downloading reverse dependencies ‘ClusTCR2’, ‘Platypus’, ‘immunarch’, ‘phangorn’, ‘Signac’ trying URL 'file:///data/Repositories/CRAN/src/contrib/ClusTCR2_1.7.3.01.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/Platypus_3.6.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/immunarch_0.10.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/phangorn_2.12.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/Signac_1.16.0.tar.gz' installing dependencies ‘airr’, ‘apex’, ‘biovizBase’, ‘chromVAR’, ‘duckplyr’, ‘ggseqlogo’, ‘immundata’, ‘iNEXT’, ‘kmer’, ‘motifmatchr’, ‘slingshot’, ‘TFBSTools’, ‘useful’, ‘VLF’, ‘wrswoR’ also installing the dependencies ‘ProtGenerics’, ‘phylogram’, ‘TrajectoryUtils’, ‘DirichletMultinomial’, ‘seqLogo’, ‘TFMPvalue’, ‘VariantAnnotation’, ‘ensembldb’, ‘AnnotationFilter’ begin installing package ‘ProtGenerics’ begin installing package ‘phylogram’ begin installing package ‘TrajectoryUtils’ begin installing package ‘DirichletMultinomial’ begin installing package ‘seqLogo’ begin installing package ‘TFMPvalue’ begin installing package ‘AnnotationFilter’ begin installing package ‘VariantAnnotation’ begin installing package ‘ggseqlogo’ begin installing package ‘VLF’ begin installing package ‘useful’ begin installing package ‘iNEXT’ begin installing package ‘duckplyr’ begin installing package ‘airr’ begin installing package ‘apex’ begin installing package ‘wrswoR’ * installing *source* package ‘phylogram’ ... ** this is package ‘phylogram’ version ‘2.1.0’ ** package ‘phylogram’ 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 (phylogram) begin installing package ‘kmer’ * installing *source* package ‘seqLogo’ ... ** this is package ‘seqLogo’ version ‘1.76.0’ ** package ‘seqLogo’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (seqLogo) * installing *source* package ‘ProtGenerics’ ... ** this is package ‘ProtGenerics’ version ‘1.42.0’ ** package ‘ProtGenerics’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘smooth’ in package ‘ProtGenerics’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ProtGenerics) * installing *source* package ‘ggseqlogo’ ... ** this is package ‘ggseqlogo’ version ‘0.2.2’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggseqlogo) * installing *source* package ‘useful’ ... ** this is package ‘useful’ version ‘1.2.6.1’ ** package ‘useful’ 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 (useful) * installing *source* package ‘VLF’ ... ** this is package ‘VLF’ version ‘1.1-3’ ** package ‘VLF’ 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 (VLF) * installing *source* package ‘airr’ ... ** this is package ‘airr’ version ‘1.5.0’ ** package ‘airr’ 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 (airr) * installing *source* package ‘DirichletMultinomial’ ... ** this is package ‘DirichletMultinomial’ version ‘1.52.0’ ** package ‘DirichletMultinomial’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjqHnii/R.INSTALL29f2295fbc8fbb/DirichletMultinomial/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 `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dirichlet_fit.c -o dirichlet_fit.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dirichlet_fit_main.c -o dirichlet_fit_main.o dirichlet_fit_main.c: In function ‘hessian’: dirichlet_fit_main.c:391:34: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 391 | adCJK0[j] += adPi[i] * n ? gsl_sf_psi(adAlpha[j] + n) : dPsiAlpha; | ~~~~~~~~^~~ dirichlet_fit_main.c:393:33: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 393 | adCJK[j] += adPi[i] * n ? gsl_sf_psi_1(adAlpha[j] + n): dPsi1Alpha; | ~~~~~~~~^~~ gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o DirichletMultinomial.so R_init_DirichletMultinomial.o dirichlet_fit.o dirichlet_fit_main.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjqHnii/R.INSTALL29f2295fbc8fbb/DirichletMultinomial/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-DirichletMultinomial/00new/DirichletMultinomial/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DirichletMultinomial) Warning: SystemRequirements specified C++11: support will be removed soon * installing *source* package ‘TFMPvalue’ ... ** this is package ‘TFMPvalue’ version ‘0.0.9’ ** package ‘TFMPvalue’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmplhC8Py/R.INSTALL29f22c41bb4824/TFMPvalue/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ArgumentException.cpp -o ArgumentException.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c FileException.cpp -o FileException.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Matrix.cpp -o Matrix.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ParseException.cpp -o ParseException.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TFMMain.cpp -o TFMMain.o TFMMain.cpp: In function ‘SEXPREC* pv2sc(SEXP, SEXP, SEXP, SEXP)’: TFMMain.cpp:159:8: warning: unused variable ‘sortColumns’ [-Wunused-variable] 159 | bool sortColumns = false; | ^~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c TFMPvalue_init.c -o TFMPvalue_init.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TFMpvalue.cpp -o TFMpvalue.o TFMpvalue.cpp: In function ‘void testLazyDistrib(Matrix, double, double)’: TFMpvalue.cpp:119:13: warning: unused variable ‘totalSize’ [-Wunused-variable] 119 | qlonglong totalSize = 0; | ^~~~~~~~~ TFMpvalue.cpp:120:13: warning: unused variable ‘totalOp’ [-Wunused-variable] 120 | qlonglong totalOp = 0; | ^~~~~~~ TFMpvalue.cpp: In function ‘void testFastPvalue(Matrix, double, double)’: TFMpvalue.cpp:185:13: warning: unused variable ‘totalSize’ [-Wunused-variable] 185 | qlonglong totalSize = 0; | ^~~~~~~~~ TFMpvalue.cpp:186:13: warning: unused variable ‘totalOp’ [-Wunused-variable] 186 | qlonglong totalOp = 0; | ^~~~~~~ TFMpvalue.cpp:190:10: warning: unused variable ‘pvalue’ [-Wunused-variable] 190 | double pvalue = m.fastPvalue(&m,(qlonglong)(score * m.granularity + m.offset)); | ^~~~~~ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o TFMPvalue.so ArgumentException.o FileException.o Matrix.o ParseException.o TFMMain.o TFMPvalue_init.o TFMpvalue.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmplhC8Py/R.INSTALL29f22c41bb4824/TFMPvalue/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TFMPvalue/00new/TFMPvalue/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (TFMPvalue) begin installing package ‘TFBSTools’ * installing *source* package ‘duckplyr’ ... ** this is package ‘duckplyr’ version ‘1.1.3’ ** package ‘duckplyr’ 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 (duckplyr) begin installing package ‘immundata’ * installing *source* package ‘wrswoR’ ... ** this is package ‘wrswoR’ version ‘1.2.0’ ** package ‘wrswoR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8Bp1Jk/R.INSTALL29f24669c383d5/wrswoR/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sample_int_crank.cpp -o sample_int_crank.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++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o wrswoR.so RcppExports.o sample_int_crank.o -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/Rtmp8Bp1Jk/R.INSTALL29f24669c383d5/wrswoR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-wrswoR/00new/wrswoR/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (wrswoR) * installing *source* package ‘AnnotationFilter’ ... ** this is package ‘AnnotationFilter’ version ‘1.34.0’ ** package ‘AnnotationFilter’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AnnotationFilter) begin installing package ‘ensembldb’ * installing *source* package ‘kmer’ ... ** this is package ‘kmer’ version ‘1.1.2’ ** package ‘kmer’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmprAiczM/R.INSTALL29f40822308701/kmer/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c distance.cpp -o distance.o distance.cpp: In function ‘Rcpp::NumericMatrix kcountDNA(Rcpp::List, int)’: distance.cpp:10:6: warning: unnecessary parentheses in declaration of ‘fourtopowerk’ [-Wparentheses] 10 | int(fourtopowerk) = 1; | ^~~~~~~~~~~~~~ distance.cpp:10:6: note: remove parentheses 10 | int(fourtopowerk) = 1; | ^~~~~~~~~~~~~~ | - - g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o kmer.so RcppExports.o distance.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmprAiczM/R.INSTALL29f40822308701/kmer/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-kmer/00new/kmer/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (kmer) * installing *source* package ‘apex’ ... ** this is package ‘apex’ version ‘1.0.7’ ** package ‘apex’ 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 (apex) * installing *source* package ‘iNEXT’ ... ** this is package ‘iNEXT’ version ‘3.0.2’ ** package ‘iNEXT’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp7EEyCj/R.INSTALL29f23b3760e470/iNEXT/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c subfuns.cpp -o subfuns.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o iNEXT.so RcppExports.o subfuns.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp7EEyCj/R.INSTALL29f23b3760e470/iNEXT/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-iNEXT/00new/iNEXT/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 (iNEXT) * installing *source* package ‘immundata’ ... ** this is package ‘immundata’ version ‘0.0.5’ ** package ‘immundata’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (immundata) * installing *source* package ‘TrajectoryUtils’ ... ** this is package ‘TrajectoryUtils’ version ‘1.18.0’ ** package ‘TrajectoryUtils’ 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 (TrajectoryUtils) begin installing package ‘slingshot’ * installing *source* package ‘slingshot’ ... ** this is package ‘slingshot’ version ‘2.18.0’ ** package ‘slingshot’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘slingshot’ with signature ‘data="ClusterExperiment"’: no definition for class “ClusterExperiment” ** 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 (slingshot) * installing *source* package ‘ensembldb’ ... ** this is package ‘ensembldb’ version ‘2.34.0’ ** package ‘ensembldb’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘.cds_for_id2’ in package ‘ensembldb’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ensembldb) * installing *source* package ‘TFBSTools’ ... ** this is package ‘TFBSTools’ version ‘1.48.0’ ** package ‘TFBSTools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHna5Wr/R.INSTALL29f66e397ba06b/TFBSTools/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 matrixAlignerDynamic.c -o matrixAlignerDynamic.o matrixAlignerDynamic.c: In function ‘score’: matrixAlignerDynamic.c:235:22: warning: ‘best_pntr’ may be used uninitialized [-Wmaybe-uninitialized] 235 | while (current_pntr->father != NULL){ // while the father of the current pointer exists, walk through the best posible alignment | ~~~~~~~~~~~~^~~~~~~~ matrixAlignerDynamic.c:115:17: note: ‘best_pntr’ was declared here 115 | struct entry *best_pntr; // pointer to the best entry so far | ^~~~~~~~~ gcc-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 R_init_TFBSTools.c -o R_init_TFBSTools.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHna5Wr/R.INSTALL29f66e397ba06b/TFBSTools/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TFBSTools/00new/TFBSTools/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘seqLogo’ in package ‘TFBSTools’ Creating a new generic function for ‘pattern’ in package ‘TFBSTools’ Creating a generic function for ‘colSums’ from package ‘base’ in package ‘TFBSTools’ Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘TFBSTools’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (TFBSTools) begin installing package ‘chromVAR’ begin installing package ‘motifmatchr’ * installing *source* package ‘VariantAnnotation’ ... ** this is package ‘VariantAnnotation’ version ‘1.56.0’ ** package ‘VariantAnnotation’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpDq7TpZ/R.INSTALL29f2284477162b/VariantAnnotation/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IRanges_stubs.c -o IRanges_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dna_hash.c -o dna_hash.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rle.c -o rle.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c strhash.c -o strhash.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utilities.c -o utilities.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcffile.c -o vcffile.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcftype.c -o vcftype.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c writevcf.c -o writevcf.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpDq7TpZ/R.INSTALL29f2284477162b/VariantAnnotation/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (VariantAnnotation) begin installing package ‘biovizBase’ Warning: SystemRequirements specified C++11: support will be removed soon * installing *source* package ‘motifmatchr’ ... ** this is package ‘motifmatchr’ version ‘1.32.0’ ** package ‘motifmatchr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpdld88P/R.INSTALL29f8243b65793c/motifmatchr/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c r_interface.cpp -o r_interface.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/scanner.cpp -o MOODS/scanner.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/motif_h.cpp -o MOODS/motif_h.o MOODS/motif_h.cpp: In member function ‘std::vector MOODS::scan::MotifH::expected_scores(const std::vector&)’: MOODS/motif_h.cpp:26:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 26 | for (int i = 0; i < cols; ++i){ | ~~^~~~~~ MOODS/motif_h.cpp:27:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 27 | for (int j = 0; j < rows; ++j){ | ~~^~~~~~ MOODS/motif_h.cpp: In member function ‘virtual std::pair MOODS::scan::MotifH::check_hit(const std::string&, const std::vector&, std::size_t, double)’: MOODS/motif_h.cpp:256:25: warning: suggest parentheses around arithmetic in operand of ‘^’ [-Wparentheses] 256 | CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]]; | ~~~~~^~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/motif_0.cpp -o MOODS/motif_0.o MOODS/motif_0.cpp: In function ‘std::vector MOODS::scan::expected_differences(const score_matrix&, const std::vector&)’: MOODS/motif_0.cpp:28:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 28 | for (int i = 0; i < m; ++i) | ~~^~~ MOODS/motif_0.cpp:31:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 31 | for (int j = 0; j < a; ++j) | ~~^~~ MOODS/motif_0.cpp:38:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 38 | for (int j = 0; j < a; ++j) | ~~^~~ MOODS/motif_0.cpp: In function ‘unsigned int MOODS::scan::window_position(const std::vector&, unsigned int, unsigned int)’: MOODS/motif_0.cpp:64:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 64 | for (int i = 0; i < m - l; ++i) | ~~^~~~~~~ MOODS/motif_0.cpp: In function ‘std::vector MOODS::scan::compute_lookahead_order(const std::vector&, unsigned int, unsigned int, unsigned int)’: MOODS/motif_0.cpp:96:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 96 | for (int i = 0; i < window_pos; ++i) | ~~^~~~~~~~~~~~ MOODS/motif_0.cpp:100:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 100 | for (int i = window_pos+l; i < m; ++i) | ~~^~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o MOODS/moods_tools.cpp: In function ‘double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector&, const double&)’: MOODS/moods_tools.cpp:155:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 155 | for (size_t i = 0; i < n; ++i) | ~~^~~ MOODS/moods_tools.cpp:157:30: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 157 | for (size_t j = 0; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp:168:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 168 | for (size_t i = 0; i < n; ++i) | ~~^~~ MOODS/moods_tools.cpp:172:30: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 172 | for (size_t j = 1; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp:190:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 190 | for (size_t j = 0; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 193 | for (size_t i = 1; i < n; ++i) | ~~^~~ MOODS/moods_tools.cpp:195:30: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 195 | for (size_t j = 0; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp: In function ‘score_matrix MOODS::tools::log_odds(const std::vector >&, const std::vector >&, const std::vector&, double, std::size_t)’: MOODS/moods_tools.cpp:320:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 320 | for (size_t PCODE = 0; PCODE < 1 << (SHIFT * r); ++PCODE ){ | ~~~~~~^~~~~~~~~~~~~~~~~~ MOODS/moods_tools.cpp:328:46: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 328 | for (size_t SCODE = 0; SCODE < 1 << (SHIFT * (q - r - 1)); ++SCODE){ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ MOODS/moods_tools.cpp: In function ‘double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector&, const double&, std::size_t)’: MOODS/moods_tools.cpp:454:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 454 | for (size_t i = 0; i < cols; ++i) | ~~^~~~~~ MOODS/moods_tools.cpp:456:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 456 | for (size_t CODE = 0; CODE < rows; ++CODE) | ~~~~~^~~~~~ MOODS/moods_tools.cpp:468:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 468 | for (size_t i = 0; i < cols; ++i) | ~~^~~~~~ MOODS/moods_tools.cpp:472:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 472 | for (size_t CODE = 1; CODE < rows; ++CODE) | ~~~~~^~~~~~ MOODS/moods_tools.cpp:489:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 489 | for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE){ | ~~~~~^~~~~~~~~~~~~~~~~~~~ MOODS/moods_tools.cpp:500:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 500 | for (size_t i = 1; i < cols; ++i) | ~~^~~~~~ MOODS/moods_tools.cpp:503:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 503 | for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE) | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o MOODS/moods_scan.cpp: In function ‘std::vector > MOODS::scan::scan_best_hits_dna(const std::string&, const std::vector > >&, std::size_t, int, unsigned int, std::size_t, std::size_t)’: MOODS/moods_scan.cpp:97:14: warning: unused variable ‘done’ [-Wunused-variable] 97 | bool done = 0; | ^~~~ MOODS/moods_scan.cpp: In function ‘std::vector MOODS::scan::naive_scan_dna(const std::string&, score_matrix, double, std::size_t)’: MOODS/moods_scan.cpp:252:33: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 252 | CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]]; | ~~~~~^~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MOODS/match_types.cpp -o MOODS/match_types.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o motifmatchr.so ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpdld88P/R.INSTALL29f8243b65793c/motifmatchr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-motifmatchr/00new/motifmatchr/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (motifmatchr) * installing *source* package ‘biovizBase’ ... ** this is package ‘biovizBase’ version ‘1.58.0’ ** package ‘biovizBase’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmprpXUMy/R.INSTALL29f87a1ce1ce56/biovizBase/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 R_init_biovizBase.c -o R_init_biovizBase.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 bin_offsets.c -o bin_offsets.o bin_offsets.c: In function ‘scan_bam_bin_offsets’: bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign] 57 | if (strncmp(b, "BAI\1", 4)) | ^ | | | Rbyte * {aka unsigned char *} In file included from /home/hornik/tmp/R-d-gcc-15/include/R_ext/RS.h:34, from /home/hornik/tmp/R-d-gcc-15/include/Rdefines.h:38, from bin_offsets.h:1, from bin_offsets.c:3: /usr/include/string.h:159:33: note: expected ‘const char *’ but argument is of type ‘Rbyte *’ {aka ‘unsigned char *’} 159 | extern int strncmp (const char *__s1, const char *__s2, size_t __n) | ~~~~~~~~~~~~^~~~ gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmprpXUMy/R.INSTALL29f87a1ce1ce56/biovizBase/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-biovizBase/00new/biovizBase/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biovizBase) Warning: SystemRequirements specified C++11: support will be removed soon * installing *source* package ‘chromVAR’ ... ** this is package ‘chromVAR’ version ‘1.32.0’ ** package ‘chromVAR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRdPS9q/R.INSTALL29f8252b86ae95/chromVAR/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwm_similarity.cpp -o pwm_similarity.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c utils.cpp -o utils.o utils.cpp: In function ‘Rcpp::NumericVector row_sds(arma::mat&, bool)’: utils.cpp:12:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 12 | for( int j=0; j < X.n_rows; j++ ) { | ~~^~~~~~~~~~ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o chromVAR.so RcppExports.o pwm_similarity.o utils.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/RtmpRdPS9q/R.INSTALL29f8252b86ae95/chromVAR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-chromVAR/00new/chromVAR/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (chromVAR) checking ggseqlogo_0.2.2.tar.gz ... checking ClusTCR2_1.7.3.01.tar.gz ... checking Platypus_3.6.0.tar.gz ... checking immunarch_0.10.3.tar.gz ... checking phangorn_2.12.1.tar.gz ... checking Signac_1.16.0.tar.gz ... Depends: Package: ggseqlogo Imports: ggplot2 Timings: user system elapsed ggseqlogo 35.464 4.375 40.645 Results: Check status summary: ERROR OK Source packages 0 1 Reverse depends 1 4 Check results summary: ggseqlogo ... OK rdepends_ClusTCR2 ... OK rdepends_immunarch ... OK rdepends_phangorn ... OK rdepends_Platypus ... ERROR * checking DESCRIPTION meta-information ... NOTE * checking examples ... [5s/5s] ERROR rdepends_Signac ... OK