* using log directory ‘/home/hornik/tmp/CRAN_special_clang-san/fastQR.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘fastQR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘fastQR’ version ‘1.0.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘fastQR’ can be installed ... [174s/174s] OK * used C++ compiler: ‘Debian clang version 19.1.7 (1+b1)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [8s/8s] OK * checking Rd files ... [2s/2s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [1s/1s] ERROR Running examples in ‘fastQR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: qrdowndate > ### Title: Fast downdating of the QR factorization > ### Aliases: qrdowndate > > ### ** Examples > > ## Remove one column > ## generate sample data > set.seed(10) > n <- 10 > p <- 6 > X <- matrix(rnorm(n * p, 1), n, p) > > ## get the initial QR factorization > output <- fastQR::qr(X, type = "householder", + nb = NULL, + complete = TRUE) > Q <- output$Q > R <- output$R > > ## select the column to be deleted > ## from X and update X > k <- 2 > X1 <- X[, -k] > > ## downdate the QR decomposition > out <- fastQR::qrdowndate(Q = Q, R = R, + k = k, m = 1, + type = "column", + fast = FALSE, + complete = TRUE) ================================================================= ==2839417==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x5140001e5fd0 at pc 0x7f22e9917b4f bp 0x7fff15e54d10 sp 0x7fff15e54d08 READ of size 16 at 0x5140001e5fd0 thread T0 #0 0x7f22e9917b4e in double vector[2] Eigen::internal::ploadu(Eigen::internal::unpacket_traits::type const*) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:746:10 #1 0x7f22e9917b4e in double vector[2] Eigen::internal::ploadt(Eigen::internal::unpacket_traits::type const*) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:969:12 #2 0x7f22e9917b4e in double vector[2] Eigen::internal::evaluator>>::packet<0, double vector[2]>(long, long) const /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:238:14 #3 0x7f22e9917b4e in void Eigen::internal::generic_dense_assignment_kernel, -1, -1, false>>, Eigen::internal::evaluator>, Eigen::internal::assign_op, 0>::assignPacket<16, 0, double vector[2]>(long, long) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:675:89 #4 0x7f22e9917b4e in void Eigen::internal::generic_dense_assignment_kernel, -1, -1, false>>, Eigen::internal::evaluator>, Eigen::internal::assign_op, 0>::assignPacketByOuterInner<16, 0, double vector[2]>(long, long) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:689:5 #5 0x7f22e9917b4e in Eigen::internal::dense_assignment_loop, -1, -1, false>>, Eigen::internal::evaluator>, Eigen::internal::assign_op, 0>, 4, 0>::run(Eigen::internal::generic_dense_assignment_kernel, -1, -1, false>>, Eigen::internal::evaluator>, Eigen::internal::assign_op, 0>&) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:572:25 #6 0x7f22e9928420 in void Eigen::internal::call_dense_assignment_loop, -1, -1, false>, Eigen::Matrix, Eigen::internal::assign_op>(Eigen::Block, -1, -1, false>&, Eigen::Matrix const&, Eigen::internal::assign_op const&) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785:3 #7 0x7f22e9928420 in Eigen::internal::Assignment, -1, -1, false>, Eigen::Matrix, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Block, -1, -1, false>&, Eigen::Matrix const&, Eigen::internal::assign_op const&) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #8 0x7f22e9928420 in void Eigen::internal::call_assignment_no_alias, -1, -1, false>, Eigen::Matrix, Eigen::internal::assign_op>(Eigen::Block, -1, -1, false>&, Eigen::Matrix const&, Eigen::internal::assign_op const&) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #9 0x7f22e9928420 in void Eigen::internal::call_assignment, -1, -1, false>, Eigen::Matrix, Eigen::internal::assign_op>(Eigen::Block, -1, -1, false>&, Eigen::Matrix const&, Eigen::internal::assign_op const&, Eigen::internal::enable_if>::value, void*>::type) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:3 #10 0x7f22e9928420 in void Eigen::internal::call_assignment, -1, -1, false>, Eigen::Matrix>(Eigen::Block, -1, -1, false>&, Eigen::Matrix const&) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:3 #11 0x7f22e9928420 in Eigen::Block, -1, -1, false>& Eigen::MatrixBase, -1, -1, false>>::operator=>(Eigen::DenseBase> const&) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/Assign.h:66:3 #12 0x7f22e9928420 in Eigen::internal::BlockImpl_dense, -1, -1, false, true>& Eigen::internal::BlockImpl_dense, -1, -1, false, true>::operator=>(Eigen::DenseBase> const&) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/Block.h:341:5 #13 0x7f22e9928420 in Eigen::BlockImpl, -1, -1, false, Eigen::Dense>& Eigen::BlockImpl, -1, -1, false, Eigen::Dense>::operator=>(Eigen::DenseBase> const&) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/Block.h:161:5 #14 0x7f22e9928420 in Eigen::Block, -1, -1, false>& Eigen::Block, -1, -1, false>::operator=>(Eigen::DenseBase> const&) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/Block.h:111:5 #15 0x7f22e9928420 in qrdowndate(Eigen::Matrix const&, Eigen::Matrix const&, int, Rcpp::Nullable, Rcpp::Nullable, std::allocator>>, Rcpp::Nullable, Rcpp::Nullable) /home/hornik/tmp/CRAN_special_clang-san/fastQR.Rcheck/00_pkg_src/fastQR/src/QR_wrap.cpp:716:44 #16 0x7f22e9ab519a in _fastQR_qrdowndate /home/hornik/tmp/CRAN_special_clang-san/fastQR.Rcheck/00_pkg_src/fastQR/src/RcppExports.cpp:188:34 #17 0x7f2304954a66 in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:775:11 #18 0x7f2304b18cf9 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8672:21 #19 0x7f2304aa7994 in bcEval /home/hornik/src/R/src/main/eval.c:7505:16 #20 0x7f2304aa60cf in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #21 0x7f2304ab0825 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393:22 #22 0x7f2304aac31c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306:16 #23 0x7f2304aa6a4f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328:16 #24 0x7f2304aa6a4f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #25 0x7f2304abf3e5 in do_set /home/hornik/src/R/src/main/eval.c:3571:8 #26 0x7f2304aa649b in Rf_eval /home/hornik/src/R/src/main/eval.c:1232:12 #27 0x7f2304bea427 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265:2 #28 0x7f2304bed240 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #29 0x7f2304bed064 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1219:5 #30 0x7f2304bed30a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1226:5 #31 0x5603c6593dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #32 0x7f2303e33d67 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #33 0x7f2303e33e24 in __libc_start_main csu/../csu/libc-start.c:360:3 #34 0x5603c64b0370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 38e1ee5ef6bdb9bd5de3520a8e141c0ea669cab3) 0x5140001e5fd0 is located 0 bytes after 400-byte region [0x5140001e5e40,0x5140001e5fd0) allocated by thread T0 here: #0 0x5603c65501a3 in malloc (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0xcb1a3) (BuildId: 38e1ee5ef6bdb9bd5de3520a8e141c0ea669cab3) #1 0x7f22e9919c3c in Eigen::internal::aligned_malloc(unsigned long) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/util/Memory.h:182:14 #2 0x7f22e9919c3c in void* Eigen::internal::conditional_aligned_malloc(unsigned long) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/util/Memory.h:241:10 #3 0x7f22e9919c3c in double* Eigen::internal::conditional_aligned_new_auto(unsigned long) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/util/Memory.h:404:36 #4 0x7f22e9919c3c in Eigen::DenseStorage::resize(long, long, long) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/DenseStorage.h:486:20 #5 0x7f22e990316c in Eigen::PlainObjectBase>::resize(long, long) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:285:19 #6 0x7f22e990316c in void Eigen::PlainObjectBase>::_init2(long, long, Eigen::internal::enable_if::type*) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:810:7 #7 0x7f22e990316c in Eigen::Matrix::Matrix(int const&, int const&) /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/Matrix.h:340:22 #8 0x7f22e990316c in Rcpp::traits::MatrixExporterForEigen, double>::get() /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/RcppEigenWrap.h:157:19 #9 0x7f22e9927e97 in Eigen::Matrix Rcpp::internal::as>(SEXPREC*, Rcpp::traits::r_type_generic_tag) /home/hornik/tmp/CRAN_special_clang-san/Library/Rcpp/include/Rcpp/as.h:89:29 #10 0x7f22e9927e97 in Eigen::Matrix Rcpp::as>(SEXPREC*) /home/hornik/tmp/CRAN_special_clang-san/Library/Rcpp/include/Rcpp/as.h:152:16 #11 0x7f22e9927e97 in Rcpp::internal::generic_name_proxy<19, Rcpp::PreserveStorage>::operator Eigen::Matrix>() const /home/hornik/tmp/CRAN_special_clang-san/Library/Rcpp/include/Rcpp/vector/proxy.h:174:11 #12 0x7f22e9927e97 in qrdowndate(Eigen::Matrix const&, Eigen::Matrix const&, int, Rcpp::Nullable, Rcpp::Nullable, std::allocator>>, Rcpp::Nullable, Rcpp::Nullable) /home/hornik/tmp/CRAN_special_clang-san/fastQR.Rcheck/00_pkg_src/fastQR/src/QR_wrap.cpp:712:10 #13 0x7f22e9ab519a in _fastQR_qrdowndate /home/hornik/tmp/CRAN_special_clang-san/fastQR.Rcheck/00_pkg_src/fastQR/src/RcppExports.cpp:188:34 #14 0x7f2304954a66 in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:775:11 #15 0x7f2304b18cf9 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8672:21 #16 0x7f2304aa7994 in bcEval /home/hornik/src/R/src/main/eval.c:7505:16 #17 0x7f2304aa60cf in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #18 0x7f2304ab0825 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393:22 #19 0x7f2304aac31c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306:16 #20 0x7f2304aa6a4f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328:16 #21 0x7f2304aa6a4f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #22 0x7f2304abf3e5 in do_set /home/hornik/src/R/src/main/eval.c:3571:8 #23 0x7f2304aa649b in Rf_eval /home/hornik/src/R/src/main/eval.c:1232:12 #24 0x7f2304bea427 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265:2 #25 0x7f2304bed240 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #26 0x7f2304bed064 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1219:5 #27 0x7f2304bed30a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1226:5 #28 0x5603c6593dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #29 0x7f2303e33d67 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 SUMMARY: AddressSanitizer: heap-buffer-overflow /home/hornik/tmp/CRAN_special_clang-san/Library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:746:10 in double vector[2] Eigen::internal::ploadu(Eigen::internal::unpacket_traits::type const*) Shadow bytes around the buggy address: 0x5140001e5d00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x5140001e5d80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x5140001e5e00: fa fa fa fa fa fa fa fa 00 00 00 00 00 00 00 00 0x5140001e5e80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x5140001e5f00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x5140001e5f80: 00 00 00 00 00 00 00 00 00 00[fa]fa fa fa fa fa 0x5140001e6000: fa fa fa fa fa fa fa fa 00 00 00 00 00 00 00 00 0x5140001e6080: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x5140001e6100: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x5140001e6180: 00 00 00 00 00 00 00 00 00 00 fa fa fa fa fa fa 0x5140001e6200: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa Shadow byte legend (one shadow byte represents 8 application bytes): Addressable: 00 Partially addressable: 01 02 03 04 05 06 07 Heap left redzone: fa Freed heap region: fd Stack left redzone: f1 Stack mid redzone: f2 Stack right redzone: f3 Stack after return: f5 Stack use after scope: f8 Global redzone: f9 Global init order: f6 Poisoned by user: f7 Container overflow: fc Array cookie: ac Intra object redzone: bb ASan internal: fe Left alloca redzone: ca Right alloca redzone: cb ==2839417==ABORTING * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR