############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL S4Vectors ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'S4Vectors' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AEbufs.c -o AEbufs.o AEbufs.c: In function '_IntAEAE_toEnvir': AEbufs.c:632:50: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 632 | snprintf(key, sizeof(key), "%010lu", i + keyshift); | ~~~~~^ ~~~~~~~~~~~~ | | | | | size_t {aka long long unsigned int} | long unsigned int | %010llu gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DataFrame_class.c -o DataFrame_class.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Hits_class.c -o Hits_class.o In file included from F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41, from ../inst/include/S4Vectors_defines.h:18, from S4Vectors.h:1, from Hits_class.c:4: F:/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h: In function 'Hits_new': F:/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:886:33: warning: 'revmap' may be used uninitialized [-Wmaybe-uninitialized] 886 | #define defineVar Rf_defineVar | ^~~~~~~~~~~~ Hits_class.c:216:19: note: 'revmap' was declared here 216 | SEXP ans, revmap, symbol; | ^~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LLint_class.c -o LLint_class.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c List_class.c -o List_class.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Rle_class.c -o Rle_class.o Rle_class.c: In function 'fill_integer_runs': Rle_class.c:278:38: warning: 'val_out' may be used uninitialized [-Wmaybe-uninitialized] 278 | values_out[nrun_out] = val_out; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ Rle_class.c:245:21: note: 'val_out' was declared here 245 | int val_in, val_out; | ^~~~~~~ In function 'fill_numeric_runs', inlined from '_construct_numeric_Rle' at Rle_class.c:765:2: Rle_class.c:377:38: warning: 'val_out' may be used uninitialized [-Wmaybe-uninitialized] 377 | values_out[nrun_out] = val_out; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ Rle_class.c: In function '_construct_numeric_Rle': Rle_class.c:344:24: note: 'val_out' was declared here 344 | double val_in, val_out; | ^~~~~~~ In function 'fill_character_runs', inlined from '_construct_character_Rle' at Rle_class.c:813:2: Rle_class.c:575:17: warning: 'val_out' may be used uninitialized [-Wmaybe-uninitialized] 575 | SET_STRING_ELT(values_out, nrun_out, val_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Rle_class.c: In function '_construct_character_Rle': Rle_class.c:541:22: note: 'val_out' was declared here 541 | SEXP val_in, val_out; | ^~~~~~~ In function 'fill_raw_runs', inlined from '_construct_raw_Rle' at Rle_class.c:838:2: Rle_class.c:671:38: warning: 'val_out' may be used uninitialized [-Wmaybe-uninitialized] 671 | values_out[nrun_out] = val_out; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ Rle_class.c: In function '_construct_raw_Rle': Rle_class.c:638:23: note: 'val_out' was declared here 638 | Rbyte val_in, val_out; | ^~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Rle_utils.c -o Rle_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SEXP_utils.c -o SEXP_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SimpleList_class.c -o SimpleList_class.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c anyMissing.c -o anyMissing.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c character_utils.c -o character_utils.o character_utils.c: In function 'get_svn_time': character_utils.c:187:9: warning: 'timezone' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations] 187 | utc_offset = - (timezone / 3600); | ^~~~~~~~~~ In file included from character_utils.c:12: c:\rtools43\x86_64-w64-mingw32.static.posix\include\time.h:276:23: note: declared here 276 | _CRTIMP extern long timezone __MINGW_ATTRIB_DEPRECATED_UCRT; | ^~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c eval_utils.c -o eval_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hash_utils.c -o hash_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c integer_utils.c -o integer_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c logical_utils.c -o logical_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c raw_utils.c -o raw_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c safe_arithm.c -o safe_arithm.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sort_utils.c -o sort_utils.o sort_utils.c:263:13: warning: 'sort_uchar_array' defined but not used [-Wunused-function] 263 | static void sort_uchar_array(unsigned char *x, int nelt, int desc) | ^~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c subsetting_utils.c -o subsetting_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vector_utils.c -o vector_utils.o gcc -shared -s -static-libgcc -o S4Vectors.dll tmp.def AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-S4Vectors/00new/S4Vectors/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading in method for 'normalizeSingleBracketReplacementValue' with signature '"List"': no definition for class "List" Creating a new generic function for 'unname' in package 'S4Vectors' Creating a new generic function for 'expand.grid' in package 'S4Vectors' Creating a new generic function for 'findMatches' in package 'S4Vectors' Creating a generic function for 'setequal' from package 'base' in package 'S4Vectors' in method for 'coerce' with signature '"Hits","DFrame"': no definition for class "DFrame" Creating a generic function for 'as.factor' from package 'base' in package 'S4Vectors' Creating a generic function for 'tabulate' from package 'base' in package 'S4Vectors' Creating a generic function for 'cov' from package 'stats' in package 'S4Vectors' Creating a generic function for 'cor' from package 'stats' in package 'S4Vectors' Creating a generic function for 'smoothEnds' from package 'stats' in package 'S4Vectors' Creating a generic function for 'runmed' from package 'stats' in package 'S4Vectors' Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors' Creating a generic function for 'substr' from package 'base' in package 'S4Vectors' Creating a generic function for 'substring' from package 'base' in package 'S4Vectors' Creating a generic function for 'chartr' from package 'base' in package 'S4Vectors' Creating a generic function for 'tolower' from package 'base' in package 'S4Vectors' Creating a generic function for 'toupper' from package 'base' in package 'S4Vectors' Creating a generic function for 'sub' from package 'base' in package 'S4Vectors' Creating a generic function for 'gsub' from package 'base' in package 'S4Vectors' Creating a generic function for 'nlevels' from package 'base' in package 'S4Vectors' in method for 'coerce' with signature '"data.table","DFrame"': no definition for class "data.table" Creating a generic function for 'complete.cases' from package 'stats' in package 'S4Vectors' ** 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 (S4Vectors)