* installing *source* package 'ClusterGVis' ... ** this is package 'ClusterGVis' version '0.1.4' ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Installing package into 'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98' (as 'lib' is unspecified) trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.6/BiocManager_1.30.26.zip' Content type 'application/zip' length 507868 bytes (495 KB) ================================================== downloaded 495 KB package 'BiocManager' successfully unpacked and MD5 sums checked The downloaded binary packages are in D:\temp\2025_06_23_08_25_17_16803\RtmpWMpv1E\downloaded_packages 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://bioconductor.statistik.tu-dortmund.de/cran Bioconductor version 3.22 (BiocManager 1.30.26), R Under development (unstable) (2025-06-22 r88341 ucrt) Installing package(s) 'BiocVersion', 'SingleCellExperiment' also installing the dependencies 'sys', 'askpass', 'curl', 'openssl', 'httr', 'matrixStats', 'UCSC.utils', 'crayon', 'MatrixGenerics', 'Biobase', 'IRanges', 'GenomeInfoDb', 'S4Arrays', 'XVector', 'SparseArray', 'SummarizedExperiment', 'S4Vectors', 'BiocGenerics', 'GenomicRanges', 'DelayedArray' Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/bin/windows/contrib/4.6: cannot open URL 'https://bioconductor.org/packages/3.22/bioc/bin/windows/contrib/4.6/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/annotation/bin/windows/contrib/4.6: cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/bin/windows/contrib/4.6/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/experiment/bin/windows/contrib/4.6: cannot open URL 'https://bioconductor.org/packages/3.22/data/experiment/bin/windows/contrib/4.6/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.22/workflows/bin/windows/contrib/4.6: cannot open URL 'https://bioconductor.org/packages/3.22/workflows/bin/windows/contrib/4.6/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.22/books/bin/windows/contrib/4.6: cannot open URL 'https://bioconductor.org/packages/3.22/books/bin/windows/contrib/4.6/PACKAGES' There is a binary version available but the source version is later: binary source needs_compilation curl 6.3.0 6.4.0 TRUE Packages which are only available in source form, and may need compilation of C/C++/Fortran: 'Biobase' 'IRanges' 'S4Arrays' 'XVector' 'SparseArray' 'S4Vectors' 'GenomicRanges' 'DelayedArray' trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.6/sys_3.4.3.zip' trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.6/askpass_1.2.1.zip' trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.6/openssl_2.3.3.zip' trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.6/httr_1.4.7.zip' trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.6/matrixStats_1.5.0.zip' trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.6/crayon_1.5.3.zip' package 'sys' successfully unpacked and MD5 sums checked package 'askpass' successfully unpacked and MD5 sums checked package 'openssl' successfully unpacked and MD5 sums checked package 'httr' successfully unpacked and MD5 sums checked package 'matrixStats' successfully unpacked and MD5 sums checked package 'crayon' successfully unpacked and MD5 sums checked The downloaded binary packages are in D:\temp\2025_06_23_08_25_17_16803\RtmpWMpv1E\downloaded_packages installing the source packages 'curl', 'UCSC.utils', 'MatrixGenerics', 'Biobase', 'IRanges', 'GenomeInfoDb', 'S4Arrays', 'XVector', 'SparseArray', 'SummarizedExperiment', 'S4Vectors', 'BiocGenerics', 'GenomicRanges', 'DelayedArray', 'BiocVersion', 'SingleCellExperiment' trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/src/contrib/curl_6.4.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/UCSC.utils_1.5.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/MatrixGenerics_1.21.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/Biobase_2.69.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/IRanges_2.43.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/GenomeInfoDb_1.45.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/S4Arrays_1.9.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/XVector_0.49.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/SparseArray_1.9.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/SummarizedExperiment_1.39.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/S4Vectors_0.47.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/BiocGenerics_0.55.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/GenomicRanges_1.61.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/DelayedArray_0.35.2.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/BiocVersion_3.22.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/SingleCellExperiment_1.31.0.tar.gz' * installing *source* package 'curl' ... ** this is package 'curl' version '6.4.0' ** package 'curl' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c callbacks.c -o callbacks.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c curl.c -o curl.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c download.c -o download.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c dryrun.c -o dryrun.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c escape.c -o escape.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c fetch.c -o fetch.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c findport.c -o findport.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c form.c -o form.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c getdate.c -o getdate.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c handle.c -o handle.o In file included from curl-common.h:6, from handle.c:1: handle.c: In function 'R_handle_setopt': ../.deps/libcurl/include/curl/typecheck-gcc.h:84:15: warning: call to '_curl_easy_setopt_err_xferinfo_cb' declared with attribute warning: curl_easy_setopt expects a curl_xferinfo_callback argument [-Wattribute-warning] 84 | _curl_easy_setopt_err_xferinfo_cb(); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../.deps/libcurl/include/curl/curl.h:59:49: note: in definition of macro 'CURL_IGNORE_DEPRECATION' 59 | #define CURL_IGNORE_DEPRECATION(statements) statements | ^~~~~~~~~~ handle.c:110:54: note: in expansion of macro 'curl_easy_setopt' 110 | #define set_user_option(option, value) assert_setopt(curl_easy_setopt(handle, option, value), option, optname) | ^~~~~~~~~~~~~~~~ handle.c:284:7: note: in expansion of macro 'set_user_option' 284 | set_user_option(CURLOPT_XFERINFOFUNCTION, (curl_progress_callback) R_curl_callback_xferinfo); | ^~~~~~~~~~~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ieproxy.c -o ieproxy.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c interrupt.c -o interrupt.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c multi.c -o multi.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c nslookup.c -o nslookup.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c options.c -o options.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c reflist.c -o reflist.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c split.c -o split.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ssl.c -o ssl.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c typechecking.c -o typechecking.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c urlparser.c -o urlparser.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c version.c -o version.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c winidn.c -o winidn.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I../.deps/libcurl/include -DCURL_STATICLIB -DSTRICT_R_HEADERS -DR_NO_REMAP -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c writer.c -o writer.o gcc -shared -s -static-libgcc -o curl.dll tmp.def callbacks.o curl.o download.o dryrun.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o urlparser.o utils.o version.o winidn.o writer.o -L../.deps/libcurl/lib-14.2.0/x64 -L../.deps/libcurl/lib -lwinhttp -lcurl -lnghttp2 -lssh2 -lz -lssl -lcrypto -pthread -lgdi32 -lws2_32 -lcrypt32 -lbcrypt -lwldap32 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/00LOCK-curl/00new/curl/libs/x64 ** 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 (curl) * installing *source* package 'MatrixGenerics' ... ** this is package 'MatrixGenerics' version '1.21.0' ** package 'MatrixGenerics' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'rowAlls' in package 'MatrixGenerics' Creating a new generic function for 'colAlls' in package 'MatrixGenerics' Creating a new generic function for 'rowAnyNAs' in package 'MatrixGenerics' Creating a new generic function for 'colAnyNAs' in package 'MatrixGenerics' Creating a new generic function for 'rowAnys' in package 'MatrixGenerics' Creating a new generic function for 'colAnys' in package 'MatrixGenerics' Creating a new generic function for 'rowAvgsPerColSet' in package 'MatrixGenerics' Creating a new generic function for 'colAvgsPerRowSet' in package 'MatrixGenerics' Creating a new generic function for 'rowCollapse' in package 'MatrixGenerics' Creating a new generic function for 'colCollapse' in package 'MatrixGenerics' Creating a new generic function for 'rowCounts' in package 'MatrixGenerics' Creating a new generic function for 'colCounts' in package 'MatrixGenerics' Creating a new generic function for 'rowCummaxs' in package 'MatrixGenerics' Creating a new generic function for 'colCummaxs' in package 'MatrixGenerics' Creating a new generic function for 'rowCummins' in package 'MatrixGenerics' Creating a new generic function for 'colCummins' in package 'MatrixGenerics' Creating a new generic function for 'rowCumprods' in package 'MatrixGenerics' Creating a new generic function for 'colCumprods' in package 'MatrixGenerics' Creating a new generic function for 'rowCumsums' in package 'MatrixGenerics' Creating a new generic function for 'colCumsums' in package 'MatrixGenerics' Creating a new generic function for 'rowDiffs' in package 'MatrixGenerics' Creating a new generic function for 'colDiffs' in package 'MatrixGenerics' Creating a new generic function for 'rowIQRDiffs' in package 'MatrixGenerics' Creating a new generic function for 'colIQRDiffs' in package 'MatrixGenerics' Creating a new generic function for 'rowIQRs' in package 'MatrixGenerics' Creating a new generic function for 'colIQRs' in package 'MatrixGenerics' Creating a new generic function for 'rowLogSumExps' in package 'MatrixGenerics' Creating a new generic function for 'colLogSumExps' in package 'MatrixGenerics' Creating a new generic function for 'rowMadDiffs' in package 'MatrixGenerics' Creating a new generic function for 'colMadDiffs' in package 'MatrixGenerics' Creating a new generic function for 'rowMads' in package 'MatrixGenerics' Creating a new generic function for 'colMads' in package 'MatrixGenerics' Creating a new generic function for 'rowMaxs' in package 'MatrixGenerics' Creating a new generic function for 'colMaxs' in package 'MatrixGenerics' Creating a new generic function for 'rowMeans2' in package 'MatrixGenerics' Creating a new generic function for 'colMeans2' in package 'MatrixGenerics' Creating a new generic function for 'rowMedians' in package 'MatrixGenerics' Creating a new generic function for 'colMedians' in package 'MatrixGenerics' Creating a new generic function for 'rowMins' in package 'MatrixGenerics' Creating a new generic function for 'colMins' in package 'MatrixGenerics' Creating a new generic function for 'rowOrderStats' in package 'MatrixGenerics' Creating a new generic function for 'colOrderStats' in package 'MatrixGenerics' Creating a new generic function for 'rowProds' in package 'MatrixGenerics' Creating a new generic function for 'colProds' in package 'MatrixGenerics' Creating a new generic function for 'rowQuantiles' in package 'MatrixGenerics' Creating a new generic function for 'colQuantiles' in package 'MatrixGenerics' Creating a new generic function for 'rowRanges' in package 'MatrixGenerics' Creating a new generic function for 'colRanges' in package 'MatrixGenerics' Creating a new generic function for 'rowRanks' in package 'MatrixGenerics' Creating a new generic function for 'colRanks' in package 'MatrixGenerics' Creating a new generic function for 'rowSdDiffs' in package 'MatrixGenerics' Creating a new generic function for 'colSdDiffs' in package 'MatrixGenerics' Creating a new generic function for 'rowSds' in package 'MatrixGenerics' Creating a new generic function for 'colSds' in package 'MatrixGenerics' Creating a new generic function for 'rowSums2' in package 'MatrixGenerics' Creating a new generic function for 'colSums2' in package 'MatrixGenerics' Creating a new generic function for 'rowTabulates' in package 'MatrixGenerics' Creating a new generic function for 'colTabulates' in package 'MatrixGenerics' Creating a new generic function for 'rowVarDiffs' in package 'MatrixGenerics' Creating a new generic function for 'colVarDiffs' in package 'MatrixGenerics' Creating a new generic function for 'rowVars' in package 'MatrixGenerics' Creating a new generic function for 'colVars' in package 'MatrixGenerics' Creating a new generic function for 'rowWeightedMads' in package 'MatrixGenerics' Creating a new generic function for 'colWeightedMads' in package 'MatrixGenerics' Creating a new generic function for 'rowWeightedMeans' in package 'MatrixGenerics' Creating a new generic function for 'colWeightedMeans' in package 'MatrixGenerics' Creating a new generic function for 'rowWeightedMedians' in package 'MatrixGenerics' Creating a new generic function for 'colWeightedMedians' in package 'MatrixGenerics' Creating a new generic function for 'rowWeightedSds' in package 'MatrixGenerics' Creating a new generic function for 'colWeightedSds' in package 'MatrixGenerics' Creating a new generic function for 'rowWeightedVars' in package 'MatrixGenerics' Creating a new generic function for 'colWeightedVars' in package 'MatrixGenerics' ** 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 (MatrixGenerics) * installing *source* package 'BiocGenerics' ... ** this is package 'BiocGenerics' version '0.55.0' ** package 'BiocGenerics' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'aperm' in package 'BiocGenerics' Creating a new generic function for 'append' in package 'BiocGenerics' Creating a new generic function for 'as.data.frame' in package 'BiocGenerics' Creating a new generic function for 'cbind' in package 'BiocGenerics' Creating a new generic function for 'rbind' in package 'BiocGenerics' Creating a new generic function for 'do.call' in package 'BiocGenerics' Creating a new generic function for 'duplicated' in package 'BiocGenerics' Creating a new generic function for 'anyDuplicated' in package 'BiocGenerics' Creating a new generic function for 'eval' in package 'BiocGenerics' Creating a new generic function for 'pmax' in package 'BiocGenerics' Creating a new generic function for 'pmin' in package 'BiocGenerics' Creating a new generic function for 'pmax.int' in package 'BiocGenerics' Creating a new generic function for 'pmin.int' in package 'BiocGenerics' Creating a new generic function for 'Reduce' in package 'BiocGenerics' Creating a new generic function for 'Filter' in package 'BiocGenerics' Creating a new generic function for 'Find' in package 'BiocGenerics' Creating a new generic function for 'Map' in package 'BiocGenerics' Creating a new generic function for 'Position' in package 'BiocGenerics' Creating a new generic function for 'get' in package 'BiocGenerics' Creating a new generic function for 'mget' in package 'BiocGenerics' Creating a new generic function for 'grep' in package 'BiocGenerics' Creating a new generic function for 'grepl' in package 'BiocGenerics' Creating a new generic function for 'is.unsorted' in package 'BiocGenerics' Creating a new generic function for 'lapply' in package 'BiocGenerics' Creating a new generic function for 'sapply' in package 'BiocGenerics' Creating a new generic function for 'mapply' in package 'BiocGenerics' Creating a new generic function for 'match' in package 'BiocGenerics' Creating a new generic function for 'order' in package 'BiocGenerics' Creating a new generic function for 'paste' in package 'BiocGenerics' Creating a new generic function for 'rank' in package 'BiocGenerics' Creating a new generic function for 'rownames' in package 'BiocGenerics' Creating a new generic function for 'colnames' in package 'BiocGenerics' Creating a new generic function for 'saveRDS' in package 'BiocGenerics' Creating a new generic function for 'table' in package 'BiocGenerics' Creating a new generic function for 'tapply' in package 'BiocGenerics' Creating a new generic function for 'unique' in package 'BiocGenerics' Creating a new generic function for 'unsplit' in package 'BiocGenerics' Creating a new generic function for 'which.min' in package 'BiocGenerics' Creating a new generic function for 'which.max' in package 'BiocGenerics' Creating a new generic function for 'IQR' in package 'BiocGenerics' Creating a new generic function for 'mad' in package 'BiocGenerics' Creating a new generic function for 'var' in package 'BiocGenerics' Creating a new generic function for 'sd' in package 'BiocGenerics' Creating a new generic function for 'xtabs' in package 'BiocGenerics' Creating a new generic function for 'basename' in package 'BiocGenerics' Creating a new generic function for 'dirname' in package 'BiocGenerics' ** 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 (BiocGenerics) * installing *source* package 'BiocVersion' ... ** this is package 'BiocVersion' version '3.22.0' ** package 'BiocVersion' successfully unpacked and MD5 sums checked ** using staged installation ** 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 (BiocVersion) * installing *source* package 'Biobase' ... ** this is package 'Biobase' version '2.69.0' ** package 'Biobase' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c anyMissing.c -o anyMissing.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c envir.c -o envir.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c matchpt.c -o matchpt.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c rowMedians.c -o rowMedians.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c sublist_extract.c -o sublist_extract.o gcc -shared -s -static-libgcc -o Biobase.dll tmp.def Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/00LOCK-Biobase/00new/Biobase/libs/x64 ** 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 (Biobase) * installing *source* package 'S4Vectors' ... ** this is package 'S4Vectors' version '0.47.0' ** package 'S4Vectors' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c AEbufs.c -o AEbufs.o AEbufs.c: In function '_IntAEAE_toEnvir': AEbufs.c:634:50: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 634 | snprintf(key, sizeof(key), "%010lu", i + keyshift); | ~~~~~^ ~~~~~~~~~~~~ | | | | | size_t {aka long long unsigned int} | long unsigned int | %010llu gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c DataFrame_class.c -o DataFrame_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Hits_class.c -o Hits_class.o Hits_class.c: In function 'tsort_hits': Hits_class.c:113:17: warning: 'memcpy' specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 113 | memcpy(from_in, from_out, sizeof(int) * nLnode); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Hits_class.c: In function 'qsort_hits': Hits_class.c:74:25: warning: 'memcpy' specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 74 | memcpy(from_in, revmap, sizeof(int) * nhit); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Hits_class.c:74:25: warning: 'memcpy' specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] In file included from D:/RCompile/recent/R/include/Rdefines.h:41, from ../inst/include/S4Vectors_defines.h:18, from S4Vectors.h:1, from Hits_class.c:4: Hits_class.c: In function 'Hits_new': D:/RCompile/recent/R/include/Rinternals.h:926:33: warning: 'revmap' may be used uninitialized [-Wmaybe-uninitialized] 926 | #define defineVar Rf_defineVar Hits_class.c:244:9: note: in expansion of macro 'defineVar' 244 | defineVar(install(translateChar(symbol)), revmap, revmap_envir); | ^~~~~~~~~ Hits_class.c:219:19: note: 'revmap' was declared here 219 | SEXP ans, revmap, symbol; | ^~~~~~ Hits_class.c: In function 'select_hits': Hits_class.c:348:48: warning: 'is_used' may be used uninitialized [-Wmaybe-uninitialized] 348 | is_used->elts[ans_elt - 1] = 1; | ~~~~~~~^~~~~~ Hits_class.c:313:17: note: 'is_used' was declared here 313 | CharAE *is_used; | ^~~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c LLint_class.c -o LLint_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c List_class.c -o List_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Rle_class.c -o Rle_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Rle_utils.c -o Rle_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SEXP_utils.c -o SEXP_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SimpleList_class.c -o SimpleList_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c anyMissing.c -o anyMissing.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -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: D:/rtools45/x86_64-w64-mingw32.static.posix/include/time.h:286:23: note: declared here 286 | _CRTIMP extern long timezone __MINGW_ATTRIB_DEPRECATED_UCRT; | ^~~~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c eval_utils.c -o eval_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c hash_utils.c -o hash_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c integer_utils.c -o integer_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c logical_utils.c -o logical_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c raw_utils.c -o raw_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c safe_arithm.c -o safe_arithm.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c sort_utils.c -o sort_utils.o sort_utils.c:267:13: warning: 'sort_uchar_array' defined but not used [-Wunused-function] 267 | static void sort_uchar_array(unsigned char *x, int nelt, int desc) | ^~~~~~~~~~~~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c subsetting_utils.c -o subsetting_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -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 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/00LOCK-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' 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) * installing *source* package 'UCSC.utils' ... ** this is package 'UCSC.utils' version '1.5.0' ** package 'UCSC.utils' 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 (UCSC.utils) * installing *source* package 'IRanges' ... ** this is package 'IRanges' version '2.43.0' ** package 'IRanges' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c CompressedList_class.c -o CompressedList_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Grouping_class.c -o Grouping_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c IPosRanges_comparison.c -o IPosRanges_comparison.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c IRanges_class.c -o IRanges_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c IRanges_constructor.c -o IRanges_constructor.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c NCList.c -o NCList.o NCList.c:1173:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function] 1173 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist, | ^~~~~~~~~~~~~~~~~~~~~~~~~ NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function] 202 | static const NCList *next_top_down(const NCList *nclist) | ^~~~~~~~~~~~~ NCList.c: In function 'C_find_overlaps_in_groups_NCList': NCList.c:1608:24: warning: 'ans' may be used uninitialized [-Wmaybe-uninitialized] 1608 | return ans; | ^~~ NCList.c:1546:14: note: 'ans' was declared here 1546 | SEXP ans; | ^~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_init_IRanges.c -o R_init_IRanges.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Ranges_class.c -o Ranges_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c RleViews_utils.c -o RleViews_utils.o In function 'viewWhichMaxs_int_RleViews', inlined from 'viewWhichMaxs_RleViews' at RleViews_utils.c:579:3, inlined from 'C_summarize_RleViews' at RleViews_utils.c:694:9: RleViews_utils.c:325:54: warning: 'max' may be used uninitialized [-Wmaybe-uninitialized] 325 | if (!max_is_initialized || v > max) { | ~~^~~~~ RleViews_utils.c: In function 'C_summarize_RleViews': RleViews_utils.c:316:21: note: 'max' was declared here 316 | int max; /* uninitialized */ | ^~~ In function 'viewWhichMins_int_RleViews', inlined from 'viewWhichMins_RleViews' at RleViews_utils.c:546:3, inlined from 'C_summarize_RleViews' at RleViews_utils.c:686:9: RleViews_utils.c:293:54: warning: 'min' may be used uninitialized [-Wmaybe-uninitialized] 293 | if (!min_is_initialized || v < min) { | ~~^~~~~ RleViews_utils.c: In function 'C_summarize_RleViews': RleViews_utils.c:284:21: note: 'min' was declared here 284 | int min; /* uninitialized */ | ^~~ In function 'viewMaxs_int_RleViews', inlined from 'viewMaxs_RleViews' at RleViews_utils.c:443:3, inlined from 'C_summarize_RleViews' at RleViews_utils.c:665:9: RleViews_utils.c:67:54: warning: 'max' may be used uninitialized [-Wmaybe-uninitialized] 67 | if (!max_is_initialized || v > max) { | ~~^~~~~ RleViews_utils.c: In function 'C_summarize_RleViews': RleViews_utils.c:54:21: note: 'max' was declared here 54 | int max; /* uninitialized */ | ^~~ In function 'viewMins_int_RleViews', inlined from 'viewMins_RleViews' at RleViews_utils.c:413:3, inlined from 'C_summarize_RleViews' at RleViews_utils.c:660:9: RleViews_utils.c:36:54: warning: 'min' may be used uninitialized [-Wmaybe-uninitialized] 36 | if (!min_is_initialized || v < min) { | ~~^~~~~ RleViews_utils.c: In function 'C_summarize_RleViews': RleViews_utils.c:23:21: note: 'min' was declared here 23 | int min; /* uninitialized */ | ^~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c coverage_methods.c -o coverage_methods.o In function 'shift_and_clip_ranges', inlined from 'compute_coverage_from_IRanges_holder' at coverage_methods.c:609:12: coverage_methods.c:579:35: warning: 'x_end' may be used uninitialized [-Wmaybe-uninitialized] 579 | if (*out_ranges_are_tiles && x_end != cvg_len) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ coverage_methods.c: In function 'compute_coverage_from_IRanges_holder': coverage_methods.c:495:28: note: 'x_end' was declared here 495 | i, j, x_start, x_end, shift_elt, tmp; | ^~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c extractListFragments.c -o extractListFragments.o extractListFragments.c: In function 'C_find_partition_overlaps': extractListFragments.c:85:25: warning: 'split_partitions_buf' may be used uninitialized [-Wmaybe-uninitialized] 85 | IntAE_insert_at(split_partitions_buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 | IntAE_get_nelt(split_partitions_buf), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 | q_prev_end); | ~~~~~~~~~~~ extractListFragments.c:35:16: note: 'split_partitions_buf' was declared here 35 | IntAE *split_partitions_buf; | ^~~~~~~~~~~~~~~~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c inter_range_methods.c -o inter_range_methods.o inter_range_methods.c: In function 'reduce_ranges.isra': inter_range_methods.c:154:39: warning: 'gapwidth' may be used uninitialized [-Wmaybe-uninitialized] 154 | delta += gapwidth; | ~~~~~~^~~~~~~~~~~ inter_range_methods.c:102:38: note: 'gapwidth' was declared here 102 | append_or_drop, max_end, gapwidth, delta, width_inc; | ^~~~~~~~ gcc -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/00LOCK-IRanges/00new/IRanges/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'drop' from package 'base' in package 'IRanges' Creating a generic function for 'runmed' from package 'stats' in package 'IRanges' Creating a generic function for 'chartr' from package 'base' in package 'IRanges' Creating a generic function for 'toupper' from package 'base' in package 'IRanges' Creating a generic function for 'tolower' from package 'base' in package 'IRanges' Creating a generic function for 'sub' from package 'base' in package 'IRanges' Creating a generic function for 'gsub' from package 'base' in package 'IRanges' Creating a generic function for 'startsWith' from package 'base' in package 'IRanges' Creating a generic function for 'endsWith' from package 'base' in package 'IRanges' Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges' Creating a new generic function for 'windows' in package 'IRanges' ** 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 (IRanges) * installing *source* package 'GenomeInfoDb' ... ** this is package 'GenomeInfoDb' version '1.45.4' ** package 'GenomeInfoDb' 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 (GenomeInfoDb) * installing *source* package 'S4Arrays' ... ** this is package 'S4Arrays' version '1.9.1' ** package 'S4Arrays' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_init_S4Arrays.c -o R_init_S4Arrays.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c abind.c -o abind.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c array_selection.c -o array_selection.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c dim_tuning_utils.c -o dim_tuning_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c rowsum.c -o rowsum.o gcc -shared -s -static-libgcc -o S4Arrays.dll tmp.def R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o rowsum.o -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/00LOCK-S4Arrays/00new/S4Arrays/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'rowsum' in package 'S4Arrays' Creating a new generic function for 'abind' in package 'S4Arrays' ** 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 (S4Arrays) * installing *source* package 'XVector' ... ** this is package 'XVector' version '0.49.0' ** package 'XVector' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c RDS_random_access.c -o RDS_random_access.o RDS_random_access.c: In function 'RDS_extract_subarray': RDS_random_access.c:796:25: warning: unused variable 'ans' [-Wunused-variable] 796 | SEXP subscript, ans; | ^~~ RDS_random_access.c:793:18: warning: variable 'x_type' set but not used [-Wunused-but-set-variable] 793 | SEXPTYPE x_type; | ^~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_init_XVector.c -o R_init_XVector.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SharedDouble_class.c -o SharedDouble_class.o SharedDouble_class.c: In function 'SharedDouble_get_show_string': SharedDouble_class.c:42:82: warning: format '%p' expects argument of type 'void *', but argument 5 has type 'double *' [-Wformat=] 42 | "%d-number SharedDouble object (data starting at memory address %p)", | ~^ | | | void * 43 | tag_length, REAL(tag)); | ~~~~~~~~~ | | | double * gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SharedInteger_class.c -o SharedInteger_class.o SharedInteger_class.c: In function 'SharedInteger_get_show_string': SharedInteger_class.c:41:84: warning: format '%p' expects argument of type 'void *', but argument 5 has type 'int *' [-Wformat=] 41 | "%d-integer SharedInteger object (data starting at memory address %p)", | ~^ | | | void * | %n 42 | tag_length, INTEGER(tag)); | ~~~~~~~~~~~~ | | | int * gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SharedRaw_class.c -o SharedRaw_class.o SharedRaw_class.c: In function 'SharedRaw_read_complexes_from_subscript': SharedRaw_class.c:396:20: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable] 396 | SEXP dest, src_tag; | ^~~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SharedVector_class.c -o SharedVector_class.o SharedVector_class.c: In function 'address_as_CHARSXP': SharedVector_class.c:22:38: warning: format '%p' expects argument of type 'void *', but argument 4 has type 'SEXP' {aka 'struct SEXPREC *'} [-Wformat=] 22 | snprintf(buf, sizeof(buf), "%p", x); | ~^ ~ | | | | | SEXP {aka struct SEXPREC *} | void * SharedVector_class.c: In function 'externalptr_show': SharedVector_class.c:110:32: warning: format '%p' expects argument of type 'void *', but argument 2 has type 'SEXP' {aka 'struct SEXPREC *'} [-Wformat=] 110 | Rprintf(" x address: %p\n", x); | ~^ ~ | | | | | SEXP {aka struct SEXPREC *} | void * SharedVector_class.c:114:42: warning: format '%p' expects argument of type 'void *', but argument 2 has type 'SEXP' {aka 'struct SEXPREC *'} [-Wformat=] 114 | Rprintf(" R_ExternalPtrTag(x): %p\n", s); | ~^ ~ | | | | | SEXP {aka struct SEXPREC *} | void * SharedVector_class.c:118:48: warning: format '%p' expects argument of type 'void *', but argument 2 has type 'SEXP' {aka 'struct SEXPREC *'} [-Wformat=] 118 | Rprintf(" R_ExternalPtrProtected(x): %p\n", s); | ~^ ~ | | | | | SEXP {aka struct SEXPREC *} | void * gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c XDouble_class.c -o XDouble_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c XInteger_class.c -o XInteger_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c XRawList_comparison.c -o XRawList_comparison.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c XRaw_class.c -o XRaw_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c XVectorList_class.c -o XVectorList_class.o XVectorList_class.c: In function '_new_XRawList_from_CharAEAE': XVectorList_class.c:459:17: warning: 'lkup_length' may be used uninitialized [-Wmaybe-uninitialized] 459 | _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 460 | (char *) dest.ptr, dest.length, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 461 | src->elts, CharAE_get_nelt(src), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 462 | lkup0, lkup_length); | ~~~~~~~~~~~~~~~~~~~ XVectorList_class.c:434:13: note: 'lkup_length' was declared here 434 | int lkup_length, nelt, i; | ^~~~~~~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c XVector_class.c -o XVector_class.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c io_utils.c -o io_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c slice_methods.c -o slice_methods.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c vector_copy.c -o vector_copy.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c view_summarization_methods.c -o view_summarization_methods.o view_summarization_methods.c: In function 'get_which_min_from_Ints_holder': view_summarization_methods.c:219:45: warning: 'cur_min' may be used uninitialized [-Wmaybe-uninitialized] 219 | if (which_min == NA_INTEGER || x < cur_min) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:208:19: note: 'cur_min' was declared here 208 | int xlen, cur_min, which_min, i, x; | ^~~~~~~ view_summarization_methods.c: In function 'get_which_min_from_Doubles_holder': view_summarization_methods.c:246:45: warning: 'cur_min' may be used uninitialized [-Wmaybe-uninitialized] 246 | if (which_min == NA_INTEGER || x < cur_min) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:235:16: note: 'cur_min' was declared here 235 | double cur_min, x; | ^~~~~~~ view_summarization_methods.c: In function 'get_which_max_from_Ints_holder': view_summarization_methods.c:269:45: warning: 'cur_max' may be used uninitialized [-Wmaybe-uninitialized] 269 | if (which_max == NA_INTEGER || x > cur_max) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:258:19: note: 'cur_max' was declared here 258 | int xlen, cur_max, which_max, i, x; | ^~~~~~~ view_summarization_methods.c: In function 'get_which_max_from_Doubles_holder': view_summarization_methods.c:296:45: warning: 'cur_max' may be used uninitialized [-Wmaybe-uninitialized] 296 | if (which_max == NA_INTEGER || x > cur_max) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:285:16: note: 'cur_max' was declared here 285 | double cur_max, x; | ^~~~~~~ gcc -shared -s -static-libgcc -o XVector.dll tmp.def IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/00LOCK-XVector/00new/XVector/libs/x64 ** 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 (XVector) * installing *source* package 'SparseArray' ... ** this is package 'SparseArray' version '1.9.0' ** package 'SparseArray' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o ExtendableJaggedArray.c: In function '_move_ExtendableJaggedArrays_to_SVT': ExtendableJaggedArray.c:129:25: warning: 'nzvals_p' may be used uninitialized [-Wmaybe-uninitialized] 129 | free(nzvals_p); | ^~~~~~~~~~~~~~ ExtendableJaggedArray.c:111:22: note: 'nzvals_p' was declared here 111 | int *nzvals_p, *nzoffs_p; | ^~~~~~~~ ExtendableJaggedArray.c:125:25: warning: 'nzoffs_p' may be used uninitialized [-Wmaybe-uninitialized] 125 | free(nzoffs_p); | ^~~~~~~~~~~~~~ ExtendableJaggedArray.c:111:33: note: 'nzoffs_p' was declared here 111 | int *nzvals_p, *nzoffs_p; | ^~~~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c OPBufTree.c -o OPBufTree.o OPBufTree.c: In function 'print_OPBuf': OPBufTree.c:271:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 271 | Rprintf("%4lu", opbuf->xLoffs[k]); | ~~~^ ~~~~~~~~~~~~~~~~ | | | | | R_xlen_t {aka long long int} | long unsigned int | %4llu gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Rvector_summarization.c -o Rvector_summarization.o Rvector_summarization.c:1370:12: warning: 'count_NA_list_elts' defined but not used [-Wunused-function] 1370 | static int count_NA_list_elts(SEXP x) | ^~~~~~~~~~~~~~~~~~ Rvector_summarization.c:1360:12: warning: 'any_NA_list_elt' defined but not used [-Wunused-function] 1360 | static int any_NA_list_elt(SEXP x) | ^~~~~~~~~~~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Rvector_utils.c -o Rvector_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SBT_utils.c -o SBT_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o SVT_SparseArray_class.c: In function 'C_from_SVT_SparseMatrix_to_CsparseMatrix': SVT_SparseArray_class.c:645:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 645 | error("SVT_SparseMatrix object contains too many nonzero " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 646 | "values (%ld) to \"fit\" in a CsparseMatrix derivative", 647 | x_nzcount); | ~~~~~~~~~ | | | R_xlen_t {aka long long int} SVT_SparseArray_class.c:646:34: note: format string is defined here 646 | "values (%ld) to \"fit\" in a CsparseMatrix derivative", | ~~^ | | | long int | %lld gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_abind.c -o SparseArray_abind.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_subassignment_OLD.c -o SparseArray_subassignment_OLD.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseMatrix_mult.c -o SparseMatrix_mult.o SparseMatrix_mult.c:346:13: warning: 'crossprod2_doublemat_doubleSV' defined but not used [-Wunused-function] 346 | static void crossprod2_doublemat_doubleSV( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SparseMatrix_mult.c:306:13: warning: 'crossprod2_doubleSV_doublemat' defined but not used [-Wunused-function] 306 | static void crossprod2_doubleSV_doublemat( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec.c -o SparseVec.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec_Arith.c -o SparseVec_Arith.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec_Compare.c -o SparseVec_Compare.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec_Logic.c -o SparseVec_Logic.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec_Math.c -o SparseVec_Math.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec_dotprod.c -o SparseVec_dotprod.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c argcheck_utils.c -o argcheck_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c coerceVector2.c -o coerceVector2.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c leaf_utils.c -o leaf_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c randomSparseArray.c -o randomSparseArray.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c readSparseCSV.c -o readSparseCSV.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c rowsum_methods.c -o rowsum_methods.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c test.c -o test.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/XVector/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c thread_control.c -o thread_control.o gcc -shared -s -static-libgcc -o SparseArray.dll tmp.def ExtendableJaggedArray.o IRanges_stubs.o OPBufTree.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Arith_methods.o SparseArray_Compare_methods.o SparseArray_Complex_methods.o SparseArray_Logic_methods.o SparseArray_Math_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_dim_tuning.o SparseArray_matrixStats.o SparseArray_misc_methods.o SparseArray_subassignment.o SparseArray_subassignment_OLD.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o XVector_stubs.o argcheck_utils.o coerceVector2.o leaf_utils.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -fopenmp -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/00LOCK-SparseArray/00new/SparseArray/libs/x64 ** 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 (SparseArray) * installing *source* package 'GenomicRanges' ... ** this is package 'GenomicRanges' version '1.61.0' ** package 'GenomicRanges' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/IRanges/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c transcript_utils.c -o transcript_utils.o In function 'tloc2rloc', inlined from 'tlocs2rlocs' at transcript_utils.c:208:26: transcript_utils.c:143:45: warning: 'start' may be used uninitialized [-Wmaybe-uninitialized] 143 | return on_minus_strand ? end - tloc : start + tloc; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ transcript_utils.c: In function 'tlocs2rlocs': transcript_utils.c:120:24: note: 'start' was declared here 120 | int nexons, j, start, end, width; | ^~~~~ In function 'tloc2rloc', inlined from 'tlocs2rlocs' at transcript_utils.c:208:26: transcript_utils.c:143:45: warning: 'end' may be used uninitialized [-Wmaybe-uninitialized] 143 | return on_minus_strand ? end - tloc : start + tloc; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ transcript_utils.c: In function 'tlocs2rlocs': transcript_utils.c:120:31: note: 'end' was declared here 120 | int nexons, j, start, end, width; | ^~~ gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/00LOCK-GenomicRanges/00new/GenomicRanges/libs/x64 ** 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 (GenomicRanges) * installing *source* package 'DelayedArray' ... ** this is package 'DelayedArray' version '0.35.2' ** package 'DelayedArray' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_init_DelayedArray.c -o R_init_DelayedArray.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/S4Vectors/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c compress_atomic_vector.c -o compress_atomic_vector.o gcc -shared -s -static-libgcc -o DelayedArray.dll tmp.def R_init_DelayedArray.o S4Vectors_stubs.o compress_atomic_vector.o -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to D:/temp/2025_06_23_08_25_17_16803/RtmpKGWad7/RLIBS_f4b43e335c98/00LOCK-DelayedArray/00new/DelayedArray/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'apply' in package 'DelayedArray' Creating a new generic function for 'sweep' in package 'DelayedArray' Creating a new generic function for 'scale' in package 'DelayedArray' Creating a generic function for 'dnorm' from package 'stats' in package 'DelayedArray' Creating a generic function for 'pnorm' from package 'stats' in package 'DelayedArray' Creating a generic function for 'qnorm' from package 'stats' in package 'DelayedArray' Creating a generic function for 'dbinom' from package 'stats' in package 'DelayedArray' Creating a generic function for 'pbinom' from package 'stats' in package 'DelayedArray' Creating a generic function for 'qbinom' from package 'stats' in package 'DelayedArray' Creating a generic function for 'dpois' from package 'stats' in package 'DelayedArray' Creating a generic function for 'ppois' from package 'stats' in package 'DelayedArray' Creating a generic function for 'qpois' from package 'stats' in package 'DelayedArray' Creating a generic function for 'dlogis' from package 'stats' in package 'DelayedArray' Creating a generic function for 'plogis' from package 'stats' in package 'DelayedArray' Creating a generic function for 'qlogis' from package 'stats' in package 'DelayedArray' ** 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 (DelayedArray) * installing *source* package 'SummarizedExperiment' ... ** this is package 'SummarizedExperiment' version '1.39.0' ** package 'SummarizedExperiment' 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 (SummarizedExperiment) * installing *source* package 'SingleCellExperiment' ... ** this is package 'SingleCellExperiment' version '1.31.0' ** package 'SingleCellExperiment' 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 (SingleCellExperiment) The downloaded source packages are in 'D:\temp\2025_06_23_08_25_17_16803\RtmpWMpv1E\downloaded_packages' Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, : no definition was found for superclass "BiocVersion" in the specification of class "cell_data_set" Error: unable to load R code in package 'ClusterGVis' Execution halted ERROR: lazy loading failed for package 'ClusterGVis' * removing 'd:/RCompile/CRANincoming/R-devel/lib/ClusterGVis'