downloading reverse dependencies ‘ProbeDeveloper’ trying URL 'file:///data/Repositories/CRAN/src/contrib/ProbeDeveloper_1.1.0.tar.gz' Content type 'unknown' length 22318 bytes (21 KB) ================================================== installing dependencies ‘BSgenome.Hsapiens.UCSC.hg38’, ‘ggbio’, ‘Gviz’, ‘karyoploteR’, ‘TmCalculator’ also installing the dependencies ‘biovizBase’, ‘OrganismDbi’, ‘regioneR’, ‘bamsignals’ begin installing package ‘biovizBase’ begin installing package ‘OrganismDbi’ begin installing package ‘bamsignals’ begin installing package ‘regioneR’ begin installing package ‘BSgenome.Hsapiens.UCSC.hg38’ * installing *source* package ‘bamsignals’ ... ** this is package ‘bamsignals’ version ‘1.43.0’ ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-14) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-14) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpWOUTY2/R.INSTALL2cd6871206a00f/bamsignals/src' g++-15 -std=gnu++20 -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/Rcpp/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 -pedantic -mtune=native -c CountSignals.cpp -o CountSignals.o g++-15 -std=gnu++20 -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/Rcpp/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 -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++20 -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/Rcpp/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 -pedantic -mtune=native -c bamsignals.cpp -o bamsignals.o bamsignals.cpp: In function ‘bool writeSamAsBamAndIndex(const std::string&, const std::string&)’: bamsignals.cpp:499:9: warning: variable ‘iorval’ set but not used [-Wunused-but-set-variable] 499 | int iorval; | ^~~~~~ 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/Rcpp/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 bamsignals_init.c -o bamsignals_init.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o bamsignals.so CountSignals.o RcppExports.o bamsignals.o bamsignals_init.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/RtmpWOUTY2/R.INSTALL2cd6871206a00f/bamsignals/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-bamsignals/00new/bamsignals/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 (bamsignals) * installing *source* package ‘regioneR’ ... ** this is package ‘regioneR’ version ‘1.43.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (regioneR) * installing *source* package ‘OrganismDbi’ ... ** this is package ‘OrganismDbi’ version ‘1.53.2’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (OrganismDbi) * installing *source* package ‘biovizBase’ ... ** this is package ‘biovizBase’ version ‘1.59.0’ ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-14) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp2KW72t/R.INSTALL2cd68315e5af9e/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/Rtmp2KW72t/R.INSTALL2cd68315e5af9e/biovizBase/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-biovizBase/00new/biovizBase/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biovizBase) begin installing package ‘Gviz’ begin installing package ‘karyoploteR’ begin installing package ‘ggbio’ * 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 ‘karyoploteR’ ... ** this is package ‘karyoploteR’ version ‘1.37.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (karyoploteR) * installing *source* package ‘ggbio’ ... ** this is package ‘ggbio’ version ‘1.59.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'rescale' in package 'ggbio' Creating a new generic function for 'xlim' in package 'ggbio' Creating a new generic function for 'geom_rect' in package 'ggbio' Creating a new generic function for 'geom_segment' in package 'ggbio' Creating a new generic function for 'geom_bar' in package 'ggbio' Creating a new generic function for 'stat_identity' in package 'ggbio' Creating a new generic function for 'stat_bin' in package 'ggbio' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggbio) * installing *source* package ‘Gviz’ ... ** this is package ‘Gviz’ version ‘1.55.0’ ** 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 (Gviz) begin installing package ‘TmCalculator’ * installing *source* package ‘TmCalculator’ ... ** this is package ‘TmCalculator’ version ‘1.0.4’ ** 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 (TmCalculator) checking TmCalculator_1.0.4.tar.gz ... checking ProbeDeveloper_1.1.0.tar.gz ... Depends: Package: TmCalculator Depends: R (>= 3.5) Imports: seqinr, BSgenome, Biostrings, GenomicRanges, IRanges, S4Vectors, GenomeInfoDb, Gviz, dplyr, ggbio, ggplot2, karyoploteR, viridis, rlang, plotly Timings: user system elapsed TmCalculator 368.545 22.462 398.704 Results: Check status summary: ERROR NOTE Source packages 0 1 Reverse depends 1 0 Check results summary: TmCalculator ... NOTE * checking CRAN incoming feasibility ... [4s/6s] NOTE rdepends_ProbeDeveloper ... ERROR * checking whether package ‘ProbeDeveloper’ can be installed ... [13s/13s] ERROR Check results changes: Package: ProbeDeveloper Check: CRAN incoming feasibility Old result: NOTE Package: ProbeDeveloper Check: whether package can be installed New result: ERROR