ok downloading TAD_1.0.0.tar.gz ... ok downloading thematic_0.1.7.tar.gz ... ok downloading viscomplexr_1.1.2.tar.gz ... ok downloading WeightedCluster_1.8-1.tar.gz ... ok installing dependencies ‘aroma.light’, ‘BLR’, ‘Cairo’, ‘cmocean’, ‘cubble’, ‘cubelyr’, ‘dexter’, ‘DirichletReg’, ‘EnsDb.Hsapiens.v75’, ‘ensembldb’, ‘equate’, ‘expectile’, ‘GLAD’, ‘GMMAT’, ‘HaarSeg’, ‘HardyWeinberg’, ‘mblm’, ‘mpcbs’, ‘nbpMatching’, ‘ncdfgeom’, ‘nullabor’, ‘OpenStreetMap’, ‘PASWR’, ‘PCICt’, ‘plotlyGeoAssets’, ‘powerEQTL’, ‘PSCBS’, ‘R.filesets’, ‘randomNames’, ‘reactlog’, ‘regress’, ‘rerddap’, ‘Rserve’, ‘seqminer’, ‘sfit’, ‘SGPdata’, ‘shinysurveys’, ‘SNPassoc’, ‘starsdata’, ‘toOrdinal’, ‘vegclust’, ‘watcher’ Warning: packages ‘sfit’, ‘expectile’, ‘HaarSeg’, ‘mpcbs’, ‘shinysurveys’, ‘PCICt’, ‘starsdata’ are not available for this version of R Versions of these packages for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages also installing the dependencies ‘awsMethods’, ‘aws’, ‘AnnotationFilter’, ‘ProtGenerics’, ‘poisbinom’, ‘areal’ begin installing package ‘AnnotationFilter’ begin installing package ‘awsMethods’ begin installing package ‘ProtGenerics’ begin installing package ‘poisbinom’ begin installing package ‘areal’ begin installing package ‘dexter’ begin installing package ‘Rserve’ begin installing package ‘equate’ begin installing package ‘toOrdinal’ begin installing package ‘SGPdata’ begin installing package ‘R.filesets’ begin installing package ‘aroma.light’ begin installing package ‘PASWR’ begin installing package ‘BLR’ begin installing package ‘GMMAT’ begin installing package ‘HardyWeinberg’ begin installing package ‘powerEQTL’ begin installing package ‘regress’ begin installing package ‘seqminer’ begin installing package ‘nbpMatching’ begin installing package ‘nullabor’ begin installing package ‘cmocean’ begin installing package ‘rerddap’ begin installing package ‘plotlyGeoAssets’ begin installing package ‘reactlog’ begin installing package ‘watcher’ begin installing package ‘OpenStreetMap’ begin installing package ‘cubble’ * installing *source* package ‘plotlyGeoAssets’ ... ** this is package ‘plotlyGeoAssets’ version ‘0.0.2’ ** package ‘plotlyGeoAssets’ 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 ** 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 (plotlyGeoAssets) begin installing package ‘cubelyr’ * installing *source* package ‘cmocean’ ... ** this is package ‘cmocean’ version ‘0.3-2’ ** package ‘cmocean’ 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 (cmocean) begin installing package ‘mblm’ * installing *source* package ‘reactlog’ ... ** this is package ‘reactlog’ version ‘1.1.1’ ** package ‘reactlog’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (reactlog) begin installing package ‘vegclust’ * installing *source* package ‘awsMethods’ ... ** this is package ‘awsMethods’ version ‘1.1-1’ ** package ‘awsMethods’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpuJpDgc/R.INSTALL9dea36f125667/awsMethods/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c omp_funcs.c -o omp_funcs.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o awsMethods.so init.o omp_funcs.o -fopenmp -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpuJpDgc/R.INSTALL9dea36f125667/awsMethods/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-awsMethods/00new/awsMethods/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 (awsMethods) begin installing package ‘DirichletReg’ * installing *source* package ‘BLR’ ... ** this is package ‘BLR’ version ‘1.6’ ** package ‘BLR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpNC8jSV/R.INSTALL9dece855416f/BLR/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sample_betas.c -o sample_betas.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o BLR.so init.o sample_betas.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpNC8jSV/R.INSTALL9dece855416f/BLR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BLR/00new/BLR/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 (BLR) begin installing package ‘Cairo’ * installing *source* package ‘powerEQTL’ ... ** this is package ‘powerEQTL’ version ‘0.3.6’ ** package ‘powerEQTL’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (powerEQTL) begin installing package ‘aws’ * installing *source* package ‘toOrdinal’ ... ** this is package ‘toOrdinal’ version ‘1.3-0.0’ ** package ‘toOrdinal’ 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 (toOrdinal) begin installing package ‘randomNames’ * installing *source* package ‘regress’ ... ** this is package ‘regress’ version ‘1.3-22’ ** package ‘regress’ 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 ** 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 (regress) * installing *source* package ‘ProtGenerics’ ... ** this is package ‘ProtGenerics’ version ‘1.40.0’ ** using staged installation ** R ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘smooth’ in package ‘ProtGenerics’ ** 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 (ProtGenerics) * installing *source* package ‘mblm’ ... ** this is package ‘mblm’ version ‘0.12.1’ ** package ‘mblm’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mblm) * installing *source* package ‘equate’ ... ** this is package ‘equate’ version ‘2.0.8’ ** package ‘equate’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (equate) * installing *source* package ‘aroma.light’ ... ** this is package ‘aroma.light’ version ‘3.38.0’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (aroma.light) begin installing package ‘PSCBS’ * installing *source* package ‘cubelyr’ ... ** this is package ‘cubelyr’ version ‘1.0.2’ ** package ‘cubelyr’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cubelyr) * installing *source* package ‘PASWR’ ... ** this is package ‘PASWR’ version ‘1.3’ ** package ‘PASWR’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PASWR) * installing *source* package ‘R.filesets’ ... ** this is package ‘R.filesets’ version ‘2.15.1’ ** package ‘R.filesets’ 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 ** 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 (R.filesets) * installing *source* package ‘randomNames’ ... ** this is package ‘randomNames’ version ‘1.6-0.0’ ** package ‘randomNames’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (randomNames) * installing *source* package ‘areal’ ... ** this is package ‘areal’ version ‘0.1.8’ ** package ‘areal’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (areal) begin installing package ‘ncdfgeom’ * installing *source* package ‘rerddap’ ... ** this is package ‘rerddap’ version ‘1.2.1’ ** package ‘rerddap’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rerddap) * installing *source* package ‘DirichletReg’ ... ** this is package ‘DirichletReg’ version ‘0.7-2’ ** package ‘DirichletReg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmptyUieH/R.INSTALL9ea241dd90d9b/DirichletReg/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ddirichlet.c -o ddirichlet.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rdirichlet.c -o rdirichlet.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wght_LL.c -o wght_LL.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wght_LL_grad_alternative.c -o wght_LL_grad_alternative.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wght_LL_grad_common.c -o wght_LL_grad_common.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o DirichletReg.so ddirichlet.o init.o rdirichlet.o wght_LL.o wght_LL_grad_alternative.o wght_LL_grad_common.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmptyUieH/R.INSTALL9ea241dd90d9b/DirichletReg/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-DirichletReg/00new/DirichletReg/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DirichletReg) * installing *source* package ‘nbpMatching’ ... ** this is package ‘nbpMatching’ version ‘1.5.6’ ** package ‘nbpMatching’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmph3cGCv/R.INSTALL9def2521f1d17/nbpMatching/src' gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c fcorematch.f -o fcorematch.o fcorematch.f:275:5: 275 | 500 CONTINUE | 1 Warning: Label 500 at (1) defined but not used [-Wunused-label] fcorematch.f:638:5: 638 | 400 CONTINUE | 1 Warning: Label 400 at (1) defined but not used [-Wunused-label] fcorematch.f:415:56: 415 | DOUBLE PRECISION DPLUS(N),DMINUS(N),Y1(N),Y2(N),C0,D,DBEST,YB, | 1 Warning: Unused variable ‘c0’ declared at (1) [-Wunused-variable] fcorematch.f:415:64: 415 | DOUBLE PRECISION DPLUS(N),DMINUS(N),Y1(N),Y2(N),C0,D,DBEST,YB, | 1 Warning: Unused variable ‘dbest’ declared at (1) [-Wunused-variable] fcorematch.f:410:48: 410 | 1 BASIS,KA,KB,DPLUS,DMINUS,Y1,Y2) | 1 Warning: Unused dummy argument ‘dminus’ at (1) [-Wunused-dummy-argument] fcorematch.f:633:55: 633 | DOUBLE PRECISION Y1(N),Y2(N),DMINUS(N),DPLUS(N),D,DBEST,Y1B,Y2B, | 1 Warning: Unused variable ‘d’ declared at (1) [-Wunused-variable] fcorematch.f:627:48: 627 | F Y1,Y2,DPLUS,DMINUS,SUP,EPS,NBL,INDEX,NBEST,DBEST, | 1 Warning: Unused dummy argument ‘eps’ at (1) [-Wunused-dummy-argument] fcorematch.f:633:69: 633 | DOUBLE PRECISION Y1(N),Y2(N),DMINUS(N),DPLUS(N),D,DBEST,Y1B,Y2B, | 1 Warning: Unused variable ‘y2b’ declared at (1) [-Wunused-variable] fcorematch.f:629:48: 629 | INTEGER BASIS(N),MEM(N),KA(N),KB(N),ZFW | 1 Warning: Unused variable ‘zfw’ declared at (1) [-Wunused-variable] fcorematch.f:528:54: 528 | SUBROUTINE SCAN1(NB1,N,SUP,CC,BASIS,MEM,KA,KB,SM,TMA,TMB, | 1 Warning: Unused dummy argument ‘sm’ at (1) [-Wunused-dummy-argument] fcorematch.f:528:62: 528 | SUBROUTINE SCAN1(NB1,N,SUP,CC,BASIS,MEM,KA,KB,SM,TMA,TMB, | 1 Warning: Unused dummy argument ‘tmb’ at (1) [-Wunused-dummy-argument] fcorematch.f:211:56: 211 | DOUBLE PRECISION Y1(N),Y2(N),DMINUS(N),DPLUS(N),C0,D,DBEST,Y1B, | 1 Warning: Unused variable ‘c0’ declared at (1) [-Wunused-variable] fcorematch.f:204:39: 204 | SUBROUTINE AUGMNT(N,TOP,NMATCH,CC,BASIS,MEM,KA,KB,SM,TMA,TMB, | 1 Warning: Unused dummy argument ‘cc’ at (1) [-Wunused-dummy-argument] fcorematch.f:205:48: 205 | F Y1,Y2,DPLUS,DMINUS,SUP,EPS,NBL,INDEX,DBEST,N1,N2, | 1 Warning: Unused dummy argument ‘eps’ at (1) [-Wunused-dummy-argument] fcorematch.f:205:58: 205 | F Y1,Y2,DPLUS,DMINUS,SUP,EPS,NBL,INDEX,DBEST,N1,N2, | 1 Warning: Unused dummy argument ‘index’ at (1) [-Wunused-dummy-argument] fcorematch.f:204:52: 204 | SUBROUTINE AUGMNT(N,TOP,NMATCH,CC,BASIS,MEM,KA,KB,SM,TMA,TMB, | 1 Warning: Unused dummy argument ‘ka’ at (1) [-Wunused-dummy-argument] fcorematch.f:204:55: 204 | SUBROUTINE AUGMNT(N,TOP,NMATCH,CC,BASIS,MEM,KA,KB,SM,TMA,TMB, | 1 Warning: Unused dummy argument ‘kb’ at (1) [-Wunused-dummy-argument] fcorematch.f:204:49: 204 | SUBROUTINE AUGMNT(N,TOP,NMATCH,CC,BASIS,MEM,KA,KB,SM,TMA,TMB, | 1 Warning: Unused dummy argument ‘mem’ at (1) [-Wunused-dummy-argument] fcorematch.f:205:52: 205 | F Y1,Y2,DPLUS,DMINUS,SUP,EPS,NBL,INDEX,DBEST,N1,N2, | 1 Warning: Unused dummy argument ‘nbl’ at (1) [-Wunused-dummy-argument] fcorematch.f:211:68: 211 | DOUBLE PRECISION Y1(N),Y2(N),DMINUS(N),DPLUS(N),C0,D,DBEST,Y1B, | 1 Warning: Unused variable ‘y1b’ declared at (1) [-Wunused-variable] fcorematch.f:205:27: 205 | F Y1,Y2,DPLUS,DMINUS,SUP,EPS,NBL,INDEX,DBEST,N1,N2, | 1 Warning: Unused dummy argument ‘y2’ at (1) [-Wunused-dummy-argument] fcorematch.f:212:26: 212 | * Y2B,YB | 1 Warning: Unused variable ‘y2b’ declared at (1) [-Wunused-variable] fcorematch.f:212:29: 212 | * Y2B,YB | 1 Warning: Unused variable ‘yb’ declared at (1) [-Wunused-variable] fcorematch.f:207:48: 207 | INTEGER BASIS(N),MEM(N),KA(N),KB(N),ZFW | 1 Warning: Unused variable ‘zfw’ declared at (1) [-Wunused-variable] fcorematch.f:389:45: 389 | F Y2,DPLUS,DMINUS,SUP,EPS,NBL,INDEX,NBEST,DBEST) | 1 Warning: Unused dummy argument ‘eps’ at (1) [-Wunused-dummy-argument] fcorematch.f:388:28: 388 | SUBROUTINE GROW (N,TOP,NMATCH,CC,BASIS,MEM,KA,KB,SM,TMA,TMB,Y1, | 1 Warning: Unused dummy argument ‘top’ at (1) [-Wunused-dummy-argument] fcorematch.f:391:48: 391 | INTEGER BASIS(N),MEM(N),KA(N),KB(N),ZFW | 1 Warning: Unused variable ‘zfw’ declared at (1) [-Wunused-variable] fcorematch.f:270:56: 270 | DOUBLE PRECISION Y1(N),Y2(N),DMINUS(N),DPLUS(N),C0,D,DBEST,Y1B, | 1 Warning: Unused variable ‘c0’ declared at (1) [-Wunused-variable] fcorematch.f:270:58: 270 | DOUBLE PRECISION Y1(N),Y2(N),DMINUS(N),DPLUS(N),C0,D,DBEST,Y1B, | 1 Warning: Unused variable ‘d’ declared at (1) [-Wunused-variable] fcorematch.f:265:47: 265 | F Y2,DPLUS,DMINUS,SUP,EPS,NBL,INDEX,NBEST,DBEST) | 1 Warning: Unused dummy argument ‘eps’ at (1) [-Wunused-dummy-argument] fcorematch.f:264:27: 264 | SUBROUTINE EXPAND(N,M,TOP,NMATCH,CC,BASIS,MEM,KA,KB,SM,TMA,TMB,Y1, | 1 Warning: Unused dummy argument ‘m’ at (1) [-Wunused-dummy-argument] fcorematch.f:271:26: 271 | * Y2B,YB | 1 Warning: Unused variable ‘y2b’ declared at (1) [-Wunused-variable] fcorematch.f:271:29: 271 | * Y2B,YB | 1 Warning: Unused variable ‘yb’ declared at (1) [-Wunused-variable] fcorematch.f:266:48: 266 | INTEGER BASIS(N),MEM(N),KA(N),KB(N),ZFW | 1 Warning: Unused variable ‘zfw’ declared at (1) [-Wunused-variable] fcorematch.f:580:57: 580 | SUBROUTINE SCAN2(NB,N,SUP,CC,BASIS,MEM,KA,KB,SM,TMA,TMB, | 1 Warning: Unused dummy argument ‘tma’ at (1) [-Wunused-dummy-argument] fcorematch.f:69:29: 69 | * Y2B,YB | 1 Warning: Unused variable ‘yb’ declared at (1) [-Wunused-variable] gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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 mwrap.f -o mwrap.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o nbpMatching.so fcorematch.o init.o mwrap.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmph3cGCv/R.INSTALL9def2521f1d17/nbpMatching/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-nbpMatching/00new/nbpMatching/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 (nbpMatching) * installing *source* package ‘poisbinom’ ... ** this is package ‘poisbinom’ version ‘1.0.2’ ** package ‘poisbinom’ successfully unpacked and MD5 sums checked ** using staged installation ** 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’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzhFy3l/R.INSTALL9de93359e3cc3/poisbinom/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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 gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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 -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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 poisbinom.cpp -o poisbinom.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o poisbinom.so RcppExports.o init.o poisbinom.o -lfftw3 -lm -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzhFy3l/R.INSTALL9de93359e3cc3/poisbinom/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-poisbinom/00new/poisbinom/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 (poisbinom) begin installing package ‘SNPassoc’ * installing *source* package ‘cubble’ ... ** this is package ‘cubble’ version ‘1.0.0’ ** package ‘cubble’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cubble) * installing *source* package ‘Cairo’ ... ** this is package ‘Cairo’ version ‘1.6-4’ ** using staged installation 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 for sys/wait.h that is POSIX.1 compatible... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... yes checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender checking whether --static is needed... no configure: CAIRO_CFLAGS=-I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 checking if R was compiled with the RConn patch... no checking for cairo.h... yes checking for PNG support in Cairo... yes checking for ATS font support in Cairo... no configure: CAIRO_LIBS=-lfreetype -lpng16 -lz -lXext -lcairo -lXrender -lX11 checking for library containing deflate... none required checking whether Cairo programs can be compiled... yes checking for gcc-14 -std=gnu23 options needed to detect all undeclared functions... none needed checking whether cairo_image_surface_get_format is declared... no checking whether FreeType support is desired... auto checking for FreeType support in cairo... yes checking whether FreeType needs additional flags... no checking whether pkg-config knows about Xt... no checking whether libjpeg works... yes checking whether Harfbuzz layout is desired... auto checking whether Harfbuzz + ICU works... yes checking whether libtiff works... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/cconfig.h ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQ1dbMC/R.INSTALL9ecfc2e6fd804/Cairo/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I. -Iinclude -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cairobem.c -o cairobem.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I. -Iinclude -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cairogd.c -o cairogd.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I. -Iinclude -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cairotalk.c -o cairotalk.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I. -Iinclude -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c img-backend.c -o img-backend.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I. -Iinclude -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c img-jpeg.c -o img-jpeg.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I. -Iinclude -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c img-tiff.c -o img-tiff.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I. -Iinclude -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pdf-backend.c -o pdf-backend.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I. -Iinclude -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ps-backend.c -o ps-backend.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I. -Iinclude -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c svg-backend.c -o svg-backend.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I. -Iinclude -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c w32-backend.c -o w32-backend.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I. -Iinclude -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c xlib-backend.c -o xlib-backend.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o Cairo.so cairobem.o cairogd.o cairotalk.o img-backend.o img-jpeg.o img-tiff.o pdf-backend.o ps-backend.o svg-backend.o w32-backend.o xlib-backend.o -Wl,-O1 -lfreetype -lpng16 -lz -lXext -lcairo -lXrender -lX11 -ljpeg -lharfbuzz-icu -lharfbuzz -licuuc -licudata -lstdc++ -ltiff -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpQ1dbMC/R.INSTALL9ecfc2e6fd804/Cairo/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Cairo/00new/Cairo/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 (Cairo) * installing *source* package ‘nullabor’ ... ** this is package ‘nullabor’ version ‘0.3.15’ ** package ‘nullabor’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** demo ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (nullabor) * installing *source* package ‘vegclust’ ... ** this is package ‘vegclust’ version ‘2.0.3’ ** package ‘vegclust’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (vegclust) * installing *source* package ‘AnnotationFilter’ ... ** this is package ‘AnnotationFilter’ version ‘1.32.0’ ** 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 (AnnotationFilter) begin installing package ‘ensembldb’ * installing *source* package ‘ncdfgeom’ ... ** this is package ‘ncdfgeom’ version ‘1.1.6’ ** package ‘ncdfgeom’ 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 (ncdfgeom) * installing *source* package ‘PSCBS’ ... ** this is package ‘PSCBS’ version ‘0.68.0’ ** package ‘PSCBS’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PSCBS) * installing *source* package ‘aws’ ... ** this is package ‘aws’ version ‘2.5-6’ ** package ‘aws’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLXl0cI/R.INSTALL9ed221497c825/aws/src' gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ICIsmooth.f -o ICIsmooth.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rentries.c -o Rentries.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c awslp.f -o awslp.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c awswghts.f -o awswghts.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c caws.f -o caws.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cawsmask.f -o cawsmask.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c esiglike.f -o esiglike.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c estimateComplexSigma.f -o estimateComplexSigma.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c misc.f -o misc.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c nlmeans.f -o nlmeans.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c pcaws.f -o pcaws.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c segment.f -o segment.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c smooth3d.f -o smooth3d.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c smse3.f -o smse3.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c varest.f -o varest.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o aws.so ICIsmooth.o Rentries.o awslp.o awswghts.o caws.o cawsmask.o esiglike.o estimateComplexSigma.o init.o misc.o nlmeans.o pcaws.o segment.o smooth3d.o smse3.o varest.o -fopenmp -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLXl0cI/R.INSTALL9ed221497c825/aws/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-aws/00new/aws/libs ** R ** demo ** 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 (aws) begin installing package ‘GLAD’ * installing *source* package ‘SNPassoc’ ... ** this is package ‘SNPassoc’ version ‘2.1-2’ ** package ‘SNPassoc’ 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 ** 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 (SNPassoc) * installing *source* package ‘OpenStreetMap’ ... ** this is package ‘OpenStreetMap’ version ‘0.4.0’ ** package ‘OpenStreetMap’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘raster’ with signature ‘"osmtile"’: no definition for class “osmtile” in method for ‘raster’ with signature ‘"OpenStreetMap"’: no definition for class “OpenStreetMap” ** 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 (OpenStreetMap) * installing *source* package ‘Rserve’ ... ** this is package ‘Rserve’ version ‘1.8-15’ ** package ‘Rserve’ successfully unpacked and MD5 sums checked ** using staged installation checking whether to compile the server... yes checking whether to compile the client... no 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 for sys/wait.h that is POSIX.1 compatible... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for vfork.h... no checking for limits.h... yes checking for string.h... (cached) yes checking for memory.h... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for sys/socket.h... yes checking for sys/un.h... yes checking for netinet/in.h... yes checking for netinet/tcp.h... yes checking for an ANSI C-conforming const... yes checking whether byte ordering is bigendian... no checking size of size_t... 8 checking for pid_t... yes checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking return type of signal handlers... void checking for memset... yes checking for mkdir... yes checking for rmdir... yes checking for select... yes checking for socket... yes checking for srandomdev... no checking for library containing crypt... -lcrypt checking for crypt.h... yes checking for socklen_t... yes checking for connect... yes checking whether to enable IPv6... no checking for dlopen in -ldl... yes checking for openssl/rsa.h... yes checking for library containing RSA_generate_key... -lcrypto checking for openssl/ssl.h... yes checking for library containing SSL_CTX_load_verify_locations... -lssl checking whether threads are desired... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for working threads support... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/client/cxx/Makefile config.status: creating src/config.h ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpycoQHe/R.INSTALL9debf4a3e3313/Rserve/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RSserver.c -o RSserver.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rserv.c -o Rserv.o Rserv.c: In function ‘auth_user’: Rserv.c:2447:21: warning: variable ‘ctrl_flag’ set but not used [-Wunused-but-set-variable] 2447 | int ctrl_flag = 0, u_uid = 0, u_gid = 0; | ^~~~~~~~~ Rserv.c: In function ‘Rserve_fork_compute’: Rserv.c:3312:25: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3312 | int rn, cmd; | ^~~ Rserv.c: In function ‘OCAP_iteration’: Rserv.c:3468:29: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3468 | int cmd; | ^~~ Rserv.c: In function ‘Rserve_QAP1_connected’: Rserv.c:3915:9: warning: variable ‘unaligned’ set but not used [-Wunused-but-set-variable] 3915 | int unaligned=0; | ^~~~~~~~~ Rserv.c: In function ‘handle_server_event’: Rserv.c:5030:13: warning: unused variable ‘succ’ [-Wunused-variable] 5030 | int succ = 0; | ^~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c base64.c -o base64.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c date.c -o date.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c http.c -o http.o In file included from http.c:10: bsdcmpt.h:17:20: warning: ‘strnstr’ defined but not used [-Wunused-function] 17 | static const char *strnstr(const char *haystack, const char *needle, size_t len) { | ^~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ioc.c -o ioc.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c md5.c -o md5.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c oc.c -o oc.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c qap_decode.c -o qap_decode.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c qap_encode.c -o qap_encode.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c session.c -o session.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sha1.c -o sha1.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c standalone.c -o standalone.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tls.c -o tls.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ulog.c -o ulog.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utils.c -o utils.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c websockets.c -o websockets.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c winembed.c -o winembed.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o Rserve.so RSserver.o Rserv.o base64.o date.o http.o ioc.o md5.o oc.o qap_decode.o qap_encode.o session.o sha1.o standalone.o tls.o ulog.o utils.o websockets.o winembed.o -lssl -lcrypto -ldl -lcrypt -L/home/hornik/tmp/R/lib -lR gcc-14 -std=gnu23 -DSTANDALONE_RSERVE -DDAEMON -I. -Iinclude -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I/usr/local/include -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/home/hornik/tmp/R/include -o Rserve standalone.c md5.c session.c qap_decode.c qap_encode.c sha1.c base64.c websockets.c RSserver.c tls.c http.c oc.c ulog.c ioc.c utils.c date.c -Wl,-O1 -lssl -lcrypto -ldl -lcrypt -L"/home/hornik/tmp/R/lib" -lR -lssl -lcrypto -ldl -lcrypt In file included from standalone.c:6: Rserv.c: In function ‘auth_user’: Rserv.c:2447:21: warning: variable ‘ctrl_flag’ set but not used [-Wunused-but-set-variable] 2447 | int ctrl_flag = 0, u_uid = 0, u_gid = 0; | ^~~~~~~~~ Rserv.c: In function ‘Rserve_fork_compute’: Rserv.c:3312:25: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3312 | int rn, cmd; | ^~~ Rserv.c: In function ‘OCAP_iteration’: Rserv.c:3468:29: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3468 | int cmd; | ^~~ Rserv.c: In function ‘Rserve_QAP1_connected’: Rserv.c:3915:9: warning: variable ‘unaligned’ set but not used [-Wunused-but-set-variable] 3915 | int unaligned=0; | ^~~~~~~~~ Rserv.c: In function ‘handle_server_event’: Rserv.c:5030:13: warning: unused variable ‘succ’ [-Wunused-variable] 5030 | int succ = 0; | ^~~~ In file included from http.c:10: bsdcmpt.h:17:20: warning: ‘strnstr’ defined but not used [-Wunused-function] 17 | static const char *strnstr(const char *haystack, const char *needle, size_t len) { | ^~~~~~~ gcc-14 -std=gnu23 -DSTANDALONE_RSERVE -DRSERV_DEBUG -DNODAEMON -I. -Iinclude -I"/home/hornik/tmp/R/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/home/hornik/tmp/R/include -o Rserve.dbg standalone.c md5.c session.c qap_decode.c qap_encode.c sha1.c base64.c websockets.c RSserver.c tls.c http.c oc.c ulog.c ioc.c utils.c date.c -Wl,-O1 -lssl -lcrypto -ldl -lcrypt -L"/home/hornik/tmp/R/lib" -lR -lssl -lcrypto -ldl -lcrypt In file included from standalone.c:6: Rserv.c: In function ‘auth_user’: Rserv.c:2447:21: warning: variable ‘ctrl_flag’ set but not used [-Wunused-but-set-variable] 2447 | int ctrl_flag = 0, u_uid = 0, u_gid = 0; | ^~~~~~~~~ Rserv.c: In function ‘Rserve_fork_compute’: Rserv.c:3312:25: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3312 | int rn, cmd; | ^~~ Rserv.c: In function ‘OCAP_iteration’: Rserv.c:3468:29: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3468 | int cmd; | ^~~ Rserv.c: In function ‘Rserve_QAP1_connected’: Rserv.c:3915:9: warning: variable ‘unaligned’ set but not used [-Wunused-but-set-variable] 3915 | int unaligned=0; | ^~~~~~~~~ Rserv.c: In function ‘handle_server_event’: Rserv.c:5030:13: warning: unused variable ‘succ’ [-Wunused-variable] 5030 | int succ = 0; | ^~~~ standalone.c: In function ‘main’: standalone.c:38:16: warning: variable ‘rs_silent’ set but not used [-Wunused-but-set-variable] 38 | int rs_silent = 0; | ^~~~~~~~~ In file included from http.c:10: bsdcmpt.h:17:20: warning: ‘strnstr’ defined but not used [-Wunused-function] 17 | static const char *strnstr(const char *haystack, const char *needle, size_t len) { | ^~~~~~~ ./mergefat Rserve "/home/hornik/tmp/R/bin/Rserve" ./mergefat Rserve.dbg "/home/hornik/tmp/R/bin/Rserve.dbg" make -C proxy 'CC=gcc-14 -std=gnu23' 'CPPFLAGS=-I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include ' CFLAGS='-g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native ' 'LDFLAGS=-Wl,-O1' 'LIBS=-lssl -lcrypto -ldl -lcrypt ' && cp -p proxy/forward . make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpycoQHe/R.INSTALL9debf4a3e3313/Rserve/src/proxy' ln -sfn ../ulog.h ulog.h gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o forward.o forward.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o http.o http.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o http_tools.o http_tools.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o server.o server.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o tls.o tls.c ln -sfn ../md5.h md5.h ln -sfn ../sha1.h sha1.h ln -sfn ../base64.c base64.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o websockets.o websockets.c websockets.c: In function ‘WS_connected’: websockets.c:343:47: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic] 343 | ws_connected_fn_t connected = (ws_connected_fn_t) arg->srv->aux; | ^ websockets.c: In function ‘WS13_upgrade’: websockets.c:378:34: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic] 378 | srv->aux = (void*) connected; | ^ websockets.c:411:47: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic] 411 | ws_connected_fn_t connected = (ws_connected_fn_t) srv->aux; | ^ websockets.c: In function ‘create_WS_server’: websockets.c:868:34: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic] 868 | srv->aux = (void*) connected; | ^ ln -sfn ../md5.c md5.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o md5.o md5.c ln -sfn ../sha1.c sha1.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o sha1.o sha1.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o base64.o base64.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o date.o date.c ln -sfn ../ulog.c ulog.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o ulog.o ulog.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o chandler.o chandler.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o rscript.o rscript.c gcc-14 -std=gnu23 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -Wl,-O1 -o forward forward.o http.o http_tools.o server.o tls.o websockets.o md5.o sha1.o base64.o date.o ulog.o chandler.o rscript.o -lssl -lcrypto -ldl -lcrypt make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpycoQHe/R.INSTALL9debf4a3e3313/Rserve/src/proxy' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpycoQHe/R.INSTALL9debf4a3e3313/Rserve/src' installing via 'install.libs.R' to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rserve/00new/Rserve ** 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 (Rserve) * installing *source* package ‘HardyWeinberg’ ... ** this is package ‘HardyWeinberg’ version ‘1.7.8’ ** package ‘HardyWeinberg’ 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/Rtmp0cuXua/R.INSTALL9deda4f0cac5c/HardyWeinberg/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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 HWxChromosomal.cpp -o HWxChromosomal.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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 -I"/home/hornik/tmp/R/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 SNPHWEX.cpp -o SNPHWEX.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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 support.cpp -o support.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o HardyWeinberg.so HWxChromosomal.o RcppExports.o SNPHWEX.o support.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0cuXua/R.INSTALL9deda4f0cac5c/HardyWeinberg/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-HardyWeinberg/00new/HardyWeinberg/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 (HardyWeinberg) * installing *source* package ‘watcher’ ... ** this is package ‘watcher’ version ‘0.1.4’ ** package ‘watcher’ successfully unpacked and MD5 sums checked ** using staged installation Compiling 'libfswatch' from source... Detecting 'cmake'... /usr/bin/cmake -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc-14 - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++-14 - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Gettext: /usr/bin/msgmerge (found version "0.23.1") -- Found Intl: built in to C library -- Looking for C++ include getopt.h -- Looking for C++ include getopt.h - found -- Looking for getopt_long -- Looking for getopt_long - found -- Performing Test HAVE_STRUCT_STAT_ST_MTIME -- Performing Test HAVE_STRUCT_STAT_ST_MTIME - Success -- Performing Test HAVE_STRUCT_STAT_ST_MTIMESPEC -- Performing Test HAVE_STRUCT_STAT_ST_MTIMESPEC - Failed -- Looking for C++ include sys/inotify.h -- Looking for C++ include sys/inotify.h - found -- Looking for C++ include sys/event.h -- Looking for C++ include sys/event.h - not found -- Looking for C++ include port.h -- Looking for C++ include port.h - not found -- Looking for FindFirstChangeNotification -- Looking for FindFirstChangeNotification - not found -- Configuring done (1.7s) -- Generating done (0.0s) -- Build files have been written to: /home/hornik/tmp/scratch/Rtmp66UVPH/R.INSTALL9defa1da5fa35/watcher/fswatch-5c443d2 gmake[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp66UVPH/R.INSTALL9defa1da5fa35/watcher/fswatch-5c443d2' [ 7%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c/cevent.cpp.o [ 15%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c/libfswatch.cpp.o [ 23%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c/libfswatch_log.cpp.o [ 30%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c++/event.cpp.o [ 38%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c++/filter.cpp.o [ 46%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c++/libfswatch_exception.cpp.o [ 53%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c++/monitor.cpp.o [ 61%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c++/monitor_factory.cpp.o [ 69%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c++/path_utils.cpp.o [ 76%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c++/poll_monitor.cpp.o [ 84%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c++/string/string_utils.cpp.o [ 92%] Building CXX object libfswatch/CMakeFiles/libfswatch.dir/src/libfswatch/c++/inotify_monitor.cpp.o [100%] Linking CXX static library libfswatch.b [100%] Built target libfswatch Install the project... -- Install configuration: "Release" gmake[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp66UVPH/R.INSTALL9defa1da5fa35/watcher/fswatch-5c443d2' ** 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’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp66UVPH/R.INSTALL9defa1da5fa35/watcher/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../install/include -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c link.cpp -o link.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../install/include -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c watcher.c -o watcher.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o watcher.so init.o link.o watcher.o ../install/lib/libfswatch.b -lpthread -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp66UVPH/R.INSTALL9defa1da5fa35/watcher/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-watcher/00new/watcher/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 (watcher) * installing *source* package ‘GLAD’ ... ** this is package ‘GLAD’ version ‘2.72.0’ ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... yes GSL has been found on the operating system operating system: Linux configure: creating ./config.status config.status: creating src/Makevars src/Makevars file PKG_LIBS = -lgsl -lgslcblas -lm PKG_CPPFLAGS = -I/usr/local/include ** 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’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpNUeYcT/R.INSTALL9f8474db376c2/GLAD/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BkpInfo.cpp -o BkpInfo.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HaarSeg.cpp -o HaarSeg.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MoveBkp.cpp -o MoveBkp.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c OutliersGNL.cpp -o OutliersGNL.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c chrBreakpoints.cpp -o chrBreakpoints.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cutree.cpp -o cutree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c daglad.cpp -o daglad.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c distance.cpp -o distance.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c filterBkp.cpp -o filterBkp.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c findCluster.cpp -o findCluster.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glad-utils.cpp -o glad-utils.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hclust.cpp -o hclust.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c laws.c -o laws.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c loopRemove.cpp -o loopRemove.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -lgsl -lgslcblas -lm -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpNUeYcT/R.INSTALL9f8474db376c2/GLAD/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-GLAD/00new/GLAD/libs ** R ** data ** demo ** 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 (GLAD) * installing *source* package ‘GMMAT’ ... ** this is package ‘GMMAT’ version ‘1.4.2’ ** package ‘GMMAT’ 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 g++-14 -std=gnu++17 accepts -g... yes checking how to run the C++ preprocessor... g++-14 -std=gnu++17 -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 ZSTD_decompress 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 libdeflate_zlib_decompress in -ldeflate... yes checking libdeflate.h usability... yes checking libdeflate.h presence... yes checking for libdeflate.h... yes configure: Will use system-wide libdeflate library configure: creating ./config.status config.status: creating src/Makevars ** 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’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpENRaWD/R.INSTALL9ded513077ee7/GMMAT/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -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 -DARMA_64BIT_WORD -fpic -g -O2 -Wall -pedantic -mtune=native -c fitglmm.cpp -o fitglmm.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -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 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o GMMAT.so fitglmm.o registerDynamicSymbol.o -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -lz -lbz2 -lzstd -ldeflate -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpENRaWD/R.INSTALL9ded513077ee7/GMMAT/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-GMMAT/00new/GMMAT/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 (GMMAT) * installing *source* package ‘ensembldb’ ... ** this is package ‘ensembldb’ version ‘2.32.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘.cds_for_id2’ in package ‘ensembldb’ ** 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 (ensembldb) begin installing package ‘EnsDb.Hsapiens.v75’ * installing *source* package ‘SGPdata’ ... ** this is package ‘SGPdata’ version ‘28.0-0.0’ ** package ‘SGPdata’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SGPdata) * 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/RtmpJ5pa2I/R.INSTALL9dee836f07b5c/seqminer/src' have SQLite have bzip2 g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpJ5pa2I/R.INSTALL9dee836f07b5c/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 ‘EnsDb.Hsapiens.v75’ ... ** this is package ‘EnsDb.Hsapiens.v75’ version ‘2.99.0’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (EnsDb.Hsapiens.v75) * installing *source* package ‘dexter’ ... ** this is package ‘dexter’ version ‘1.6.2’ ** package ‘dexter’ 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/Rtmp63YTi9/R.INSTALL9dec27d5c1b3f/dexter/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/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++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ability.cpp -o ability.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c binning.cpp -o binning.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c data.cpp -o data.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c elsym.cpp -o elsym.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c elsymBinom.cpp -o elsymBinom.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c enrm.cpp -o enrm.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c enrmBayes.cpp -o enrmBayes.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c priors.cpp -o priors.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c pv.cpp -o pv.o pv.cpp: In function ‘Rcpp::List pv_chain_normal(const arma::mat&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::mat&, const arma::vec&, int, arma::ivec, int, int, int)’: pv.cpp:173:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 173 | if(bcol >= bmat.n_cols) bcol = chain; | ~~~~~^~~~~~~~~~~~~~ pv.cpp: In function ‘Rcpp::List pv_chain_mix(const arma::mat&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::ivec&, const arma::mat&, const arma::mat&, const arma::vec&, int, arma::ivec, int, int, int)’: pv.cpp:346:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 346 | if(bcol >= bmat.n_cols) bcol = chain; | ~~~~~^~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c shared.cpp -o shared.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/dqrng/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/sitmo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c simulation.cpp -o simulation.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o dexter.so RcppExports.o ability.o binning.o data.o elsym.o elsymBinom.o enrm.o enrmBayes.o priors.o pv.o shared.o simulation.o -fopenmp -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp63YTi9/R.INSTALL9dec27d5c1b3f/dexter/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-dexter/00new/dexter/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dexter) checking Cairo_1.6-4.tar.gz ... checking adepro_4.2.7.tar.gz ... checking airship_1.4.3.tar.gz ... checking dextergui_1.0.0.tar.gz ... checking FastRWeb_1.2-1.tar.gz ... checking forsearch_6.4.0.tar.gz ... checking ggrastr_1.0.2.tar.gz ... checking iSTATS_1.7.tar.gz ... checking memery_0.6.0.tar.gz ... checking MetaComp_1.1.2.tar.gz ... checking mmaqshiny_1.0.0.tar.gz ... checking rcssci_0.4.0.tar.gz ... checking SGP_2.2-0.0.tar.gz ... checking ultrapolaRplot_0.1.1.tar.gz ... checking valhallr_0.1.0.tar.gz ... checking visStatistics_0.1.7.tar.gz ... checking visvow_1.3.11.tar.gz ... checking aroma.core_3.3.2.tar.gz ... checking BoutrosLab.plotting.general_7.1.2.tar.gz ... checking corclass_0.2.1.tar.gz ... checking cowplot_1.2.0.tar.gz ... checking dexter_1.6.2.tar.gz ... checking dplR_1.7.8.tar.gz ... checking gaawr2_0.0.3.tar.gz ... checking ggmcmc_1.5.1.1.tar.gz ... checking hamlet_0.9.6.tar.gz ... checking hetu_1.1.0.tar.gz ... checking htmltools_0.5.8.1.tar.gz ... checking StanMoMo_1.2.0.tar.gz ... checking viscomplexr_1.1.2.tar.gz ... checking plotly_4.11.0.tar.gz ... checking shiny_1.11.1.tar.gz ... checking imager_1.0.5.tar.gz ... checking sorvi_0.8.21.tar.gz ... checking WeightedCluster_1.8-1.tar.gz ... checking thematic_0.1.7.tar.gz ... checking repr_1.1.7.tar.gz ... checking QurvE_1.1.1.tar.gz ... checking patternplot_1.0.0.tar.gz ... checking metaviz_0.3.1.tar.gz ... checking stars_0.6-8.tar.gz ... checking plotdap_1.1.0.tar.gz ... checking R.devices_2.17.2.tar.gz ... checking TAD_1.0.0.tar.gz ... Depends: Package: Cairo Depends: R (>= 2.4.0) Imports: grDevices, graphics Timings: user system elapsed Cairo 30.095 4.733 37.682 Results: Check status summary: ERROR NOTE OK Source packages 0 0 1 Reverse depends 2 9 32 Check results summary: Cairo ... OK rdepends_adepro ... OK rdepends_airship ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_aroma.core ... OK rdepends_BoutrosLab.plotting.general ... OK rdepends_corclass ... OK rdepends_cowplot ... OK rdepends_dexter ... OK rdepends_dextergui ... OK rdepends_dplR ... OK rdepends_FastRWeb ... NOTE * checking R code for possible problems ... [4s/4s] NOTE * checking Rd cross-references ... NOTE * checking compiled code ... NOTE rdepends_forsearch ... OK rdepends_gaawr2 ... OK rdepends_ggmcmc ... OK rdepends_ggrastr ... OK rdepends_hamlet ... NOTE * checking dependencies in R code ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_hetu ... OK rdepends_htmltools ... NOTE * checking compiled code ... NOTE rdepends_imager ... OK rdepends_iSTATS ... OK rdepends_memery ... OK rdepends_MetaComp ... ERROR * checking examples ... [2s/2s] ERROR * checking tests ... [3s/3s] ERROR rdepends_metaviz ... OK rdepends_mmaqshiny ... OK rdepends_patternplot ... NOTE * checking C++ specification ... NOTE rdepends_plotdap ... OK rdepends_plotly ... OK rdepends_QurvE ... NOTE * checking Rd cross-references ... NOTE rdepends_R.devices ... OK rdepends_rcssci ... OK rdepends_repr ... OK rdepends_SGP ... OK rdepends_shiny ... OK rdepends_sorvi ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_StanMoMo ... OK rdepends_stars ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_TAD ... OK rdepends_thematic ... OK rdepends_ultrapolaRplot ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_valhallr ... OK rdepends_viscomplexr ... OK rdepends_visStatistics ... ERROR * checking examples ... [2s/2s] ERROR * checking re-building of vignette outputs ... [12s/13s] ERROR rdepends_visvow ... OK rdepends_WeightedCluster ... OK Check results changes: Package: aroma.core [Old version: 3.3.1, New version: 3.3.2] Check: Rd cross-references Old result: NOTE New result: OK Package: corclass Check: CRAN incoming feasibility Old result: NOTE Package: FastRWeb Check: CRAN incoming feasibility Old result: NOTE Package: hamlet Check: CRAN incoming feasibility Old result: NOTE Package: iSTATS Check: CRAN incoming feasibility Old result: NOTE Package: MetaComp Check: examples New result: ERROR Package: MetaComp Check: tests New result: ERROR Package: patternplot Check: CRAN incoming feasibility Old result: NOTE Package: QurvE Check: DESCRIPTION meta-information Old result: NOTE New result: OK Package: valhallr Check: CRAN incoming feasibility Old result: NOTE Package: visStatistics Check: examples New result: ERROR Package: visStatistics Check: re-building of vignette outputs New result: ERROR