downloading reverse dependencies ... downloading CDMConnector_1.5.0.tar.gz ... ok downloading constructive_1.0.1.tar.gz ... ok downloading testthat_3.2.1.1.tar.gz ... ok downloading typed_0.0.1.tar.gz ... ok downloading airGRiwrm_0.7.0.tar.gz ... ok downloading bmm_1.0.1.tar.gz ... ok downloading corrtable_0.1.1.tar.gz ... ok downloading crosstable_0.8.1.tar.gz ... ok downloading dm_1.0.10.tar.gz ... ok downloading dtplyr_1.3.1.tar.gz ... ok downloading geosapi_0.7-1.tar.gz ... ok downloading ggside_0.3.1.tar.gz ... ok downloading glue_1.8.0.tar.gz ... ok downloading HDShOP_0.1.5.tar.gz ... ok downloading ibawds_1.0.0.tar.gz ... ok downloading knitxl_0.1.0.tar.gz ... ok downloading latex2exp_0.9.6.tar.gz ... ok downloading mark_0.8.1.tar.gz ... ok downloading mixvlmc_0.2.1.tar.gz ... ok downloading mlfit_0.5.3.tar.gz ... ok downloading mlr3torch_0.1.2.tar.gz ... ok downloading MOCHA_1.1.0.tar.gz ... ok downloading openxlsx2_1.10.tar.gz ... ok downloading petersenlab_1.0.0.tar.gz ... ok downloading plume_0.2.5.tar.gz ... ok downloading readr_2.1.5.tar.gz ... ok downloading renv_1.0.11.tar.gz ... ok downloading Require_1.0.1.tar.gz ... ok downloading srppp_1.0.1.tar.gz ... ok downloading tidyUSDA_0.4.1.tar.gz ... ok downloading vctrs_0.6.5.tar.gz ... ok downloading vroom_1.6.5.tar.gz ... ok installing dependencies ‘airGR’, ‘archive’, ‘ArchR’, ‘bib2df’, ‘BSgenome.Hsapiens.UCSC.hg19’, ‘chromVAR’, ‘CirceR’, ‘cmdstanr’, ‘DatabaseConnector’, ‘diffviewer’, ‘dm’, ‘dslabs’, ‘echo’, ‘ensembldb’, ‘EstimDiagnostics’, ‘expss’, ‘fpCompare’, ‘fuj’, ‘ggbio’, ‘gutenbergr’, ‘HistData’, ‘kimisc’, ‘mix’, ‘mixtur’, ‘modules’, ‘motifmatchr’, ‘mschart’, ‘MultiAssayExperiment’, ‘pixarfilms’, ‘plyranges’, ‘prettycode’, ‘RaggedExperiment’, ‘rmarkdown’, ‘S7’, ‘sloop’, ‘titanic’, ‘torchvision’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘TxDb.Hsapiens.UCSC.hg38.refGene’, ‘waldo’, ‘wCorr’, ‘wrswoR’, ‘zlib’ Warning: packages ‘cmdstanr’, ‘ArchR’ 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 ‘txdbmaker’, ‘CNEr’, ‘DirichletMultinomial’, ‘seqLogo’, ‘TFMPvalue’, ‘maditr’, ‘humaniformat’, ‘BiocBaseUtils’, ‘biovizBase’, ‘VariantAnnotation’, ‘OrganismDbi’, ‘AnnotationFilter’, ‘ProtGenerics’, ‘TFBSTools’ begin installing package ‘txdbmaker’ begin installing package ‘CNEr’ begin installing package ‘DirichletMultinomial’ begin installing package ‘seqLogo’ begin installing package ‘TFMPvalue’ begin installing package ‘maditr’ begin installing package ‘humaniformat’ begin installing package ‘BiocBaseUtils’ begin installing package ‘VariantAnnotation’ begin installing package ‘AnnotationFilter’ begin installing package ‘ProtGenerics’ begin installing package ‘S7’ begin installing package ‘CirceR’ begin installing package ‘DatabaseConnector’ begin installing package ‘dm’ begin installing package ‘pixarfilms’ begin installing package ‘prettycode’ begin installing package ‘airGR’ begin installing package ‘rmarkdown’ begin installing package ‘zlib’ begin installing package ‘mixtur’ begin installing package ‘sloop’ begin installing package ‘waldo’ begin installing package ‘dslabs’ begin installing package ‘gutenbergr’ begin installing package ‘HistData’ begin installing package ‘titanic’ begin installing package ‘fuj’ * installing *source* package ‘titanic’ ... ** package ‘titanic’ 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 ** 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 (titanic) begin installing package ‘echo’ * installing *source* package ‘BiocBaseUtils’ ... ** package ‘BiocBaseUtils’ 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 (BiocBaseUtils) begin installing package ‘kimisc’ * installing *source* package ‘prettycode’ ... ** package ‘prettycode’ 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 (prettycode) begin installing package ‘wrswoR’ * installing *source* package ‘fuj’ ... ** package ‘fuj’ 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 ** 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 (fuj) begin installing package ‘torchvision’ * installing *source* package ‘HistData’ ... ** package ‘HistData’ 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 (HistData) begin installing package ‘plyranges’ * installing *source* package ‘sloop’ ... ** package ‘sloop’ 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 (sloop) begin installing package ‘wCorr’ * installing *source* package ‘CirceR’ ... ** package ‘CirceR’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CirceR) begin installing package ‘TxDb.Hsapiens.UCSC.hg38.refGene’ * installing *source* package ‘echo’ ... ** package ‘echo’ 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 (echo) begin installing package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ * installing *source* package ‘dslabs’ ... ** package ‘dslabs’ 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 ** 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 (dslabs) begin installing package ‘BSgenome.Hsapiens.UCSC.hg19’ * installing *source* package ‘maditr’ ... ** package ‘maditr’ 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 (maditr) begin installing package ‘mschart’ * installing *source* package ‘pixarfilms’ ... ** package ‘pixarfilms’ 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 (pixarfilms) begin installing package ‘mix’ * installing *source* package ‘ProtGenerics’ ... ** package ‘ProtGenerics’ successfully unpacked and MD5 sums checked ** 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) begin installing package ‘modules’ * installing *source* package ‘seqLogo’ ... ** package ‘seqLogo’ 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 (seqLogo) begin installing package ‘fpCompare’ * installing *source* package ‘S7’ ... ** package ‘S7’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpgp4t0O/R.INSTALLa572e47e9eda9/S7/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c method-dispatch.c -o method-dispatch.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o S7.so init.o method-dispatch.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpgp4t0O/R.INSTALLa572e47e9eda9/S7/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-S7/00new/S7/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (S7) begin installing package ‘archive’ * installing *source* package ‘waldo’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (waldo) begin installing package ‘RaggedExperiment’ * installing *source* package ‘kimisc’ ... ** package ‘kimisc’ 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 (kimisc) begin installing package ‘MultiAssayExperiment’ * installing *source* package ‘fpCompare’ ... ** package ‘fpCompare’ 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 (fpCompare) begin installing package ‘EstimDiagnostics’ * installing *source* package ‘modules’ ... ** package ‘modules’ 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 (modules) * installing *source* package ‘gutenbergr’ ... ** package ‘gutenbergr’ 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 (gutenbergr) * installing *source* package ‘mix’ ... ** package ‘mix’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0SEMPI/R.INSTALLa5bd271e394cf/mix/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c mix.f -o mix.o mix.f:1209:60: 1209 | / n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz,l3) | 1 Warning: Unused dummy argument ‘mcz’ at (1) [-Wunused-dummy-argument] mix.f:1209:65: 1209 | / n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz,l3) | 1 Warning: Unused dummy argument ‘nmcz’ at (1) [-Wunused-dummy-argument] mix.f:1057:34: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘c’ at (1) [-Wunused-dummy-argument] mix.f:1057:36: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘d’ at (1) [-Wunused-dummy-argument] mix.f:1057:45: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘dmis’ at (1) [-Wunused-dummy-argument] mix.f:1057:40: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘jmp’ at (1) [-Wunused-dummy-argument] mix.f:1057:27: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘mcw’ at (1) [-Wunused-dummy-argument] mix.f:1057:32: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘nmcw’ at (1) [-Wunused-dummy-argument] mix.f:1057:15: 1057 | / t3,n,z,i,p,mcw,nmcw,c,d,jmp,dmis,mobs,ocz,nocz,mcz,nmcz) | 1 Warning: Unused dummy argument ‘t3’ at (1) [-Wunused-dummy-argument] mix.f:1056:60: 1056 | subroutine addstat1(q,psi,npsi,ncells,sigma,mu,theta,t1,t2, | 1 Warning: Unused dummy argument ‘theta’ at (1) [-Wunused-dummy-argument] mix.f:458:56: 458 | subroutine pstepm(q,psi,npsi,ncells,t1,t2,t3,n,p,prior,chf, | 1 Warning: Unused dummy argument ‘p’ at (1) [-Wunused-dummy-argument] mix.f:999:72: 999 | theta(m)=theta(m)*g/sumf | ^ Warning: ‘g’ may be used uninitialized [-Wmaybe-uninitialized] mix.f:961:64: 961 | double precision sumt,sumf,table(ncells),theta(ncells),g | ^ note: ‘g’ was declared here gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o mix.so init.o mix.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0SEMPI/R.INSTALLa5bd271e394cf/mix/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mix/00new/mix/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mix) * installing *source* package ‘mschart’ ... ** package ‘mschart’ 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 ** 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 (mschart) * installing *source* package ‘mixtur’ ... ** package ‘mixtur’ 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 *** copying figures ** 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 (mixtur) * installing *source* package ‘DatabaseConnector’ ... ** package ‘DatabaseConnector’ 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 (DatabaseConnector) * installing *source* package ‘EstimDiagnostics’ ... ** package ‘EstimDiagnostics’ 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 (EstimDiagnostics) * installing *source* package ‘DirichletMultinomial’ ... ** package ‘DirichletMultinomial’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUrWWdt/R.INSTALLa5701206f2d96/DirichletMultinomial/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dirichlet_fit.c -o dirichlet_fit.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dirichlet_fit_main.c -o dirichlet_fit_main.o dirichlet_fit_main.c: In function ‘hessian’: dirichlet_fit_main.c:391:34: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 391 | adCJK0[j] += adPi[i] * n ? gsl_sf_psi(adAlpha[j] + n) : dPsiAlpha; | ~~~~~~~~^~~ dirichlet_fit_main.c:393:33: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 393 | adCJK[j] += adPi[i] * n ? gsl_sf_psi_1(adAlpha[j] + n): dPsi1Alpha; | ~~~~~~~~^~~ gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o DirichletMultinomial.so R_init_DirichletMultinomial.o dirichlet_fit.o dirichlet_fit_main.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpUrWWdt/R.INSTALLa5701206f2d96/DirichletMultinomial/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-DirichletMultinomial/00new/DirichletMultinomial/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 (DirichletMultinomial) * installing *source* package ‘airGR’ ... ** package ‘airGR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpnTZwXd/R.INSTALLa57401cff9e45/airGR/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c airGR.c -o airGR.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c frun_CEMANEIGE.f90 -o frun_CEMANEIGE.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c frun_GR1A.f90 -o frun_GR1A.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c frun_GR2M.f90 -o frun_GR2M.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c frun_GR4H.f90 -o frun_GR4H.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c frun_GR4J.f90 -o frun_GR4J.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c frun_GR5H.f90 -o frun_GR5H.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c frun_GR5J.f90 -o frun_GR5J.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c frun_GR6J.f90 -o frun_GR6J.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c frun_PE.f90 -o frun_PE.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c utils_D.f90 -o utils_D.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c utils_H.f90 -o utils_H.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o airGR.so airGR.o frun_CEMANEIGE.o frun_GR1A.o frun_GR2M.o frun_GR4H.o frun_GR4J.o frun_GR5H.o frun_GR5J.o frun_GR6J.o frun_PE.o utils_D.o utils_H.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpnTZwXd/R.INSTALLa57401cff9e45/airGR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-airGR/00new/airGR/libs ** 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 ** 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 (airGR) * installing *source* package ‘TFMPvalue’ ... ** package ‘TFMPvalue’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpjmih69/R.INSTALLa572040661d59/TFMPvalue/src' g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ArgumentException.cpp -o ArgumentException.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c FileException.cpp -o FileException.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Matrix.cpp -o Matrix.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ParseException.cpp -o ParseException.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TFMMain.cpp -o TFMMain.o TFMMain.cpp: In function ‘SEXPREC* pv2sc(SEXP, SEXP, SEXP, SEXP)’: TFMMain.cpp:159:8: warning: unused variable ‘sortColumns’ [-Wunused-variable] 159 | bool sortColumns = false; | ^~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c TFMPvalue_init.c -o TFMPvalue_init.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TFMpvalue.cpp -o TFMpvalue.o TFMpvalue.cpp: In function ‘void testLazyDistrib(Matrix, double, double)’: TFMpvalue.cpp:119:13: warning: unused variable ‘totalSize’ [-Wunused-variable] 119 | qlonglong totalSize = 0; | ^~~~~~~~~ TFMpvalue.cpp:120:13: warning: unused variable ‘totalOp’ [-Wunused-variable] 120 | qlonglong totalOp = 0; | ^~~~~~~ TFMpvalue.cpp: In function ‘void testFastPvalue(Matrix, double, double)’: TFMpvalue.cpp:185:13: warning: unused variable ‘totalSize’ [-Wunused-variable] 185 | qlonglong totalSize = 0; | ^~~~~~~~~ TFMpvalue.cpp:186:13: warning: unused variable ‘totalOp’ [-Wunused-variable] 186 | qlonglong totalOp = 0; | ^~~~~~~ TFMpvalue.cpp:190:10: warning: unused variable ‘pvalue’ [-Wunused-variable] 190 | double pvalue = m.fastPvalue(&m,(qlonglong)(score * m.granularity + m.offset)); | ^~~~~~ g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o TFMPvalue.so ArgumentException.o FileException.o Matrix.o ParseException.o TFMMain.o TFMPvalue_init.o TFMpvalue.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpjmih69/R.INSTALLa572040661d59/TFMPvalue/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TFMPvalue/00new/TFMPvalue/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 (TFMPvalue) * installing *source* package ‘rmarkdown’ ... ** package ‘rmarkdown’ 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 (rmarkdown) begin installing package ‘diffviewer’ begin installing package ‘expss’ * installing *source* package ‘torchvision’ ... ** package ‘torchvision’ 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 (torchvision) * installing *source* package ‘diffviewer’ ... ** package ‘diffviewer’ 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 (diffviewer) * installing *source* package ‘wrswoR’ ... ** package ‘wrswoR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpqT6sUh/R.INSTALLa5a0928b5388a/wrswoR/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sample_int_crank.cpp -o sample_int_crank.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o wrswoR.so RcppExports.o sample_int_crank.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpqT6sUh/R.INSTALLa5a0928b5388a/wrswoR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-wrswoR/00new/wrswoR/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 (wrswoR) * installing *source* package ‘dm’ ... ** package ‘dm’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 (dm) * installing *source* package ‘AnnotationFilter’ ... ** package ‘AnnotationFilter’ 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 (AnnotationFilter) begin installing package ‘ensembldb’ * installing *source* package ‘humaniformat’ ... ** package ‘humaniformat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpnOW0Nl/R.INSTALLa571b4627c10e/humaniformat/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c human_format.cpp -o human_format.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c human_getset.cpp -o human_getset.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c human_parse.cpp -o human_parse.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c humaniformat.cpp -o humaniformat.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o humaniformat.so RcppExports.o human_format.o human_getset.o human_parse.o humaniformat.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpnOW0Nl/R.INSTALLa571b4627c10e/humaniformat/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-humaniformat/00new/humaniformat/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (humaniformat) begin installing package ‘bib2df’ * installing *source* package ‘zlib’ ... ** package ‘zlib’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpm62gXi/R.INSTALLa574b27e1c4f1/zlib/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I/home/hornik/tmp/R-d-gcc-14/include -I../inst/include -I./ `/home/hornik/tmp/R-d-gcc-14/bin/Rscript -e "Rcpp:::CxxFlags()"` -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I/home/hornik/tmp/R-d-gcc-14/include -I../inst/include -I./ `/home/hornik/tmp/R-d-gcc-14/bin/Rscript -e "Rcpp:::CxxFlags()"` -fpic -g -O2 -Wall -pedantic -mtune=native -c compressor.cpp -o compressor.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I/home/hornik/tmp/R-d-gcc-14/include -I../inst/include -I./ `/home/hornik/tmp/R-d-gcc-14/bin/Rscript -e "Rcpp:::CxxFlags()"` -fpic -g -O2 -Wall -pedantic -mtune=native -c constants.cpp -o constants.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I/home/hornik/tmp/R-d-gcc-14/include -I../inst/include -I./ `/home/hornik/tmp/R-d-gcc-14/bin/Rscript -e "Rcpp:::CxxFlags()"` -fpic -g -O2 -Wall -pedantic -mtune=native -c decompressor.cpp -o decompressor.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I/home/hornik/tmp/R-d-gcc-14/include -I../inst/include -I./ `/home/hornik/tmp/R-d-gcc-14/bin/Rscript -e "Rcpp:::CxxFlags()"` -fpic -g -O2 -Wall -pedantic -mtune=native -c validate.cpp -o validate.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o zlib.so RcppExports.o compressor.o constants.o decompressor.o validate.o -lz -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpm62gXi/R.INSTALLa574b27e1c4f1/zlib/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-zlib/00new/zlib/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 (zlib) * installing *source* package ‘expss’ ... ** package ‘expss’ 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 (expss) * installing *source* package ‘archive’ ... ** package ‘archive’ successfully unpacked and MD5 sums checked ** using staged installation ** Running ./configure Found pkg-config cflags and libs! PKG_CONFIG_PATH= PKG_CFLAGS= PKG_LIBS=-larchive ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzPQQCE/R.INSTALLa5c6c772caaf1/archive/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Icpp11/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cli/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c archive.cpp -o archive.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Icpp11/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cli/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c archive_extract.cpp -o archive_extract.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Icpp11/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cli/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c archive_read.cpp -o archive_read.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Icpp11/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cli/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c archive_write.cpp -o archive_write.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Icpp11/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cli/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c archive_write_direct.cpp -o archive_write_direct.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Icpp11/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cli/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c archive_write_files.cpp -o archive_write_files.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Icpp11/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cli/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cpp11.cpp -o cpp11.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Icpp11/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cli/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c r_archive.cpp -o r_archive.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -Icpp11/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cli/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c connection/connection.c -o connection/connection.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o archive.so archive.o archive_extract.o archive_read.o archive_write.o archive_write_direct.o archive_write_files.o cpp11.o r_archive.o -larchive -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzPQQCE/R.INSTALLa5c6c772caaf1/archive/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-archive/00new/archive/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 (archive) * installing *source* package ‘bib2df’ ... ** package ‘bib2df’ 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 (bib2df) * installing *source* package ‘RaggedExperiment’ ... ** package ‘RaggedExperiment’ 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 (RaggedExperiment) * installing *source* package ‘MultiAssayExperiment’ ... ** package ‘MultiAssayExperiment’ 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 (MultiAssayExperiment) * installing *source* package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ... ** 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 (TxDb.Hsapiens.UCSC.hg19.knownGene) * installing *source* package ‘TxDb.Hsapiens.UCSC.hg38.refGene’ ... ** 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 (TxDb.Hsapiens.UCSC.hg38.refGene) * installing *source* package ‘txdbmaker’ ... ** package ‘txdbmaker’ 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 (txdbmaker) begin installing package ‘OrganismDbi’ * installing *source* package ‘plyranges’ ... ** package ‘plyranges’ 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 (plyranges) * installing *source* package ‘wCorr’ ... ** package ‘wCorr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpbW5jXQ/R.INSTALLa5ae57fc8d57a/wCorr/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c contCorrHelpers.cpp -o contCorrHelpers.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c helpers.cpp -o helpers.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c polycHelpers.cpp -o polycHelpers.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpparma_hello_world.cpp -o rcpparma_hello_world.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o wCorr.so RcppExports.o contCorrHelpers.o helpers.o polycHelpers.o rcpparma_hello_world.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpbW5jXQ/R.INSTALLa5ae57fc8d57a/wCorr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-wCorr/00new/wCorr/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (wCorr) * installing *source* package ‘CNEr’ ... ** package ‘CNEr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpzq8yLp/R.INSTALLa57029fa7d81/CNEr/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IRanges_stubs.c -o IRanges_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_CNEr.c -o R_init_CNEr.o In file included from CNEr.h:3, from R_init_CNEr.c:1: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from CNEr.h:5: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ In file included from CNEr.h:6: ucsc/obscure.h:154:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 154 | void dotForUser(); | ^~~~ ucsc/obscure.h:169:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 169 | void printVmPeak(); | ^~~~ In file included from CNEr.h:7: ucsc/options.h:93:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 93 | void optionFree(); | ^~~~ In file included from ucsc/dnaseq.h:10, from ucsc/axt.h:28, from CNEr.h:8: ucsc/dnautil.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | void dnaUtilOpen(); /* Good idea to call this before using any arrays | ^~~~ In file included from ucsc/dnaseq.h:14: ucsc/bits.h:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 92 | void bitsInByteInit(); | ^~~~ In file included from ucsc/axt.h:32: ucsc/chain.h:107:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 107 | void chainIdReset(); | ^~~~ ucsc/axt.h:96:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 96 | struct axtScoreScheme *axtScoreSchemeDefault(); | ^~~~~~~~~~~~~~ ucsc/axt.h:103:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 103 | struct axtScoreScheme *axtScoreSchemeRnaDefault(); | ^~~~~~~~~~~~~~ ucsc/axt.h:112:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 112 | struct axtScoreScheme *axtScoreSchemeRnaFill(); | ^~~~~~~~~~~~~~ ucsc/axt.h:116:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 116 | struct axtScoreScheme *axtScoreSchemeProteinDefault(); | ^~~~~~~~~~~~~~ In file included from CNEr.h:14: ucsc/binRange.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | int binLevelsExtended(); | ^~~ ucsc/binRange.h:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 22 | int binLevels(); | ^~~ ucsc/binRange.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 25 | int binFirstShift(); | ^~~ ucsc/binRange.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 28 | int binNextShift(); | ^~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utils.c -o utils.o In file included from CNEr.h:3, from utils.c:5: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from CNEr.h:5: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ In file included from CNEr.h:6: ucsc/obscure.h:154:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 154 | void dotForUser(); | ^~~~ ucsc/obscure.h:169:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 169 | void printVmPeak(); | ^~~~ In file included from CNEr.h:7: ucsc/options.h:93:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 93 | void optionFree(); | ^~~~ In file included from ucsc/dnaseq.h:10, from ucsc/axt.h:28, from CNEr.h:8: ucsc/dnautil.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | void dnaUtilOpen(); /* Good idea to call this before using any arrays | ^~~~ In file included from ucsc/dnaseq.h:14: ucsc/bits.h:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 92 | void bitsInByteInit(); | ^~~~ In file included from ucsc/axt.h:32: ucsc/chain.h:107:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 107 | void chainIdReset(); | ^~~~ ucsc/axt.h:96:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 96 | struct axtScoreScheme *axtScoreSchemeDefault(); | ^~~~~~~~~~~~~~ ucsc/axt.h:103:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 103 | struct axtScoreScheme *axtScoreSchemeRnaDefault(); | ^~~~~~~~~~~~~~ ucsc/axt.h:112:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 112 | struct axtScoreScheme *axtScoreSchemeRnaFill(); | ^~~~~~~~~~~~~~ ucsc/axt.h:116:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 116 | struct axtScoreScheme *axtScoreSchemeProteinDefault(); | ^~~~~~~~~~~~~~ In file included from CNEr.h:14: ucsc/binRange.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | int binLevelsExtended(); | ^~~ ucsc/binRange.h:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 22 | int binLevels(); | ^~~ ucsc/binRange.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 25 | int binFirstShift(); | ^~~ ucsc/binRange.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 28 | int binNextShift(); | ^~~ utils.c: In function ‘bin_ranges_from_coord_range_standard’: utils.c:50:7: warning: unused variable ‘_binNextShift’ [-Wunused-variable] 50 | int _binNextShift = binNextShift(); | ^~~~~~~~~~~~~ utils.c:49:7: warning: unused variable ‘_binFirstShift’ [-Wunused-variable] 49 | int _binFirstShift = binFirstShift(); | ^~~~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io.c -o io.o In file included from CNEr.h:3, from io.c:5: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from CNEr.h:5: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ In file included from CNEr.h:6: ucsc/obscure.h:154:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 154 | void dotForUser(); | ^~~~ ucsc/obscure.h:169:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 169 | void printVmPeak(); | ^~~~ In file included from CNEr.h:7: ucsc/options.h:93:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 93 | void optionFree(); | ^~~~ In file included from ucsc/dnaseq.h:10, from ucsc/axt.h:28, from CNEr.h:8: ucsc/dnautil.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | void dnaUtilOpen(); /* Good idea to call this before using any arrays | ^~~~ In file included from ucsc/dnaseq.h:14: ucsc/bits.h:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 92 | void bitsInByteInit(); | ^~~~ In file included from ucsc/axt.h:32: ucsc/chain.h:107:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 107 | void chainIdReset(); | ^~~~ ucsc/axt.h:96:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 96 | struct axtScoreScheme *axtScoreSchemeDefault(); | ^~~~~~~~~~~~~~ ucsc/axt.h:103:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 103 | struct axtScoreScheme *axtScoreSchemeRnaDefault(); | ^~~~~~~~~~~~~~ ucsc/axt.h:112:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 112 | struct axtScoreScheme *axtScoreSchemeRnaFill(); | ^~~~~~~~~~~~~~ ucsc/axt.h:116:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 116 | struct axtScoreScheme *axtScoreSchemeProteinDefault(); | ^~~~~~~~~~~~~~ In file included from CNEr.h:14: ucsc/binRange.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | int binLevelsExtended(); | ^~~ ucsc/binRange.h:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 22 | int binLevels(); | ^~~ ucsc/binRange.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 25 | int binFirstShift(); | ^~~ ucsc/binRange.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 28 | int binNextShift(); | ^~~ io.c: In function ‘myReadAxt’: io.c:94:26: warning: unused variable ‘curAxt’ [-Wunused-variable] 94 | struct axt *axt=NULL, *curAxt; | ^~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ceScan.c -o ceScan.o In file included from CNEr.h:3, from ceScan.c:3: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from CNEr.h:5: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ In file included from CNEr.h:6: ucsc/obscure.h:154:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 154 | void dotForUser(); | ^~~~ ucsc/obscure.h:169:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 169 | void printVmPeak(); | ^~~~ In file included from CNEr.h:7: ucsc/options.h:93:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 93 | void optionFree(); | ^~~~ In file included from ucsc/dnaseq.h:10, from ucsc/axt.h:28, from CNEr.h:8: ucsc/dnautil.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | void dnaUtilOpen(); /* Good idea to call this before using any arrays | ^~~~ In file included from ucsc/dnaseq.h:14: ucsc/bits.h:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 92 | void bitsInByteInit(); | ^~~~ In file included from ucsc/axt.h:32: ucsc/chain.h:107:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 107 | void chainIdReset(); | ^~~~ ucsc/axt.h:96:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 96 | struct axtScoreScheme *axtScoreSchemeDefault(); | ^~~~~~~~~~~~~~ ucsc/axt.h:103:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 103 | struct axtScoreScheme *axtScoreSchemeRnaDefault(); | ^~~~~~~~~~~~~~ ucsc/axt.h:112:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 112 | struct axtScoreScheme *axtScoreSchemeRnaFill(); | ^~~~~~~~~~~~~~ ucsc/axt.h:116:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 116 | struct axtScoreScheme *axtScoreSchemeProteinDefault(); | ^~~~~~~~~~~~~~ In file included from CNEr.h:14: ucsc/binRange.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | int binLevelsExtended(); | ^~~ ucsc/binRange.h:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 22 | int binLevels(); | ^~~ ucsc/binRange.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 25 | int binFirstShift(); | ^~~ ucsc/binRange.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 28 | int binNextShift(); | ^~~ ceScan.c: In function ‘ceScan’: ceScan.c:615:8: warning: unused variable ‘rest’ [-Wunused-variable] 615 | char rest, path[PATH_LEN]; | ^~~~ ceScan.c:613:10: warning: unused variable ‘n’ [-Wunused-variable] 613 | int i, n; | ^ ceScan.c: In function ‘freeSlThreshold’: ceScan.c:674:17: warning: unused variable ‘CNE’ [-Wunused-variable] 674 | struct slCNE *CNE, *nextCNE, *el_CNE; | ^~~ ceScan.c:673:23: warning: unused variable ‘thresholds’ [-Wunused-variable] 673 | struct slThreshold *thresholds, *nextThreshold, *el_threshold; | ^~~~~~~~~~ ceScan.c: In function ‘myCeScan’: ceScan.c:868:28: warning: unused variable ‘i’ [-Wunused-variable] 868 | int nrCNE[nrThresholds], i; | ^ ceScan.c:868:7: warning: unused variable ‘nrCNE’ [-Wunused-variable] 868 | int nrCNE[nrThresholds], i; | ^~~~~ ceScan.c:865:17: warning: unused variable ‘CNE’ [-Wunused-variable] 865 | struct slCNE *CNE; | ^~~ ceScan.c: In function ‘myCeScanFile’: ceScan.c:898:7: warning: unused variable ‘nrThresholds’ [-Wunused-variable] 898 | int nrThresholds = GET_LENGTH(winSize); | ^~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/axt.c -o ucsc/axt.o In file included from ucsc/axt.c:17: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/axt.c:18: ucsc/obscure.h:154:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 154 | void dotForUser(); | ^~~~ ucsc/obscure.h:169:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 169 | void printVmPeak(); | ^~~~ In file included from ucsc/axt.c:20: ucsc/dnautil.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | void dnaUtilOpen(); /* Good idea to call this before using any arrays | ^~~~ In file included from ucsc/dnaseq.h:14, from ucsc/axt.h:28, from ucsc/axt.c:21: ucsc/bits.h:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 92 | void bitsInByteInit(); | ^~~~ In file included from ucsc/axt.h:32: ucsc/chain.h:107:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 107 | void chainIdReset(); | ^~~~ ucsc/axt.h:96:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 96 | struct axtScoreScheme *axtScoreSchemeDefault(); | ^~~~~~~~~~~~~~ ucsc/axt.h:103:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 103 | struct axtScoreScheme *axtScoreSchemeRnaDefault(); | ^~~~~~~~~~~~~~ ucsc/axt.h:112:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 112 | struct axtScoreScheme *axtScoreSchemeRnaFill(); | ^~~~~~~~~~~~~~ ucsc/axt.h:116:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 116 | struct axtScoreScheme *axtScoreSchemeProteinDefault(); | ^~~~~~~~~~~~~~ ucsc/axt.c:423:24: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 423 | struct axtScoreScheme *axtScoreSchemeDefault() | ^~~~~~~~~~~~~~~~~~~~~ ucsc/axt.c:493:24: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 493 | struct axtScoreScheme *axtScoreSchemeRnaDefault() | ^~~~~~~~~~~~~~~~~~~~~~~~ ucsc/axt.c:503:24: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 503 | struct axtScoreScheme *axtScoreSchemeRnaFill() | ^~~~~~~~~~~~~~~~~~~~~ ucsc/axt.c:657:24: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 657 | struct axtScoreScheme *axtScoreSchemeProteinDefault() | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/base64.c -o ucsc/base64.o In file included from ucsc/base64.c:4: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/binRange.c -o ucsc/binRange.o In file included from ucsc/binRange.c:13: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/binRange.c:14: ucsc/binRange.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | int binLevelsExtended(); | ^~~ ucsc/binRange.h:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 22 | int binLevels(); | ^~~ ucsc/binRange.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 25 | int binFirstShift(); | ^~~ ucsc/binRange.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 28 | int binNextShift(); | ^~~ ucsc/binRange.c:27:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 27 | int binLevelsExtended() | ^~~~~~~~~~~~~~~~~ ucsc/binRange.c:33:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 33 | int binLevels() | ^~~~~~~~~ ucsc/binRange.c:39:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 39 | int binFirstShift() | ^~~~~~~~~~~~~ ucsc/binRange.c:45:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 45 | int binNextShift() | ^~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/bits.c -o ucsc/bits.o In file included from ucsc/bits.c:6: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/bits.c:7: ucsc/bits.h:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 92 | void bitsInByteInit(); | ^~~~ ucsc/bits.c:18:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 18 | void bitsInByteInit() | ^~~~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/chain.c -o ucsc/chain.o In file included from ucsc/chain.c:7: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/chain.c:9: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ In file included from ucsc/dnaseq.h:10, from ucsc/chain.c:10: ucsc/dnautil.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | void dnaUtilOpen(); /* Good idea to call this before using any arrays | ^~~~ In file included from ucsc/dnaseq.h:14: ucsc/bits.h:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 92 | void bitsInByteInit(); | ^~~~ In file included from ucsc/chain.c:12: ucsc/chain.h:107:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 107 | void chainIdReset(); | ^~~~ ucsc/chain.c:188:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 188 | void chainIdReset() | ^~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o In file included from ucsc/_cheapcgi.c:9: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/_cheapcgi.c: In function ‘cgiDecode’: ucsc/_cheapcgi.c:26:29: warning: format ‘%x’ expects argument of type ‘unsigned int *’, but argument 3 has type ‘int *’ [-Wformat=] 26 | if (sscanf(in, "%2x", &code) != 1) | ~~^ ~~~~~ | | | | | int * | unsigned int * | %2x gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/cirTree.c -o ucsc/cirTree.o In file included from ucsc/cirTree.c:14: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/cirTree.c:17: ucsc/udc.h:106:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 106 | char *udcDefaultDir(); | ^~~~ ucsc/udc.h:133:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 133 | int udcCacheTimeout(); | ^~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/common.c -o ucsc/common.o In file included from ucsc/common.c:7: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/common.c:8: ucsc/errabort.h:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 21 | boolean isErrAbortInProgress(); | ^~~~~~~ ucsc/errabort.h:43:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 43 | typedef void (*AbortHandler)(); | ^~~~~~~ ucsc/errabort.h:49:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 49 | void popAbortHandler(); | ^~~~ ucsc/errabort.h:52:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 52 | void noWarnAbort(); | ^~~~ ucsc/errabort.h:55:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 55 | void pushDebugAbort(); | ^~~~ ucsc/errabort.h:81:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 81 | void popWarnHandler(); | ^~~~ ucsc/errabort.h:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 84 | void pushWarnAbort(); | ^~~~ ucsc/errabort.h:87:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 87 | void pushSilentWarnHandler(); | ^~~~ ucsc/errabort.h:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 90 | void errAbortDebugnPushPopErr(); | ^~~~ In file included from ucsc/common.c:9: ucsc/portable.h:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 50 | char *getCurrentDir(); | ^~~~ ucsc/portable.h:74:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 74 | long clock1000(); | ^~~~ ucsc/portable.h:80:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 80 | long clock1(); | ^~~~ ucsc/portable.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 105 | char *cgiDir(); | ^~~~ ucsc/portable.h:108:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 108 | char *trashDir(); | ^~~~ ucsc/portable.h:114:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 114 | double machineSpeed(); | ^~~~~~ ucsc/portable.h:117:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 117 | char *mysqlHost(); | ^~~~ ucsc/portable.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 120 | char *getHost(); | ^~~~ ucsc/portable.h:123:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 123 | void uglyfBreak(); | ^~~~ ucsc/portable.h:126:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 126 | char *getUser(); | ^~~~ ucsc/portable.h:132:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 132 | int mustFork(); | ^~~ ucsc/portable.h:135:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 135 | int rawKeyIn(); | ^~~ In file included from ucsc/common.c:11: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ ucsc/common.c:344:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 344 | void slUniqify(void *pList, int (*compare )(const void *elem1, const void *elem2), void (*free)()) | ^~~~ ucsc/common.c:374:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 374 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()) | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/dlist.c -o ucsc/dlist.o In file included from ucsc/dlist.c:5: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/dlist.c:6: ucsc/dlist.h:43:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 43 | struct dlList *newDlList(); | ^~~~~~ ucsc/dlist.c:17:16: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 17 | struct dlList *newDlList() | ^~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/dnaseq.c -o ucsc/dnaseq.o In file included from ucsc/dnaseq.c:6: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/dnaseq.h:10, from ucsc/dnaseq.c:7: ucsc/dnautil.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | void dnaUtilOpen(); /* Good idea to call this before using any arrays | ^~~~ In file included from ucsc/dnaseq.h:14: ucsc/bits.h:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 92 | void bitsInByteInit(); | ^~~~ In file included from ucsc/dnaseq.c:9: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ In file included from ucsc/dnaseq.c:10: ucsc/obscure.h:154:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 154 | void dotForUser(); | ^~~~ ucsc/obscure.h:169:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 169 | void printVmPeak(); | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/dnautil.c -o ucsc/dnautil.o In file included from ucsc/dnautil.c:15: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/dnautil.c:16: ucsc/dnautil.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | void dnaUtilOpen(); /* Good idea to call this before using any arrays | ^~~~ ucsc/dnautil.c:133:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 133 | static void initNtVal() | ^~~~~~~~~ ucsc/dnautil.c:334:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 334 | static void initNtChars() | ^~~~~~~~~~~ ucsc/dnautil.c:354:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 354 | static void initNtMixedCaseChars() | ^~~~~~~~~~~~~~~~~~~~ ucsc/dnautil.c:382:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 382 | static void initNtCompTable() | ^~~~~~~~~~~~~~~ ucsc/dnautil.c:758:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 758 | static void checkSizeTypes() | ^~~~~~~~~~~~~~ ucsc/dnautil.c: In function ‘findHeadPolyTMaybeMask’: ucsc/dnautil.c:942:5: warning: variable ‘pastPoly’ set but not used [-Wunused-but-set-variable] 942 | int pastPoly = 0; | ^~~~~~~~ ucsc/dnautil.c: At top level: ucsc/dnautil.c:1091:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 1091 | static void initAaVal() | ^~~~~~~~~ ucsc/dnautil.c:1110:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 1110 | void dnaUtilOpen() | ^~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/dystring.c -o ucsc/dystring.o In file included from ucsc/dystring.c:6: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/errabort.c -o ucsc/errabort.o In file included from ucsc/errabort.c:25: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/errabort.c:26: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ In file included from ucsc/errabort.c:28: ucsc/errabort.h:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 21 | boolean isErrAbortInProgress(); | ^~~~~~~ ucsc/errabort.h:43:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 43 | typedef void (*AbortHandler)(); | ^~~~~~~ ucsc/errabort.h:49:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 49 | void popAbortHandler(); | ^~~~ ucsc/errabort.h:52:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 52 | void noWarnAbort(); | ^~~~ ucsc/errabort.h:55:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 55 | void pushDebugAbort(); | ^~~~ ucsc/errabort.h:81:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 81 | void popWarnHandler(); | ^~~~ ucsc/errabort.h:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 84 | void pushWarnAbort(); | ^~~~ ucsc/errabort.h:87:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 87 | void pushSilentWarnHandler(); | ^~~~ ucsc/errabort.h:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 90 | void errAbortDebugnPushPopErr(); | ^~~~ ucsc/errabort.c:48:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 48 | static struct perThreadAbortVars *getThreadVars(); // forward declaration | ^~~~~~~~~~~~~~~~~~ ucsc/errabort.c:148:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 148 | void popWarnHandler() | ^~~~~~~~~~~~~~ ucsc/errabort.c:163:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 163 | static void defaultAbort() | ^~~~~~~~~~~~ ucsc/errabort.c:173:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 173 | void noWarnAbort() | ^~~~~~~~~~~ ucsc/errabort.c:231:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 231 | void popAbortHandler() | ^~~~~~~~~~~~~~~ ucsc/errabort.c:246:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 246 | static void debugAbort() | ^~~~~~~~~~ ucsc/errabort.c:254:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 254 | void pushDebugAbort() | ^~~~~~~~~~~~~~ ucsc/errabort.c:267:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 267 | void pushWarnAbort() | ^~~~~~~~~~~~~ ucsc/errabort.c:273:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 273 | void pushSilentWarnHandler() | ^~~~~~~~~~~~~~~~~~~~~ ucsc/errabort.c:279:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 279 | void errAbortDebugnPushPopErr() | ^~~~~~~~~~~~~~~~~~~~~~~~ ucsc/errabort.c:286:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 286 | boolean isErrAbortInProgress() | ^~~~~~~~~~~~~~~~~~~~ ucsc/errabort.c:296:35: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 296 | static struct perThreadAbortVars *getThreadVars() | ^~~~~~~~~~~~~ ucsc/errabort.c:30:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 30 | static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $"; | ^~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/hash.c -o ucsc/hash.o In file included from ucsc/hash.c:6: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/hash.c:8: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ In file included from ucsc/hash.c:9: ucsc/obscure.h:154:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 154 | void dotForUser(); | ^~~~ ucsc/obscure.h:169:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 169 | void printVmPeak(); | ^~~~ ucsc/hash.c:614:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 614 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()) | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/https.c -o ucsc/https.o In file included from ucsc/https.c:379: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/https.c:380: ucsc/errabort.h:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 21 | boolean isErrAbortInProgress(); | ^~~~~~~ ucsc/errabort.h:43:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 43 | typedef void (*AbortHandler)(); | ^~~~~~~ ucsc/errabort.h:49:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 49 | void popAbortHandler(); | ^~~~ ucsc/errabort.h:52:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 52 | void noWarnAbort(); | ^~~~ ucsc/errabort.h:55:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 55 | void pushDebugAbort(); | ^~~~ ucsc/errabort.h:81:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 81 | void popWarnHandler(); | ^~~~ ucsc/errabort.h:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 84 | void pushWarnAbort(); | ^~~~ ucsc/errabort.h:87:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 87 | void pushSilentWarnHandler(); | ^~~~ ucsc/errabort.h:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 90 | void errAbortDebugnPushPopErr(); | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/intExp.c -o ucsc/intExp.o In file included from ucsc/intExp.c:7: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/intExp.c:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 34 | static double expression(); | ^~~~~~ ucsc/intExp.c:37:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 37 | static double number() | ^~~~~~ ucsc/intExp.c:50:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 50 | static double atom() | ^~~~ ucsc/intExp.c:74:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 74 | static double uMinus() | ^~~~~~ ucsc/intExp.c:88:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 88 | static double mulDiv() | ^~~~~~ ucsc/intExp.c:110:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 110 | static double addSub() | ^~~~~~ ucsc/intExp.c:133:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 133 | static double expression() | ^~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/kxTok.c -o ucsc/kxTok.o In file included from ucsc/kxTok.c:8: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/linefile.c -o ucsc/linefile.o In file included from ucsc/linefile.c:7: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/linefile.c:8: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ In file included from ucsc/linefile.c:11: ucsc/errabort.h:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 21 | boolean isErrAbortInProgress(); | ^~~~~~~ ucsc/errabort.h:43:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 43 | typedef void (*AbortHandler)(); | ^~~~~~~ ucsc/errabort.h:49:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 49 | void popAbortHandler(); | ^~~~ ucsc/errabort.h:52:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 52 | void noWarnAbort(); | ^~~~ ucsc/errabort.h:55:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 55 | void pushDebugAbort(); | ^~~~ ucsc/errabort.h:81:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 81 | void popWarnHandler(); | ^~~~ ucsc/errabort.h:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 84 | void pushWarnAbort(); | ^~~~ ucsc/errabort.h:87:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 87 | void pushSilentWarnHandler(); | ^~~~ ucsc/errabort.h:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 90 | void errAbortDebugnPushPopErr(); | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/localmem.c -o ucsc/localmem.o In file included from ucsc/localmem.c:11: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/localmem.c: In function ‘lmAllocMoreMem’: ucsc/localmem.c:122:23: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 122 | mb->free = pt + newSize; | ^ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/memalloc.c -o ucsc/memalloc.o In file included from ucsc/memalloc.c:11: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/memalloc.c:12: ucsc/obscure.h:154:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 154 | void dotForUser(); | ^~~~ ucsc/obscure.h:169:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 169 | void printVmPeak(); | ^~~~ In file included from ucsc/memalloc.c:13: ucsc/memalloc.h:22:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 22 | struct memHandler *popMemHandler(); | ^~~~~~~~~~ ucsc/memalloc.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 25 | void setDefaultMemHandler(); | ^~~~ ucsc/memalloc.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 32 | void carefulCheckHeap(); | ^~~~ ucsc/memalloc.h:37:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 37 | int carefulCountBlocksAllocated(); | ^~~ ucsc/memalloc.h:41:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 41 | long carefulTotalAllocated(); | ^~~~ ucsc/memalloc.h:47:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 47 | void memTrackerStart(); | ^~~~ ucsc/memalloc.h:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 51 | void memTrackerEnd(); | ^~~~ In file included from ucsc/memalloc.c:14: ucsc/dlist.h:43:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 43 | struct dlList *newDlList(); | ^~~~~~ ucsc/memalloc.c:56:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 56 | struct memHandler *popMemHandler() | ^~~~~~~~~~~~~ ucsc/memalloc.c:67:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 67 | void setDefaultMemHandler() | ^~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:341:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 341 | void carefulCheckHeap() | ^~~~~~~~~~~~~~~~ ucsc/memalloc.c:369:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 369 | int carefulCountBlocksAllocated() | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:375:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 375 | long carefulTotalAllocated() | ^~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:450:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 450 | void memTrackerStart() | ^~~~~~~~~~~~~~~ ucsc/memalloc.c:470:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 470 | void memTrackerEnd() | ^~~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/obscure.c -o ucsc/obscure.o In file included from ucsc/obscure.c:6: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/obscure.c:8: ucsc/portable.h:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 50 | char *getCurrentDir(); | ^~~~ ucsc/portable.h:74:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 74 | long clock1000(); | ^~~~ ucsc/portable.h:80:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 80 | long clock1(); | ^~~~ ucsc/portable.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 105 | char *cgiDir(); | ^~~~ ucsc/portable.h:108:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 108 | char *trashDir(); | ^~~~ ucsc/portable.h:114:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 114 | double machineSpeed(); | ^~~~~~ ucsc/portable.h:117:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 117 | char *mysqlHost(); | ^~~~ ucsc/portable.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 120 | char *getHost(); | ^~~~ ucsc/portable.h:123:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 123 | void uglyfBreak(); | ^~~~ ucsc/portable.h:126:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 126 | char *getUser(); | ^~~~ ucsc/portable.h:132:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 132 | int mustFork(); | ^~~ ucsc/portable.h:135:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 135 | int rawKeyIn(); | ^~~ In file included from ucsc/obscure.c:10: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ In file included from ucsc/obscure.c:11: ucsc/obscure.h:154:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 154 | void dotForUser(); | ^~~~ ucsc/obscure.h:169:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 169 | void printVmPeak(); | ^~~~ ucsc/obscure.c:661:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 661 | void dotForUser() | ^~~~~~~~~~ ucsc/obscure.c:689:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 689 | void printVmPeak() | ^~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/options.c -o ucsc/options.o In file included from ucsc/options.c:10: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/options.c:11: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ In file included from ucsc/options.c:12: ucsc/verbose.h:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 31 | void verboseDot(); | ^~~~ ucsc/verbose.h:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 34 | boolean verboseDotsEnabled(); | ^~~~~~~ ucsc/verbose.h:49:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 49 | FILE *verboseLogFile(); | ^~~~ In file included from ucsc/options.c:13: ucsc/options.h:93:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 93 | void optionFree(); | ^~~~ ucsc/options.c: In function ‘validateOption’: ucsc/options.c:49:11: warning: variable ‘discardMe’ set but not used [-Wunused-but-set-variable] 49 | long long discardMe = 0; | ^~~~~~~~~ ucsc/options.c: At top level: ucsc/options.c:272:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 272 | void optionFree() | ^~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/pipeline.c -o ucsc/pipeline.o In file included from ucsc/pipeline.c:10: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/pipeline.c:13: ucsc/errabort.h:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 21 | boolean isErrAbortInProgress(); | ^~~~~~~ ucsc/errabort.h:43:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 43 | typedef void (*AbortHandler)(); | ^~~~~~~ ucsc/errabort.h:49:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 49 | void popAbortHandler(); | ^~~~ ucsc/errabort.h:52:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 52 | void noWarnAbort(); | ^~~~ ucsc/errabort.h:55:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 55 | void pushDebugAbort(); | ^~~~ ucsc/errabort.h:81:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 81 | void popWarnHandler(); | ^~~~ ucsc/errabort.h:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 84 | void pushWarnAbort(); | ^~~~ ucsc/errabort.h:87:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 87 | void pushSilentWarnHandler(); | ^~~~ ucsc/errabort.h:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 90 | void errAbortDebugnPushPopErr(); | ^~~~ In file included from ucsc/pipeline.c:14: ucsc/portable.h:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 50 | char *getCurrentDir(); | ^~~~ ucsc/portable.h:74:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 74 | long clock1000(); | ^~~~ ucsc/portable.h:80:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 80 | long clock1(); | ^~~~ ucsc/portable.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 105 | char *cgiDir(); | ^~~~ ucsc/portable.h:108:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 108 | char *trashDir(); | ^~~~ ucsc/portable.h:114:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 114 | double machineSpeed(); | ^~~~~~ ucsc/portable.h:117:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 117 | char *mysqlHost(); | ^~~~ ucsc/portable.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 120 | char *getHost(); | ^~~~ ucsc/portable.h:123:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 123 | void uglyfBreak(); | ^~~~ ucsc/portable.h:126:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 126 | char *getUser(); | ^~~~ ucsc/portable.h:132:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 132 | int mustFork(); | ^~~ ucsc/portable.h:135:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 135 | int rawKeyIn(); | ^~~ ucsc/pipeline.c:157:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 157 | static void childAbortHandler() | ^~~~~~~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/_portimpl.c -o ucsc/_portimpl.o In file included from ucsc/_portimpl.c:9: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/_portimpl.c:10: ucsc/portable.h:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 50 | char *getCurrentDir(); | ^~~~ ucsc/portable.h:74:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 74 | long clock1000(); | ^~~~ ucsc/portable.h:80:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 80 | long clock1(); | ^~~~ ucsc/portable.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 105 | char *cgiDir(); | ^~~~ ucsc/portable.h:108:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 108 | char *trashDir(); | ^~~~ ucsc/portable.h:114:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 114 | double machineSpeed(); | ^~~~~~ ucsc/portable.h:117:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 117 | char *mysqlHost(); | ^~~~ ucsc/portable.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 120 | char *getHost(); | ^~~~ ucsc/portable.h:123:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 123 | void uglyfBreak(); | ^~~~ ucsc/portable.h:126:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 126 | char *getUser(); | ^~~~ ucsc/portable.h:132:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 132 | int mustFork(); | ^~~ ucsc/portable.h:135:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 135 | int rawKeyIn(); | ^~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/sqlList.c -o ucsc/sqlList.o In file included from ucsc/sqlList.c:10: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/sqlList.c:14: ucsc/hash.h:247:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 247 | void hashFreeWithVals(struct hash **pHash, void (freeFunc)()); | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/sqlNum.c -o ucsc/sqlNum.o In file included from ucsc/sqlNum.c:7: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/verbose.c -o ucsc/verbose.o In file included from ucsc/verbose.c:7: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/verbose.c:8: ucsc/portable.h:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 50 | char *getCurrentDir(); | ^~~~ ucsc/portable.h:74:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 74 | long clock1000(); | ^~~~ ucsc/portable.h:80:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 80 | long clock1(); | ^~~~ ucsc/portable.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 105 | char *cgiDir(); | ^~~~ ucsc/portable.h:108:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 108 | char *trashDir(); | ^~~~ ucsc/portable.h:114:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 114 | double machineSpeed(); | ^~~~~~ ucsc/portable.h:117:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 117 | char *mysqlHost(); | ^~~~ ucsc/portable.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 120 | char *getHost(); | ^~~~ ucsc/portable.h:123:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 123 | void uglyfBreak(); | ^~~~ ucsc/portable.h:126:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 126 | char *getUser(); | ^~~~ ucsc/portable.h:132:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 132 | int mustFork(); | ^~~ ucsc/portable.h:135:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 135 | int rawKeyIn(); | ^~~ In file included from ucsc/verbose.c:9: ucsc/verbose.h:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 31 | void verboseDot(); | ^~~~ ucsc/verbose.h:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 34 | boolean verboseDotsEnabled(); | ^~~~~~~ ucsc/verbose.h:49:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 49 | FILE *verboseLogFile(); | ^~~~ ucsc/verbose.c:68:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 68 | boolean verboseDotsEnabled() | ^~~~~~~~~~~~~~~~~~ ucsc/verbose.c:93:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 93 | void verboseDot() | ^~~~~~~~~~ ucsc/verbose.c:125:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 125 | FILE *verboseLogFile() | ^~~~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/os.c -o ucsc/os.o In file included from ucsc/osunix.c:6, from ucsc/os.c:7: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ In file included from ucsc/osunix.c:12: ucsc/portable.h:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 50 | char *getCurrentDir(); | ^~~~ ucsc/portable.h:74:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 74 | long clock1000(); | ^~~~ ucsc/portable.h:80:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 80 | long clock1(); | ^~~~ ucsc/portable.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 105 | char *cgiDir(); | ^~~~ ucsc/portable.h:108:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 108 | char *trashDir(); | ^~~~ ucsc/portable.h:114:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 114 | double machineSpeed(); | ^~~~~~ ucsc/portable.h:117:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 117 | char *mysqlHost(); | ^~~~ ucsc/portable.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 120 | char *getHost(); | ^~~~ ucsc/portable.h:123:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 123 | void uglyfBreak(); | ^~~~ ucsc/portable.h:126:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 126 | char *getUser(); | ^~~~ ucsc/portable.h:132:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 132 | int mustFork(); | ^~~ ucsc/portable.h:135:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 135 | int rawKeyIn(); | ^~~ In file included from ucsc/osunix.c:13: ucsc/portimpl.h:19:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 19 | char * (*cgiDir)(); | ^~~~ ucsc/portimpl.h:27:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 27 | double (*speed)(); | ^~~~~~ ucsc/portimpl.h:30:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 30 | char * (*trashDir)(); | ^~~~ ucsc/osunix.c:36:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 36 | long clock1000() | ^~~~~~~~~ ucsc/osunix.c:59:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 59 | long clock1() | ^~~~~~ ucsc/osunix.c:67:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 67 | void uglyfBreak() | ^~~~~~~~~~ ucsc/osunix.c:74:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 74 | char *getCurrentDir() | ^~~~~~~~~~~~~ ucsc/osunix.c:244:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 244 | char *getHost() | ^~~~~~~ ucsc/osunix.c:274:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 274 | char *mysqlHost() | ^~~~~~~~~ ucsc/osunix.c:471:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 471 | char *getUser() | ^~~~~~~ ucsc/osunix.c:481:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 481 | int mustFork() | ^~~~~~~~ ucsc/osunix.c:490:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 490 | int rawKeyIn() | ^~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ucsc/wildcmp.c -o ucsc/wildcmp.o In file included from ucsc/wildcmp.c:6: ucsc/common.h:310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 310 | void verboseDot(); | ^~~~ ucsc/common.h:313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 313 | int verboseLevel(); | ^~~ ucsc/common.h:426:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 426 | void slUniqify(void *pList, CmpFunction *compare, void (*free)()); | ^~~~ ucsc/common.h:435:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 435 | void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); | ^~~~ gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o CNEr.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lz -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpzq8yLp/R.INSTALLa57029fa7d81/CNEr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-CNEr/00new/CNEr/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 (CNEr) begin installing package ‘TFBSTools’ * installing *source* package ‘ensembldb’ ... ** package ‘ensembldb’ successfully unpacked and MD5 sums checked ** 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) * installing *source* package ‘VariantAnnotation’ ... ** package ‘VariantAnnotation’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHMCBXA/R.INSTALLa57283df4e6d5/VariantAnnotation/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IRanges_stubs.c -o IRanges_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o In file included from vcftype.h:8, from writevcf.h:4, from R_init_VariantAnnotation.c:3: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dna_hash.c -o dna_hash.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rle.c -o rle.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c strhash.c -o strhash.o In file included from strhash.c:2: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ strhash.c:5:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 5 | khash_t(strhash) *_strhash_new() | ^~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utilities.c -o utilities.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcffile.c -o vcffile.o In file included from vcftype.h:8, from vcffile.c:4: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ vcffile.c:22:27: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 22 | static khash_t(WARNINGS) *vcfwarn_new() | ^~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcftype.c -o vcftype.o In file included from vcftype.h:8, from vcftype.c:1: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c writevcf.c -o writevcf.o In file included from vcftype.h:8, from writevcf.h:4, from writevcf.c:1: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHMCBXA/R.INSTALLa57283df4e6d5/VariantAnnotation/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’ ** 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 (VariantAnnotation) begin installing package ‘biovizBase’ * installing *source* package ‘BSgenome.Hsapiens.UCSC.hg19’ ... ** 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 (BSgenome.Hsapiens.UCSC.hg19) * installing *source* package ‘OrganismDbi’ ... ** package ‘OrganismDbi’ 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 (OrganismDbi) * installing *source* package ‘TFBSTools’ ... ** package ‘TFBSTools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjsuLn7/R.INSTALLa64ff709c606a/TFBSTools/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o matrixAlignerDynamic.c: In function ‘score’: matrixAlignerDynamic.c:235:22: warning: ‘best_pntr’ may be used uninitialized [-Wmaybe-uninitialized] 235 | while (current_pntr->father != NULL){ // while the father of the current pointer exists, walk through the best posible alignment | ~~~~~~~~~~~~^~~~~~~~ matrixAlignerDynamic.c:115:17: note: ‘best_pntr’ was declared here 115 | struct entry *best_pntr; // pointer to the best entry so far | ^~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_TFBSTools.c -o R_init_TFBSTools.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjsuLn7/R.INSTALLa64ff709c606a/TFBSTools/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TFBSTools/00new/TFBSTools/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘seqLogo’ in package ‘TFBSTools’ Creating a generic function for ‘colSums’ from package ‘base’ in package ‘TFBSTools’ Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘TFBSTools’ ** 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 (TFBSTools) begin installing package ‘motifmatchr’ begin installing package ‘chromVAR’ * installing *source* package ‘biovizBase’ ... ** package ‘biovizBase’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmplB6Nyw/R.INSTALLa6614167a368e/biovizBase/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_biovizBase.c -o R_init_biovizBase.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bin_offsets.c -o bin_offsets.o bin_offsets.c: In function ‘scan_bam_bin_offsets’: bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign] 57 | if (strncmp(b, "BAI\1", 4)) | ^ | | | Rbyte * {aka unsigned char *} In file included from /home/hornik/tmp/R-d-gcc-14/include/R_ext/RS.h:34, from /home/hornik/tmp/R-d-gcc-14/include/Rdefines.h:38, from bin_offsets.h:1, from bin_offsets.c:3: /usr/include/string.h:159:33: note: expected ‘const char *’ but argument is of type ‘Rbyte *’ {aka ‘unsigned char *’} 159 | extern int strncmp (const char *__s1, const char *__s2, size_t __n) | ~~~~~~~~~~~~^~~~ gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmplB6Nyw/R.INSTALLa6614167a368e/biovizBase/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-biovizBase/00new/biovizBase/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 (biovizBase) begin installing package ‘ggbio’ * installing *source* package ‘motifmatchr’ ... ** package ‘motifmatchr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpChZ0ca/R.INSTALLa66a467bdd2c5/motifmatchr/src' g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/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++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c r_interface.cpp -o r_interface.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/scanner.cpp -o MOODS/scanner.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/motif_h.cpp -o MOODS/motif_h.o MOODS/motif_h.cpp: In member function ‘std::vector MOODS::scan::MotifH::expected_scores(const std::vector&)’: MOODS/motif_h.cpp:26:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 26 | for (int i = 0; i < cols; ++i){ | ~~^~~~~~ MOODS/motif_h.cpp:27:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 27 | for (int j = 0; j < rows; ++j){ | ~~^~~~~~ MOODS/motif_h.cpp: In member function ‘virtual std::pair MOODS::scan::MotifH::check_hit(const std::string&, const std::vector&, std::size_t, double)’: MOODS/motif_h.cpp:256:25: warning: suggest parentheses around arithmetic in operand of ‘^’ [-Wparentheses] 256 | CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]]; | ~~~~~^~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/motif_0.cpp -o MOODS/motif_0.o MOODS/motif_0.cpp: In function ‘std::vector MOODS::scan::expected_differences(const score_matrix&, const std::vector&)’: MOODS/motif_0.cpp:28:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 28 | for (int i = 0; i < m; ++i) | ~~^~~ MOODS/motif_0.cpp:31:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 31 | for (int j = 0; j < a; ++j) | ~~^~~ MOODS/motif_0.cpp:38:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 38 | for (int j = 0; j < a; ++j) | ~~^~~ MOODS/motif_0.cpp: In function ‘unsigned int MOODS::scan::window_position(const std::vector&, unsigned int, unsigned int)’: MOODS/motif_0.cpp:64:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 64 | for (int i = 0; i < m - l; ++i) | ~~^~~~~~~ MOODS/motif_0.cpp: In function ‘std::vector MOODS::scan::compute_lookahead_order(const std::vector&, unsigned int, unsigned int, unsigned int)’: MOODS/motif_0.cpp:96:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 96 | for (int i = 0; i < window_pos; ++i) | ~~^~~~~~~~~~~~ MOODS/motif_0.cpp:100:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 100 | for (int i = window_pos+l; i < m; ++i) | ~~^~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o MOODS/moods_tools.cpp: In function ‘double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector&, const double&)’: MOODS/moods_tools.cpp:155:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 155 | for (size_t i = 0; i < n; ++i) | ~~^~~ MOODS/moods_tools.cpp:157:30: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 157 | for (size_t j = 0; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp:168:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 168 | for (size_t i = 0; i < n; ++i) | ~~^~~ MOODS/moods_tools.cpp:172:30: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 172 | for (size_t j = 1; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp:190:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 190 | for (size_t j = 0; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 193 | for (size_t i = 1; i < n; ++i) | ~~^~~ MOODS/moods_tools.cpp:195:30: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 195 | for (size_t j = 0; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp: In function ‘score_matrix MOODS::tools::log_odds(const std::vector >&, const std::vector >&, const std::vector&, double, std::size_t)’: MOODS/moods_tools.cpp:320:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 320 | for (size_t PCODE = 0; PCODE < 1 << (SHIFT * r); ++PCODE ){ | ~~~~~~^~~~~~~~~~~~~~~~~~ MOODS/moods_tools.cpp:328:46: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 328 | for (size_t SCODE = 0; SCODE < 1 << (SHIFT * (q - r - 1)); ++SCODE){ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ MOODS/moods_tools.cpp: In function ‘double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector&, const double&, std::size_t)’: MOODS/moods_tools.cpp:454:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 454 | for (size_t i = 0; i < cols; ++i) | ~~^~~~~~ MOODS/moods_tools.cpp:456:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 456 | for (size_t CODE = 0; CODE < rows; ++CODE) | ~~~~~^~~~~~ MOODS/moods_tools.cpp:468:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 468 | for (size_t i = 0; i < cols; ++i) | ~~^~~~~~ MOODS/moods_tools.cpp:472:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 472 | for (size_t CODE = 1; CODE < rows; ++CODE) | ~~~~~^~~~~~ MOODS/moods_tools.cpp:489:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 489 | for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE){ | ~~~~~^~~~~~~~~~~~~~~~~~~~ MOODS/moods_tools.cpp:500:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 500 | for (size_t i = 1; i < cols; ++i) | ~~^~~~~~ MOODS/moods_tools.cpp:503:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 503 | for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE) | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o MOODS/moods_scan.cpp: In function ‘std::vector > MOODS::scan::scan_best_hits_dna(const std::string&, const std::vector > >&, std::size_t, int, unsigned int, std::size_t, std::size_t)’: MOODS/moods_scan.cpp:97:14: warning: unused variable ‘done’ [-Wunused-variable] 97 | bool done = 0; | ^~~~ MOODS/moods_scan.cpp: In function ‘std::vector MOODS::scan::naive_scan_dna(const std::string&, score_matrix, double, std::size_t)’: MOODS/moods_scan.cpp:252:33: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 252 | CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]]; | ~~~~~^~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/match_types.cpp -o MOODS/match_types.o g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o motifmatchr.so ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpChZ0ca/R.INSTALLa66a467bdd2c5/motifmatchr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-motifmatchr/00new/motifmatchr/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 (motifmatchr) * installing *source* package ‘chromVAR’ ... ** package ‘chromVAR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpxUTIZN/R.INSTALLa66a645d5365f/chromVAR/src' g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/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++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwm_similarity.cpp -o pwm_similarity.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -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 utils.cpp: In function ‘Rcpp::NumericVector row_sds(arma::mat&, bool)’: utils.cpp:12:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 12 | for( int j=0; j < X.n_rows; j++ ) { | ~~^~~~~~~~~~ g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpxUTIZN/R.INSTALLa66a645d5365f/chromVAR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-chromVAR/00new/chromVAR/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 (chromVAR) * installing *source* package ‘ggbio’ ... ** package ‘ggbio’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'rescale' in package 'ggbio' Creating a new generic function for 'xlim' in package 'ggbio' Creating a new generic function for 'geom_rect' in package 'ggbio' Creating a new generic function for 'geom_segment' in package 'ggbio' Creating a new generic function for 'geom_bar' in package 'ggbio' Creating a new generic function for 'stat_identity' in package 'ggbio' Creating a new generic function for 'stat_bin' in package 'ggbio' ** 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 (ggbio) checking waldo_0.6.0.tar.gz ... checking CDMConnector_1.5.0.tar.gz ... checking constructive_1.0.1.tar.gz ... checking testthat_3.2.1.1.tar.gz ... checking typed_0.0.1.tar.gz ... checking airGRiwrm_0.7.0.tar.gz ... checking corrtable_0.1.1.tar.gz ... checking bmm_1.0.1.tar.gz ... checking crosstable_0.8.1.tar.gz ... checking dm_1.0.10.tar.gz ... checking dtplyr_1.3.1.tar.gz ... checking geosapi_0.7-1.tar.gz ... checking ggside_0.3.1.tar.gz ... checking glue_1.8.0.tar.gz ... checking HDShOP_0.1.5.tar.gz ... checking ibawds_1.0.0.tar.gz ... checking knitxl_0.1.0.tar.gz ... checking latex2exp_0.9.6.tar.gz ... checking mark_0.8.1.tar.gz ... checking mixvlmc_0.2.1.tar.gz ... checking mlfit_0.5.3.tar.gz ... checking mlr3torch_0.1.2.tar.gz ... checking MOCHA_1.1.0.tar.gz ... checking openxlsx2_1.10.tar.gz ... checking petersenlab_1.0.0.tar.gz ... checking plume_0.2.5.tar.gz ... checking readr_2.1.5.tar.gz ... checking renv_1.0.11.tar.gz ... checking vroom_1.6.5.tar.gz ... checking Require_1.0.1.tar.gz ... checking tidyUSDA_0.4.1.tar.gz ... checking vctrs_0.6.5.tar.gz ... checking srppp_1.0.1.tar.gz ... Depends: Package: waldo Depends: R (>= 4.0) Imports: cli, diffobj (>= 0.3.4), glue, methods, rlang (>= 1.1.0) Timings: user system elapsed waldo 44.869 4.128 49.865 Results: Check status summary: ERROR NOTE OK Source packages 0 0 1 Reverse depends 1 8 23 Check results summary: waldo ... OK rdepends_airGRiwrm ... OK rdepends_bmm ... NOTE * checking Rd cross-references ... NOTE rdepends_CDMConnector ... OK rdepends_constructive ... OK rdepends_corrtable ... OK rdepends_crosstable ... OK rdepends_dm ... ERROR * checking Rd cross-references ... NOTE * checking tests ... [102s/52s] ERROR rdepends_dtplyr ... NOTE * checking Rd cross-references ... NOTE rdepends_geosapi ... NOTE * checking Rd cross-references ... NOTE rdepends_ggside ... NOTE * checking Rd cross-references ... NOTE rdepends_glue ... OK rdepends_HDShOP ... OK rdepends_ibawds ... OK rdepends_knitxl ... OK rdepends_latex2exp ... OK rdepends_mark ... OK rdepends_mixvlmc ... OK rdepends_mlfit ... OK rdepends_mlr3torch ... OK rdepends_MOCHA ... OK rdepends_openxlsx2 ... OK rdepends_petersenlab ... OK rdepends_plume ... OK rdepends_readr ... NOTE * checking Rd cross-references ... NOTE * checking compiled code ... NOTE rdepends_renv ... OK rdepends_Require ... OK rdepends_srppp ... OK rdepends_testthat ... NOTE * checking compiled code ... NOTE rdepends_tidyUSDA ... OK rdepends_typed ... OK rdepends_vctrs ... NOTE * checking compiled code ... NOTE rdepends_vroom ... NOTE * checking compiled code ... NOTE Check results changes: Package: dm Check: tests New result: ERROR