downloading reverse dependencies ‘dynafluxr’, ‘fmriqa’, ‘numbat’, ‘plinkQC’, ‘REPTILE’, ‘RIbench’, ‘artma’, ‘enveomics.R’, ‘geeLite’, ‘gwas2crispr’, ‘rbiom’, ‘SQLFormatteR’, ‘TexExamRandomizer’, ‘twbparser’, ‘VIProDesign’, ‘W4MRUtils’ trying URL 'file:///data/Repositories/CRAN/src/contrib/dynafluxr_1.0.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/fmriqa_0.5.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/numbat_1.5.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/plinkQC_1.1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/REPTILE_1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/RIbench_1.0.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/artma_0.3.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/enveomics.R_1.10.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/geeLite_1.0.6.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/gwas2crispr_0.1.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/rbiom_2.2.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/SQLFormatteR_0.0.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/TexExamRandomizer_1.2.7.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/twbparser_0.3.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/VIProDesign_0.1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/W4MRUtils_1.2.1.tar.gz' installing dependencies ‘arrApply’, ‘BMS’, ‘box.linters’, ‘BSgenome.Hsapiens.UCSC.hg38’, ‘bspline’, ‘climenu’, ‘DECIPHER’, ‘fillpattern’, ‘flux’, ‘ggdensity’, ‘gmresls’, ‘gwasrapidd’, ‘h3jsr’, ‘hahmmr’, ‘investr’, ‘ivmodel’, ‘languageserver’, ‘MAIVE’, ‘nlsic’, ‘optparse’, ‘pathviewr’, ‘precommit’, ‘prettycode’, ‘rddensity’, ‘rextendr’, ‘rgee’, ‘scistreer’, ‘tsne’ also installing the dependency ‘lpdensity’ begin installing package ‘lpdensity’ begin installing package ‘nlsic’ begin installing package ‘arrApply’ begin installing package ‘gmresls’ begin installing package ‘hahmmr’ begin installing package ‘scistreer’ begin installing package ‘flux’ begin installing package ‘climenu’ begin installing package ‘BMS’ begin installing package ‘box.linters’ begin installing package ‘ivmodel’ begin installing package ‘languageserver’ begin installing package ‘MAIVE’ begin installing package ‘investr’ begin installing package ‘h3jsr’ begin installing package ‘rgee’ begin installing package ‘gwasrapidd’ begin installing package ‘BSgenome.Hsapiens.UCSC.hg38’ begin installing package ‘fillpattern’ begin installing package ‘ggdensity’ begin installing package ‘prettycode’ begin installing package ‘tsne’ begin installing package ‘rextendr’ begin installing package ‘precommit’ begin installing package ‘DECIPHER’ begin installing package ‘pathviewr’ begin installing package ‘optparse’ * installing *source* package ‘gmresls’ ... ** this is package ‘gmresls’ version ‘0.2.3’ ** package ‘gmresls’ 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 (gmresls) * installing *source* package ‘tsne’ ... ** this is package ‘tsne’ version ‘0.2-0’ ** package ‘tsne’ 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 (tsne) * installing *source* package ‘prettycode’ ... ** this is package ‘prettycode’ version ‘1.1.0’ ** 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) * installing *source* package ‘climenu’ ... ** this is package ‘climenu’ version ‘0.1.5’ ** package ‘climenu’ 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 (climenu) * installing *source* package ‘optparse’ ... ** this is package ‘optparse’ version ‘1.8.1’ ** using staged installation ** R ** exec ** 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 (optparse) * installing *source* package ‘investr’ ... ** this is package ‘investr’ version ‘1.4.2’ ** package ‘investr’ 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 (investr) * installing *source* package ‘precommit’ ... ** this is package ‘precommit’ version ‘0.4.3’ ** package ‘precommit’ 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 (precommit) * installing *source* package ‘MAIVE’ ... ** this is package ‘MAIVE’ version ‘0.2.4’ ** package ‘MAIVE’ 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 (MAIVE) * installing *source* package ‘nlsic’ ... ** this is package ‘nlsic’ version ‘1.2.0’ ** package ‘nlsic’ 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 (nlsic) * installing *source* package ‘box.linters’ ... ** this is package ‘box.linters’ version ‘0.10.7’ ** package ‘box.linters’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ! The packages {treesitter} and {treesitter.r} are required by namespaced_function_calls(). Please install these packages if you want to use namespaced_function_calls(). They require R version >= 4.3.0. ! The packages {treesitter} and {treesitter.r} are required by namespaced_function_calls(). Please install these packages if you want to use namespaced_function_calls(). They require R version >= 4.3.0. ** 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 (box.linters) * installing *source* package ‘flux’ ... ** this is package ‘flux’ version ‘0.3-0.1’ ** package ‘flux’ 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 (flux) * installing *source* package ‘pathviewr’ ... ** this is package ‘pathviewr’ version ‘1.1.8’ ** package ‘pathviewr’ 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 (pathviewr) * installing *source* package ‘fillpattern’ ... ** this is package ‘fillpattern’ version ‘1.0.3’ ** package ‘fillpattern’ successfully unpacked and MD5 sums checked ** 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 (fillpattern) * installing *source* package ‘ggdensity’ ... ** this is package ‘ggdensity’ version ‘1.0.1’ ** package ‘ggdensity’ 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 (ggdensity) * installing *source* package ‘h3jsr’ ... ** this is package ‘h3jsr’ version ‘1.3.1’ ** package ‘h3jsr’ 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 (h3jsr) * installing *source* package ‘gwasrapidd’ ... ** this is package ‘gwasrapidd’ version ‘0.99.18’ ** package ‘gwasrapidd’ 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 (gwasrapidd) * installing *source* package ‘rextendr’ ... ** this is package ‘rextendr’ version ‘0.4.2’ ** package ‘rextendr’ 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 (rextendr) * installing *source* package ‘lpdensity’ ... ** this is package ‘lpdensity’ version ‘2.5’ ** package ‘lpdensity’ 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 (lpdensity) begin installing package ‘rddensity’ * installing *source* package ‘BMS’ ... ** this is package ‘BMS’ version ‘0.3.5’ ** package ‘BMS’ 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 (BMS) * installing *source* package ‘ivmodel’ ... ** this is package ‘ivmodel’ version ‘1.9.1’ ** package ‘ivmodel’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ivmodel) * installing *source* package ‘rddensity’ ... ** this is package ‘rddensity’ version ‘2.6’ ** package ‘rddensity’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rddensity) * installing *source* package ‘languageserver’ ... ** this is package ‘languageserver’ version ‘0.3.17’ ** package ‘languageserver’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpIx8lSQ/R.INSTALL37524f62043045/languageserver/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c encoding.c -o encoding.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fsm.c -o fsm.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c languageserver.c -o languageserver.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c match.c -o match.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c reader.c -o reader.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c search.c -o search.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c semantic.c -o semantic.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stack.c -o stack.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c token.c -o token.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o languageserver.so encoding.o fsm.o languageserver.o match.o reader.o search.o semantic.o stack.o token.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpIx8lSQ/R.INSTALL37524f62043045/languageserver/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-languageserver/00new/languageserver/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 (languageserver) * installing *source* package ‘rgee’ ... ** this is package ‘rgee’ version ‘1.1.8’ ** package ‘rgee’ 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 (rgee) * installing *source* package ‘arrApply’ ... ** this is package ‘arrApply’ version ‘2.2.1’ ** package ‘arrApply’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpjnbr8m/R.INSTALL37521a60654160/arrApply/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 arrApply.cpp -o arrApply.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o arrApply.so RcppExports.o arrApply.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpjnbr8m/R.INSTALL37521a60654160/arrApply/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-arrApply/00new/arrApply/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 (arrApply) begin installing package ‘bspline’ * installing *source* package ‘scistreer’ ... ** this is package ‘scistreer’ version ‘1.2.1’ ** package ‘scistreer’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphoOO7j/R.INSTALL37522c68d7c706/scistreer/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c scistreer.cpp -o scistreer.o scistreer.cpp: In function ‘std::vector > > allChildrenCPP(arma::Mat)’: scistreer.cpp:22:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare] 22 | for(int i = 0; i reorder_rows(arma::Mat, arma::Col)’: scistreer.cpp:52:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 52 | for (int i = 0; i < y.n_elem; ++i) { | ~~^~~~~~~~~~ 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o scistreer.so RcppExports.o scistreer.o -lpthread -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphoOO7j/R.INSTALL37522c68d7c706/scistreer/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-scistreer/00new/scistreer/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 (scistreer) * installing *source* package ‘bspline’ ... ** this is package ‘bspline’ version ‘2.5.1’ ** package ‘bspline’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpKhr1TT/R.INSTALL37586a3c8db7c9/bspline/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 bspline.cpp -o bspline.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o bspline.so RcppExports.o bspline.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpKhr1TT/R.INSTALL37586a3c8db7c9/bspline/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-bspline/00new/bspline/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 (bspline) * installing *source* package ‘hahmmr’ ... ** this is package ‘hahmmr’ version ‘1.0.0’ ** package ‘hahmmr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpoSTJNJ/R.INSTALL37522d3ffd22f0/hahmmr/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c bbinom.cpp -o bbinom.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c hmm.cpp -o hmm.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c misc.cpp -o misc.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c mle.cpp -o mle.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c poilog.cpp -o poilog.o 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o hahmmr.so RcppExports.o bbinom.o hmm.o misc.o mle.o poilog.o -lpthread -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpoSTJNJ/R.INSTALL37522d3ffd22f0/hahmmr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-hahmmr/00new/hahmmr/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 (hahmmr) * installing *source* package ‘BSgenome.Hsapiens.UCSC.hg38’ ... ** this is package ‘BSgenome.Hsapiens.UCSC.hg38’ version ‘1.4.5’ ** 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.hg38) * installing *source* package ‘DECIPHER’ ... ** this is package ‘DECIPHER’ version ‘3.7.1’ ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpBlA6sS/R.INSTALL375283f52b1ae/DECIPHER/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c AlignProfiles.c -o AlignProfiles.o AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’: AlignProfiles.c:438:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized] 438 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:62:51: note: ‘lGs’ was declared here 62 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c:436:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized] 436 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:62:46: note: ‘lGp’ was declared here 62 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’: AlignProfiles.c:1291:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized] 1291 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:820:51: note: ‘lGs’ was declared here 820 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c:1289:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized] 1289 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:820:46: note: ‘lGp’ was declared here 820 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c: In function ‘alignProfiles’: AlignProfiles.c:82:17: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized] 82 | double *subM; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c AssignIndels.c -o AssignIndels.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c CalculateDeltaG.c -o CalculateDeltaG.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c CalculateFISH.c -o CalculateFISH.o CalculateFISH.c: In function ‘calculateFISH’: CalculateFISH.c:25:30: warning: missing braces around initializer [-Wmissing-braces] 25 | double dH_DR[4][4] = { | ^ 26 | -11.5, -7.8, -7, -8.3, | { } 27 | -10.4, -12.8, -16.3, -9.1, | { } 28 | -8.6, -8, -9.3, -5.9, | { } 29 | -7.8, -5.5, -9, -7.8 | { 30 | }; | } CalculateFISH.c:31:30: warning: missing braces around initializer [-Wmissing-braces] 31 | double dS_DR[4][4] = { | ^ 32 | -36.4, -21.6, -19.7, -23.9, | { } 33 | -28.4, -31.9, -47.1, -23.5, | { } 34 | -22.9, -17.1, -23.2, -12.3, | { } 35 | -23.2, -13.5, -26.1, -21.9 | { 36 | }; | } CalculateFISH.c:37:30: warning: missing braces around initializer [-Wmissing-braces] 37 | double dH_DD[4][4] = { | ^ 38 | -7.9, -8.4, -7.8, -7.2, | { } 39 | -8.5, -8, -10.6, -7.8, | { } 40 | -8.2, -9.8, -8, -8.4, | { } 41 | -7.2, -8.2, -8.5, -7.9 | { 42 | }; | } CalculateFISH.c:43:30: warning: missing braces around initializer [-Wmissing-braces] 43 | double dS_DD[4][4] = { | ^ 44 | -22.2, -22.4, -21, -20.4, | { } 45 | -22.7, -19.9, -27.2, -21, | { } 46 | -22.2, -24.4, -19.9, -22.4, | { } 47 | -21.3, -22.2, -22.7, -22.2 | { 48 | }; | } CalculateFISH.c:49:30: warning: missing braces around initializer [-Wmissing-braces] 49 | double dH_RR[4][4] = { | ^ 50 | -6.6, -10.17, -7.65, -5.76, | { } 51 | -10.56, -12.21, -7.95, -7.65, | { } 52 | -13.37, -14.21, -12.21, -10.17, | { } 53 | -8.11, -13.37, -10.56, -6.6 | { 54 | }; | } CalculateFISH.c:55:30: warning: missing braces around initializer [-Wmissing-braces] 55 | double dS_RR[4][4] = { | ^ 56 | -18.38, -26.03, -19.18, -15.67, | { } 57 | -28.25, -30.02, -19.18, -19.18, | { } 58 | -35.68, -34.85, -30.02, -26.03, | { } 59 | -22.59, -35.68, -28.25, -18.38 | { 60 | }; | } gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ChainSegments.c -o ChainSegments.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Cluster.c -o Cluster.o Cluster.c: In function ‘cluster._omp_fn.0’: Cluster.c:439:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 439 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: ‘minC’ was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function ‘cluster._omp_fn.1’: Cluster.c:469:50: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 469 | minCs[i] = minC; | ~~~~~~~~~^~~~~~ Cluster.c:246:57: note: ‘minC’ was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function ‘cluster._omp_fn.2’: Cluster.c:493:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 493 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: ‘minC’ was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function ‘cluster’: Cluster.c:277:14: warning: ‘minCols’ may be used uninitialized [-Wmaybe-uninitialized] 277 | int *minCols; | ^~~~~~~ Cluster.c:916:43: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 916 | *rPercentComplete = floor(100*soFar/total); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ Cluster.c:248:25: note: ‘rPercentComplete’ was declared here 248 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ Cluster.c:916:45: warning: ‘total’ may be used uninitialized [-Wmaybe-uninitialized] 916 | *rPercentComplete = floor(100*soFar/total); | ^~~~~~~~~~~~~~~~~~~~~~ Cluster.c:249:23: note: ‘total’ was declared here 249 | double soFar, total, minHeight, *cut, *rans, *distanceMatrix, minH; | ^~~~~ In file included from /home/hornik/tmp/R-d-gcc-15/include/Rdefines.h:41, from Cluster.c:11: /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:916:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 916 | #define eval Rf_eval Cluster.c:920:33: note: in expansion of macro ‘eval’ 920 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ Cluster.c:250:36: note: ‘utilsPackage’ was declared here 250 | SEXP ans, percentComplete, utilsPackage; | ^~~~~~~~~~~~ /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:916:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 916 | #define eval Rf_eval Cluster.c:920:33: note: in expansion of macro ‘eval’ 920 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ Cluster.c:250:19: note: ‘percentComplete’ was declared here 250 | SEXP ans, percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ Cluster.c:283:17: warning: ‘nDiv’ may be used uninitialized [-Wmaybe-uninitialized] 283 | double *nDiv; | ^~~~ Cluster.c:413:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 413 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: ‘minC’ was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ClusterME.c -o ClusterME.o ClusterME.c: In function ‘clusterME’: ClusterME.c:311:101: warning: ‘LLRL’ may be used uninitialized [-Wmaybe-uninitialized] 311 | subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac | ~~~~~^~~~~~ ClusterME.c:273:24: note: ‘LLRL’ was declared here 273 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:311:101: warning: ‘LRRL’ may be used uninitialized [-Wmaybe-uninitialized] 311 | subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac | ~~~~~^~~~~~ ClusterME.c:273:30: note: ‘LRRL’ was declared here 273 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:312:101: warning: ‘LLRR’ may be used uninitialized [-Wmaybe-uninitialized] 312 | subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc | ~~~~~^~~~~~ ClusterME.c:273:36: note: ‘LLRR’ was declared here 273 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:312:101: warning: ‘LRRR’ may be used uninitialized [-Wmaybe-uninitialized] 312 | subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc | ~~~~~^~~~~~ ClusterME.c:273:42: note: ‘LRRR’ was declared here 273 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ClusterML.c -o ClusterML.o ClusterML.c: In function ‘clusterML’: ClusterML.c:1913:17: warning: ‘node’ may be used uninitialized [-Wmaybe-uninitialized] 1913 | double *node; | ^~~~ ClusterML.c:1959:14: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 1959 | int *Up; | ^~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ClusterMP.c -o ClusterMP.o ClusterMP.c: In function ‘clusterMP._omp_fn.0’: ClusterMP.c:190:71: warning: ‘temp_nodes’ may be used uninitialized [-Wmaybe-uninitialized] 190 | temp_nodes[j] = 0; | ~~~~~~~~~~~~~~^~~ ClusterMP.c:163:34: note: ‘temp_nodes’ was declared here 163 | int *temp_subM, *temp_nodes; | ^~~~~~~~~~ ClusterMP.c:465:49: warning: ‘temp_lengths’ may be used uninitialized [-Wmaybe-uninitialized] 465 | *(temp_lengths + j) += *(S + w*c + m)*weight; | ^~~~~~~~~~~~~~~~~~~ ClusterMP.c:162:38: note: ‘temp_lengths’ was declared here 162 | double *temp_score, *temp_lengths; | ^~~~~~~~~~~~ ClusterMP.c:485:73: warning: ‘temp_subM’ may be used uninitialized [-Wmaybe-uninitialized] 485 | *(temp_subM + c*m + w - 1) += weight; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ClusterMP.c:163:22: note: ‘temp_subM’ was declared here 163 | int *temp_subM, *temp_nodes; | ^~~~~~~~~ ClusterMP.c:202:49: warning: ‘P’ may be used uninitialized [-Wmaybe-uninitialized] 202 | allStates(R, P, S, c, j, 0, k - 1, 0, k - 1, c, only); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ClusterMP.c:185:38: note: ‘P’ was declared here 185 | int *P; | ^ ClusterMP.c:385:61: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 385 | *(R + 3*c*n + m) = 0; | ^ ClusterMP.c:105:22: note: ‘m’ was declared here 105 | int i, j, k, m, w; | ^ ClusterMP.c: In function ‘clusterMP’: ClusterMP.c:159:17: warning: ‘lengths’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:128:17: note: ‘lengths’ was declared here 128 | double *lengths, *score; | ^~~~~~~ ClusterMP.c:159:17: warning: ‘nodes’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:129:20: note: ‘nodes’ was declared here 129 | int size, *nodes, *subM; | ^~~~~ ClusterMP.c:159:17: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:129:28: note: ‘subM’ was declared here 129 | int size, *nodes, *subM; | ^~~~ ClusterMP.c:159:17: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:145:14: note: ‘Up’ was declared here 145 | int *Up; | ^~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Compositions.c -o Compositions.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Compression.c -o Compression.o Compression.c: In function ‘nbit._omp_fn.0’: Compression.c:1242:71: warning: ‘lastTriplet’ may be used uninitialized [-Wmaybe-uninitialized] 1242 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) { | ~~~^~~~~~~~~~~~~~ Compression.c:632:26: note: ‘lastTriplet’ was declared here 632 | int run, lastTriplet, lastCase; | ^~~~~~~~~~~ Compression.c:1012:62: warning: ‘word’ may be used uninitialized [-Wmaybe-uninitialized] 1012 | word = (word << 8) | (unsigned int)reorder(byte); | ~~~~~~^~~~~ Compression.c:545:37: note: ‘word’ was declared here 545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ Compression.c:1013:54: warning: ‘count’ may be used uninitialized [-Wmaybe-uninitialized] 1013 | count++; | ~~~~~^~ Compression.c:545:43: note: ‘count’ was declared here 545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~ Compression.c:1215:56: warning: ‘rev’ may be used uninitialized [-Wmaybe-uninitialized] 1215 | p[c++] = rev == 0 ? 254 : 255; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ Compression.c:546:41: note: ‘rev’ was declared here 546 | int lastTemp, currTemp, rev, len, len2, thresh = 1; | ^~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ConsensusSequence.c -o ConsensusSequence.o In function ‘runsAA’, inlined from ‘consensusProfileAA’ at ConsensusSequence.c:1836:3: ConsensusSequence.c:454:50: warning: ‘lastPos’ may be used uninitialized [-Wmaybe-uninitialized] 454 | if (lastGap < (s - 2)) // ensure continuity before the run | ~~~^~~~ ConsensusSequence.c: In function ‘consensusProfileAA’: ConsensusSequence.c:397:30: note: ‘lastPos’ was declared here 397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1; | ^~~~~~~ ConsensusSequence.c: In function ‘colScores’: ConsensusSequence.c:2043:19: warning: ‘curr’ may be used uninitialized [-Wmaybe-uninitialized] 2043 | if (tGaps && curr > 0) { | ~~~~~~^~~~~~~~~~~ ConsensusSequence.c:1930:37: note: ‘curr’ was declared here 1930 | double weight, total, prev, curr; | ^~~~ ConsensusSequence.c: In function ‘colScoresAA’: ConsensusSequence.c:2186:19: warning: ‘curr’ may be used uninitialized [-Wmaybe-uninitialized] 2186 | if (tGaps && curr > 0) { | ~~~~~~^~~~~~~~~~~ ConsensusSequence.c:2073:37: note: ‘curr’ was declared here 2073 | double weight, total, prev, curr; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c DesignProbes.c -o DesignProbes.o DesignProbes.c: In function ‘designProbes’: DesignProbes.c:71:27: warning: missing braces around initializer [-Wmissing-braces] 71 | double NN[4][4] = { | ^ 72 | -0.816507461,-2.5401714,-1.647430026,-1.184658548 | { 73 | ,-1.854740485,-2.479102613,-2.826248182,-1.647430026 | }{ 74 | ,-2.48761723,-4.694133177,-2.479102613,-2.5401714 | }{ 75 | ,-0.495794417,-2.48761723,-1.854740485,-0.816507461 | }{ 76 | }; | } DesignProbes.c:78:27: warning: missing braces around initializer [-Wmissing-braces] 78 | double PM[4][4] = { | ^ 79 | -0.141370102,-0.439805276,-0.285236035,-0.205111781 | { 80 | ,-0.321129768,-0.429231826,-0.48933661,-0.285236035 | }{ 81 | ,-0.430706047,-0.812742218,-0.429231826,-0.439805276 | }{ 82 | ,-0.085841845,-0.430706047,-0.321129768,-0.141370102 | }{ 83 | }; | } DesignProbes.c:85:34: warning: missing braces around initializer [-Wmissing-braces] 85 | double sMM[4][5][5][4] = { | ^ 86 | 0,0,0,0 | {{{ 87 | ,1.545032445,1.254355018,1.491691514,1.329138183 | }{ 88 | ,1.150635633,0.582415494,1.075877275,1.187937642 | }{ 89 | ,1.203555051,1.001540513,0.864287715,0.717125848 | }{ 90 | ,0.75,0.65,0.69,0.78 | }{ 91 | ,0.630005348,0.18553379,0.730763505,0.709272397 | - | }},{{ 92 | ,0,0,0,0 | }{ 93 | ,0.856582783,-0.143236405,0.716721488,0.603652831 | }{ 94 | ,0.851622883,0.653168672,0.676545316,1.187937642 | }{ 95 | ,0.75,0.65,0.69,0.78 | }{ 96 | ,1.231861002,0.746214538,1.087821916,0.989140748 | - | }},{{ 97 | ,1.822113278,1.270687029,1.336192565,1.364584949 | }{ 98 | ,0,0,0,0 | }{ 99 | ,1.443665704,1.385046493,1.256013166,1.329138183 | }{ 100 | ,0.75,0.65,0.69,0.78 | }{ 101 | ,1.478009492,0.882097231,1.20450984,1.061002478 | - | }},{{ 102 | ,1.496720812,0.846496194,0.967868114,0.989140748 | }{ 103 | ,0.766581547,-0.024857805,0.50754303,0.709272397 | }{ 104 | ,0,0,0,0 | }{ 105 | ,0.75,0.65,0.69,0.78 | }{ 106 | ,0.75,0.65,0.69,0.78 | - | }},{{ 107 | ,0.75,0.65,0.69,0.78 | }{ 108 | ,0.75,0.65,0.69,0.78 | }{ 109 | ,0.76,0.65,0.69,0.78 | }{ 110 | ,0,0,0,0 | }{ 111 | ,0,0,0,0 | - | }}},{{{ 112 | ,1.295827995,0.84547091,0.91019099,1.256013166 | }{ 113 | ,0.755889609,0.241428373,0.396379912,0.676545316 | }{ 114 | ,0.99945386,0.740323132,0.435659206,0.864287715 | }{ 115 | ,0.65,0.55,0.48,0.69 | }{ 116 | ,0.843147406,0.101248351,0.49063599,0.50754303 | - | }},{{ 117 | ,0,0,0,0 | }{ 118 | ,1.0651638,0.249934344,0.699352949,0.716721488 | }{ 119 | ,0.871921533,0.59458138,0.396379912,1.075877275 | }{ 120 | ,0.65,0.56,0.49,0.69 | }{ 121 | ,1.07531714,0.318907854,0.653287717,0.967868114 | - | }},{{ 122 | ,1.099899195,0.730184613,0.661798984,1.336192565 | }{ 123 | ,0,0,0,0 | }{ 124 | ,1.45897431,1.318532145,0.91019099,1.491691514 | }{ 125 | ,0.65,0.56,0.49,0.69 | }{ 126 | ,1.242135174,0.894838095,1.108555445,1.20450984 | - | }},{{ 127 | ,0.911428974,0.524430101,0.653287717,1.087821916 | }{ 128 | ,0.503209827,0.274849491,0.49063599,0.730763505 | }{ 129 | ,0,0,0,0 | }{ 130 | ,0.65,0.55,0.48,0.69 | }{ 131 | ,0.65,0.55,0.48,0.69 | - | }},{{ 132 | ,0.65,0.56,0.49,0.69 | }{ 133 | ,0.65,0.56,0.49,0.69 | }{ 134 | ,0.65,0.55,0.48,0.69 | }{ 135 | ,0,0,0,0 | }{ 136 | ,0,0,0,0 | - | }}},{{{ 137 | ,1.100661785,0.969784756,1.318532145,1.385046493 | }{ 138 | ,0.565895968,-0.060347902,0.59458138,0.653168672 | }{ 139 | ,0.782168488,0.788161238,0.740323132,1.001540513 | }{ 140 | ,0.68,0.46,0.55,0.65 | }{ 141 | ,0.468913405,-0.469855984,0.274849491,-0.024857805 | - | }},{{ 142 | ,0,0,0,0 | }{ 143 | ,0.258195131,-0.70438632,0.249934344,-0.143236405 | }{ 144 | ,0.502914193,-0.060347902,0.241428373,0.582415494 | }{ 145 | ,0.68,0.47,0.56,0.65 | }{ 146 | ,0.584083861,0.258975454,0.524430101,0.846496194 | - | }},{{ 147 | ,0.968040559,0.797499702,0.730184613,1.270687029 | }{ 148 | ,0,0,0,0 | }{ 149 | ,1.081040749,0.969784756,0.84547091,1.254355018 | }{ 150 | ,0.68,0.47,0.56,0.65 | }{ 151 | ,1.048553951,0.728354541,0.894838095,0.882097231 | - | }},{{ 152 | ,0.88611252,0.258975454,0.318907854,0.746214538 | }{ 153 | ,0.239520858,-0.469855984,0.101248351,0.18553379 | }{ 154 | ,0,0,0,0 | }{ 155 | ,0.68,0.46,0.55,0.65 | }{ 156 | ,0.68,0.46,0.55,0.65 | - | }},{{ 157 | ,0.68,0.47,0.56,0.65 | }{ 158 | ,0.68,0.47,0.56,0.65 | }{ 159 | ,0.68,0.46,0.55,0.65 | }{ 160 | ,0,0,0,0 | }{ 161 | ,0,0,0,0 | - | }}},{{{ 162 | ,1.566899704,1.081040749,1.45897431,1.443665704 | }{ 163 | ,0.976725675,0.502914193,0.871921533,0.851622883 | }{ 164 | ,1.482046826,0.782168488,0.99945386,1.203555051 | }{ 165 | ,0.85,0.68,0.65,0.76 | }{ 166 | ,0.798628781,0.239520858,0.503209827,0.766581547 | - | }},{{ 167 | ,0,0,0,0 | }{ 168 | ,1.141098246,0.258195131,1.0651638,0.856582783 | }{ 169 | ,0.976725675,0.565895968,0.755889609,1.150635633 | }{ 170 | ,0.85,0.68,0.65,0.75 | }{ 171 | ,1.125403302,0.88611252,0.911428974,1.496720812 | - | }},{{ 172 | ,1.68169282,0.968040559,1.099899195,1.822113278 | }{ 173 | ,0,0,0,0 | }{ 174 | ,1.566899704,1.100661785,1.295827995,1.545032445 | }{ 175 | ,0.85,0.68,0.65,0.75 | }{ 176 | ,1.35948517,1.048553951,1.242135174,1.478009492 | - | }},{{ 177 | ,1.125403302,0.584083861,1.07531714,1.231861002 | }{ 178 | ,0.798628781,0.468913405,0.843147406,0.630005348 | }{ 179 | ,0,0,0,0 | }{ 180 | ,0.85,0.68,0.65,0.75 | }{ 181 | ,0.85,0.68,0.65,0.75 | - | }},{{ 182 | ,0.85,0.68,0.65,0.75 | }{ 183 | ,0.85,0.68,0.65,0.75 | }{ 184 | ,0.85,0.68,0.65,0.75 | }{ 185 | ,0,0,0,0 | }{ 186 | }; | }}} DesignProbes.c: In function ‘designProbes._omp_fn.0’: DesignProbes.c:838:60: warning: ‘lastCycle’ may be used uninitialized [-Wmaybe-uninitialized] 838 | if (thisCycle < lastCycle) { | ^ DesignProbes.c:270:58: note: ‘lastCycle’ was declared here 270 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Diff.c -o Diff.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c DistanceMatrix.c -o DistanceMatrix.o DistanceMatrix.c: In function ‘firstSeqsPosEqual’: DistanceMatrix.c:1009:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1009 | if (!ci) | ^~ DistanceMatrix.c:1012:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1012 | while (i < ex) { | ^~~~~ DistanceMatrix.c:1031:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1031 | if (!cj) | ^~ DistanceMatrix.c:1034:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1034 | while (j < ey) { | ^~~~~ DistanceMatrix.c: In function ‘computeOverlap._omp_fn.0’: DistanceMatrix.c:1587:66: warning: ‘OV’ may be used uninitialized [-Wmaybe-uninitialized] 1587 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:1096:92: note: ‘OV’ was declared here 1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ DistanceMatrix.c:1587:66: warning: ‘off’ may be used uninitialized [-Wmaybe-uninitialized] 1587 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:1096:96: note: ‘off’ was declared here 1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~~ DistanceMatrix.c:1266:53: warning: ‘one’ may be used uninitialized [-Wmaybe-uninitialized] 1266 | two != one) { | ~~~~^~~~~~ DistanceMatrix.c:1241:29: note: ‘one’ was declared here 1241 | int one, two; | ^~~ DistanceMatrix.c:1603:52: warning: ‘o’ may be used uninitialized [-Wmaybe-uninitialized] 1603 | if (o == 1) { | ^ DistanceMatrix.c:1096:112: note: ‘o’ was declared here 1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^ DistanceMatrix.c:1606:91: warning: ‘ov’ may be used uninitialized [-Wmaybe-uninitialized] 1606 | sim[i] = (double)pos/((double)(ov + count + g2)); | ~~~^~~~~~~ DistanceMatrix.c:1096:88: note: ‘ov’ was declared here 1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ DistanceMatrix.c:1335:40: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1335 | keep = (int *) calloc(n, sizeof(int)); // initialized to zero (thread-safe on Windows) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from DistanceMatrix.c:32: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ DistanceMatrix.c: In function ‘distMatrix._omp_fn.0’: DistanceMatrix.c:137:25: warning: ‘m2’ may be used uninitialized [-Wmaybe-uninitialized] 137 | int i, j, I, J, m2, *counts; | ^~ DistanceMatrix.c:137:30: warning: ‘counts’ may be used uninitialized [-Wmaybe-uninitialized] 137 | int i, j, I, J, m2, *counts; | ^~~~~~ DistanceMatrix.c: In function ‘distMatrix’: DistanceMatrix.c:624:33: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 624 | #pragma omp parallel for private(j,x_j,seqLength_j,start,end,index,width) schedule(guided) num_threads(nthreads) | ^~~ DistanceMatrix.c:545:13: note: ‘m’ was declared here 545 | int m, *lkup_row, *lkup_col; | ^ DistanceMatrix.c:545:17: warning: ‘lkup_row’ may be used uninitialized [-Wmaybe-uninitialized] 545 | int m, *lkup_row, *lkup_col; | ^~~~~~~~ DistanceMatrix.c:545:28: warning: ‘lkup_col’ may be used uninitialized [-Wmaybe-uninitialized] 545 | int m, *lkup_row, *lkup_col; | ^~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c EnumerateSequence.c -o EnumerateSequence.o EnumerateSequence.c: In function ‘pop’: EnumerateSequence.c:546:15: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 546 | x = x + (x >> 4) & 0xF0F0F0F; | ~~^~~~~~~~~~ EnumerateSequence.c: In function ‘enumerateSequence’: EnumerateSequence.c:359:17: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized] 359 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:318:14: note: ‘mN’ was declared here 318 | int *mN; | ^~ EnumerateSequence.c:319:13: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized] 319 | int tot; // total number of k-mers | ^~~ EnumerateSequence.c: In function ‘enumerateSequenceReducedAA’: EnumerateSequence.c:908:14: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized] 908 | int *mN; | ^~ EnumerateSequence.c:909:13: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized] 909 | int tot; // total number of k-mers | ^~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ExpandAmbiguities.c -o ExpandAmbiguities.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c FindFrameshifts.c -o FindFrameshifts.o FindFrameshifts.c: In function ‘findFrameshifts’: FindFrameshifts.c:464:43: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 464 | *rPercentComplete = floor(100*(double)(s + 1)/f_length); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FindFrameshifts.c:160:25: note: ‘rPercentComplete’ was declared here 160 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ In file included from /home/hornik/tmp/R-d-gcc-15/include/Rdefines.h:41, from FindFrameshifts.c:11: /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:916:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 916 | #define eval Rf_eval FindFrameshifts.c:467:33: note: in expansion of macro ‘eval’ 467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ FindFrameshifts.c:162:14: note: ‘percentComplete’ was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:916:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 916 | #define eval Rf_eval FindFrameshifts.c:467:33: note: in expansion of macro ‘eval’ 467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ FindFrameshifts.c:162:31: note: ‘utilsPackage’ was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ FindFrameshifts.c:317:34: warning: ‘I’ may be used uninitialized [-Wmaybe-uninitialized] 317 | while (i > 0 && j > 0) { | ~~^~~ FindFrameshifts.c:135:28: note: ‘I’ was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ FindFrameshifts.c:317:43: warning: ‘J’ may be used uninitialized [-Wmaybe-uninitialized] 317 | while (i > 0 && j > 0) { | ~~^~~ FindFrameshifts.c:135:31: note: ‘J’ was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ FindFrameshifts.c:376:28: warning: ‘K’ may be used uninitialized [-Wmaybe-uninitialized] 376 | if (k == 1) { | ^ FindFrameshifts.c:135:34: note: ‘K’ was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c GeneFinding.c -o GeneFinding.o GeneFinding.c: In function ‘scoreCodonModel’: GeneFinding.c:422:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 422 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:389:22: note: ‘x_i.ptr’ was declared here 389 | Chars_holder x_i; | ^~~ GeneFinding.c:432:57: warning: ‘lastVal’ may be used uninitialized [-Wmaybe-uninitialized] 432 | if (val < 64 && lastVal < 64) | ~~~~~~~~^~~~ GeneFinding.c:372:32: note: ‘lastVal’ was declared here 372 | int i, j, s, fin, val, lastVal, dicodon; | ^~~~~~~ GeneFinding.c: In function ‘startCodonModel’: GeneFinding.c:798:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 798 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:772:22: note: ‘x_i.ptr’ was declared here 772 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreStartCodonModel’: GeneFinding.c:899:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 899 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:869:22: note: ‘x_i.ptr’ was declared here 869 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘initialCodonModel’: GeneFinding.c:952:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 952 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:929:22: note: ‘x_i.ptr’ was declared here 929 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreInitialCodonModel’: GeneFinding.c:1059:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1059 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1032:22: note: ‘x_i.ptr’ was declared here 1032 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘terminationCodonModel’: GeneFinding.c:1116:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1116 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1093:22: note: ‘x_i.ptr’ was declared here 1093 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreTerminationCodonModel’: GeneFinding.c:1216:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1216 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1189:22: note: ‘x_i.ptr’ was declared here 1189 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘getRegion’: GeneFinding.c:1317:81: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1317 | seq[k] = getBaseLetterRC(x_i.ptr[j--]); | ^ GeneFinding.c:1253:22: note: ‘x_i.ptr’ was declared here 1253 | Chars_holder x_i; | ^~~ GeneFinding.c:1314:51: warning: ‘x_i.length’ may be used uninitialized [-Wmaybe-uninitialized] 1314 | (s == 0 && j >= 0 && j + w <= x_i.length)) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ GeneFinding.c:1253:22: note: ‘x_i.length’ was declared here 1253 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘autocorrelationModel’: GeneFinding.c:1379:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1379 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1351:22: note: ‘x_i.ptr’ was declared here 1351 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreAutocorrelationModel’: GeneFinding.c:1496:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1496 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1462:22: note: ‘x_i.ptr’ was declared here 1462 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘couplingModel’: GeneFinding.c:1598:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1598 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1574:22: note: ‘x_i.ptr’ was declared here 1574 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreCouplingModel’: GeneFinding.c:1712:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1712 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1682:22: note: ‘x_i.ptr’ was declared here 1682 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘nucleotideBiasModel’: GeneFinding.c:1827:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1827 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1789:22: note: ‘x_i.ptr’ was declared here 1789 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreNucleotideBiasModel’: GeneFinding.c:1914:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1914 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1883:22: note: ‘x_i.ptr’ was declared here 1883 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘upstreamMotifModel’: GeneFinding.c:1993:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1993 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:1951:22: note: ‘x_i.ptr’ was declared here 1951 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreUpstreamMotifModel’: GeneFinding.c:2093:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2093 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:2058:22: note: ‘x_i.ptr’ was declared here 2058 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreRunLengthModel’: GeneFinding.c:2308:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2308 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2277:22: note: ‘x_i.ptr’ was declared here 2277 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘stopCodonModel’: GeneFinding.c:2426:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2426 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:2400:22: note: ‘x_i.ptr’ was declared here 2400 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreStopCodonModel’: GeneFinding.c:2527:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2527 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:2497:22: note: ‘x_i.ptr’ was declared here 2497 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘codonFrequencies’: GeneFinding.c:2578:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2578 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2555:22: note: ‘x_i.ptr’ was declared here 2555 | Chars_holder x_i; | ^~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c GetPools.c -o GetPools.o GetPools.c: In function ‘getPools’: GetPools.c:33:46: warning: format ‘%p’ expects argument of type ‘void *’, but argument 4 has type ‘SEXP’ {aka ‘struct SEXPREC *’} [-Wformat=] 33 | snprintf(buf, sizeof(buf), "%p", s); | ~^ ~ | | | | | SEXP {aka struct SEXPREC *} | void * gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Import.c -o Import.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c InformationContent.c -o InformationContent.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IntDist.c -o IntDist.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ManipulateXStringSet.c -o ManipulateXStringSet.o ManipulateXStringSet.c: In function ‘mergePairs._omp_fn.0’: ManipulateXStringSet.c:1106:58: warning: ‘l2’ may be used uninitialized [-Wmaybe-uninitialized] 1106 | p2 = (l2 + pow(10, ((double)q2_i.ptr[s2 + 1] - 33)/-10))/2; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ManipulateXStringSet.c:1087:36: note: ‘l2’ was declared here 1087 | double l1, l2; // last probability | ^~ ManipulateXStringSet.c:1096:58: warning: ‘l1’ may be used uninitialized [-Wmaybe-uninitialized] 1096 | p1 = (l1 + pow(10, ((double)q1_i.ptr[s1 + 1] - 33)/-10))/2; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ManipulateXStringSet.c:1087:32: note: ‘l1’ was declared here 1087 | double l1, l2; // last probability | ^~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c MeltPolymer.c -o MeltPolymer.o MeltPolymer.c: In function ‘meltPolymer’: MeltPolymer.c:79:27: warning: missing braces around initializer [-Wmissing-braces] 79 | double dH[4][4] = { | ^ 80 | -7.9,-8.4,-7.8,-7.2 | { 81 | ,-8.5,-8.0,-10.6,-7.8 | }{ 82 | ,-8.2,-9.8,-8.0,-8.4 | }{ 83 | ,-7.2,-8.2,-8.5,-7.9 | }{ 84 | }; | } MeltPolymer.c:88:27: warning: missing braces around initializer [-Wmissing-braces] 88 | double dS[4][4] = { | ^ 89 | -22.2,-22.4,-21.0,-20.4 | { 90 | ,-22.7,-19.9,-27.2,-21.0 | }{ 91 | ,-22.2,-24.4,-19.9,-22.4 | }{ 92 | ,-21.3,-22.2,-22.7,-22.2 | }{ 93 | }; | } MeltPolymer.c:406:25: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 406 | SET_VECTOR_ELT(ret, s, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ MeltPolymer.c:53:19: note: ‘ans’ was declared here 53 | SEXP ret, ans; | ^~~ MeltPolymer.c:358:41: warning: ‘rans’ may be used uninitialized [-Wmaybe-uninitialized] 358 | *(rans + k + l*s) += 1; | ^~~~~~~~~~~~~~~~~ MeltPolymer.c:54:17: note: ‘rans’ was declared here 54 | double *rans; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c MovingAverage.c -o MovingAverage.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c NNLS.c -o NNLS.o NNLS.c: In function ‘NNLS’: NNLS.c:78:51: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 78 | *rPercentComplete = floor(100*((double)i + 1)/(double)l); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NNLS.c:40:34: note: ‘rPercentComplete’ was declared here 40 | int i, j, k, before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ In file included from /home/hornik/tmp/R-d-gcc-15/include/Rdefines.h:41, from NNLS.c:17: /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:916:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 916 | #define eval Rf_eval NNLS.c:82:41: note: in expansion of macro ‘eval’ 82 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:48:14: note: ‘percentComplete’ was declared here 48 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:916:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 916 | #define eval Rf_eval NNLS.c:82:41: note: in expansion of macro ‘eval’ 82 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:48:31: note: ‘utilsPackage’ was declared here 48 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Order.c -o Order.o Order.c: In function ‘radixOrder’: Order.c:99:19: warning: ‘bounds’ may be used uninitialized [-Wmaybe-uninitialized] 99 | R_xlen_t *bounds; | ^~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PairwiseAlignment.c -o PairwiseAlignment.o PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’: PairwiseAlignment.c:446:39: warning: ‘p3’ may be used uninitialized [-Wmaybe-uninitialized] 446 | p3[0] = l1; | ~~~~~~^~~~ PairwiseAlignment.c:176:24: note: ‘p3’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:447:39: warning: ‘p4’ may be used uninitialized [-Wmaybe-uninitialized] 447 | p4[0] = l2 - j1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:176:29: note: ‘p4’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:450:39: warning: ‘p1’ may be used uninitialized [-Wmaybe-uninitialized] 450 | p1[0] = l2; | ~~~~~~^~~~ PairwiseAlignment.c:176:14: note: ‘p1’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:451:39: warning: ‘p2’ may be used uninitialized [-Wmaybe-uninitialized] 451 | p2[0] = l1 - i1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:176:19: note: ‘p2’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c: In function ‘alignPairs’: PairwiseAlignment.c:1036:25: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 1036 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ PairwiseAlignment.c:1038:14: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 1038 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ PairwiseAlignment.c:1038:31: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 1038 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PopulationGenetics.c -o PopulationGenetics.o PopulationGenetics.c: In function ‘correlationProfile’: PopulationGenetics.c:140:51: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 140 | *rPercentComplete = floor(100*soFar/tot); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ PopulationGenetics.c:40:68: note: ‘rPercentComplete’ was declared here 40 | int i, j, k, p, I, J, minL, warn = NA_INTEGER, v, before, *rPercentComplete; | ^~~~~~~~~~~~~~~~ PopulationGenetics.c:140:53: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized] 140 | *rPercentComplete = floor(100*soFar/tot); | ^~~~~~~~~~~~~~~~~~~~ PopulationGenetics.c:41:31: note: ‘tot’ was declared here 41 | double weight, soFar, tot; | ^~~ In file included from /home/hornik/tmp/R-d-gcc-15/include/Rdefines.h:41, from PopulationGenetics.c:11: /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:916:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 916 | #define eval Rf_eval PopulationGenetics.c:143:41: note: in expansion of macro ‘eval’ 143 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ PopulationGenetics.c:50:14: note: ‘percentComplete’ was declared here 50 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ /home/hornik/tmp/R-d-gcc-15/include/Rinternals.h:916:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 916 | #define eval Rf_eval PopulationGenetics.c:143:41: note: in expansion of macro ‘eval’ 143 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ PopulationGenetics.c:50:31: note: ‘utilsPackage’ was declared here 50 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PredictDBN.c -o PredictDBN.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PredictHEC.c -o PredictHEC.o PredictHEC.c: In function ‘predictHEC’: PredictHEC.c:51:31: warning: ‘rans’ may be used uninitialized [-Wmaybe-uninitialized] 51 | double HEC[N], temp, *rans; | ^~~~ PredictHEC.c:247:43: warning: ‘states’ may be used uninitialized [-Wmaybe-uninitialized] 247 | states[j] = nms[0]; | ~~~~~~~~~~^~~~~~~~ PredictHEC.c:52:15: note: ‘states’ was declared here 52 | char *states; | ^~~~~~ PredictHEC.c:273:25: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 273 | SET_VECTOR_ELT(ret, i, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictHEC.c:59:19: note: ‘ans’ was declared here 59 | SEXP ret, ans; | ^~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_decipher.c -o R_init_decipher.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Search.c -o Search.o Search.c: In function ‘searchIndex._omp_fn.0’: Search.c:574:92: warning: ‘subScores’ may be used uninitialized [-Wmaybe-uninitialized] 574 | if (lkup != NA_INTEGER && subScores[p1*l_i.length + lkup] != R_NegInf) | ^ Search.c:317:33: note: ‘subScores’ was declared here 317 | double *subScores; // substitution scores (if maxIt > 0) | ^~~~~~~~~ Search.c:445:66: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized] 445 | score2[j] = score[o1[j]]; | ^ Search.c:282:33: note: ‘score’ was declared here 282 | double *score, *addScore, *score2, *addScore2; | ^~~~~ Search.c:446:72: warning: ‘addScore’ may be used uninitialized [-Wmaybe-uninitialized] 446 | addScore2[j] = addScore[o1[j]]; | ^ Search.c:282:41: note: ‘addScore’ was declared here 282 | double *score, *addScore, *score2, *addScore2; | ^~~~~~~~ Search.c:583:83: warning: ‘maxLen’ may be used uninitialized [-Wmaybe-uninitialized] 583 | if (deltaTarget >= maxSep + maxLen) { | ~~~~~~~^~~~~~~~ Search.c:556:45: note: ‘maxLen’ was declared here 556 | int maxLen; // maximum observed length | ^~~~~~ Search.c:551:59: warning: ‘s_j.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 551 | Chars_holder p_i, s_j; | ^~~ Search.c:622:55: warning: ‘s_j.length’ may be used uninitialized [-Wmaybe-uninitialized] 622 | bound = s_j.length - 1; // right bound | ~~~~~~^~~~~~~~~~~~~~~~ Search.c:551:59: note: ‘s_j.length’ was declared here 551 | Chars_holder p_i, s_j; | ^~~ Search.c:878:59: warning: ‘s_j.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 878 | Chars_holder p_i, s_j; | ^~~ Search.c:367:30: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized] 367 | int *res; // indices of results | ^~~ Search.c:1147:72: warning: ‘len’ may be used uninitialized [-Wmaybe-uninitialized] 1147 | anchor[k++] = posQuery[p] + len[p] - 1; | ^ Search.c:366:30: note: ‘len’ was declared here 366 | int *len; // length of each hit | ^~~ Search.c:1136:58: warning: ‘chain’ may be used uninitialized [-Wmaybe-uninitialized] 1136 | while (p != chain[p]) { | ^ Search.c:365:30: note: ‘chain’ was declared here 365 | int *chain; // set of joined hits per match | ^~~~~ Search.c: In function ‘searchIndex’: Search.c:224:17: warning: ‘sM’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:111:17: note: ‘sM’ was declared here 111 | double *sM, dS; | ^~ Search.c:224:17: warning: ‘dS’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:111:21: note: ‘dS’ was declared here 111 | double *sM, dS; | ^~ Search.c:112:14: warning: ‘lkup_row’ may be used uninitialized [-Wmaybe-uninitialized] 112 | int *lkup_row, *lkup_col, *pwv; | ^~~~~~~~ Search.c:112:25: warning: ‘lkup_col’ may be used uninitialized [-Wmaybe-uninitialized] 112 | int *lkup_row, *lkup_col, *pwv; | ^~~~~~~~ Search.c:112:36: warning: ‘pwv’ may be used uninitialized [-Wmaybe-uninitialized] 112 | int *lkup_row, *lkup_col, *pwv; | ^~~ Search.c:113:17: warning: ‘scores’ may be used uninitialized [-Wmaybe-uninitialized] 113 | double *scores, *addScores; | ^~~~~~ Search.c:224:17: warning: ‘addScores’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:113:26: note: ‘addScores’ was declared here 113 | double *scores, *addScores; | ^~~~~~~~~ Search.c:224:17: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:174:25: note: ‘rPercentComplete’ was declared here 174 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ Search.c:176:14: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 176 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ Search.c:176:31: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 176 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ Search.c:224:17: warning: ‘matrices’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:217:16: note: ‘matrices’ was declared here 217 | int ***matrices; | ^~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c TerminalMismatch.c -o TerminalMismatch.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Translate.c -o Translate.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Utils.c -o Utils.o Utils.c: In function ‘splitPartitions’: Utils.c:990:35: warning: ‘change’ may be used uninitialized [-Wmaybe-uninitialized] 990 | } else if (change - j >= m && // large enough partition | ~~~~~~~^~~ Utils.c:984:13: note: ‘change’ was declared here 984 | int change; // index before start of partition | ^~~~~~ Utils.c: In function ‘matchColumns’: Utils.c:1198:55: warning: ‘lkup’ may be used uninitialized [-Wmaybe-uninitialized] 1198 | int val = lkup[(unsigned char)x_i.ptr[o[j]]]; | ^ Utils.c:1130:14: note: ‘lkup’ was declared here 1130 | int *lkup; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c VectorSums.c -o VectorSums.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterME.o ClusterML.o ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PopulationGenetics.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o Search.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -fopenmp -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpBlA6sS/R.INSTALL375283f52b1ae/DECIPHER/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-DECIPHER/00new/DECIPHER/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 (DECIPHER) checking optparse_1.8.1.tar.gz ... checking dynafluxr_1.0.1.tar.gz ... checking fmriqa_0.5.0.tar.gz ... checking numbat_1.5.2.tar.gz ... checking plinkQC_1.1.0.tar.gz ... checking REPTILE_1.0.tar.gz ... checking RIbench_1.0.2.tar.gz ... checking artma_0.3.3.tar.gz ... checking enveomics.R_1.10.0.tar.gz ... checking geeLite_1.0.6.tar.gz ... checking gwas2crispr_0.1.2.tar.gz ... checking rbiom_2.2.1.tar.gz ... checking SQLFormatteR_0.0.2.tar.gz ... checking TexExamRandomizer_1.2.7.tar.gz ... checking twbparser_0.3.1.tar.gz ... checking VIProDesign_0.1.0.tar.gz ... checking W4MRUtils_1.2.1.tar.gz ... Depends: Package: optparse Depends: R (>= 3.6.0) Imports: methods Timings: user system elapsed optparse 26.65 4.079 32.617 Results: Check status summary: ERROR NOTE OK Source packages 0 0 1 Reverse depends 1 1 14 Check results summary: optparse ... OK rdepends_artma ... OK rdepends_dynafluxr ... OK rdepends_enveomics.R ... OK rdepends_fmriqa ... OK rdepends_geeLite ... OK rdepends_gwas2crispr ... OK rdepends_numbat ... OK rdepends_plinkQC ... OK rdepends_rbiom ... OK rdepends_REPTILE ... OK rdepends_RIbench ... OK rdepends_SQLFormatteR ... NOTE * checking compiled code ... NOTE rdepends_TexExamRandomizer ... OK rdepends_twbparser ... OK rdepends_VIProDesign ... OK rdepends_W4MRUtils ... ERROR * checking examples ... [1s/1s] ERROR * checking tests ... [2s/2s] ERROR Check results changes: Package: REPTILE Check: CRAN incoming feasibility Old result: NOTE Package: TexExamRandomizer Check: CRAN incoming feasibility Old result: NOTE Package: W4MRUtils Check: examples New result: ERROR Package: W4MRUtils Check: tests New result: ERROR