* using log directory ‘/srv/hornik/tmp/CRAN_pretest/PerRegMod.Rcheck’ * using R Under development (unstable) (2024-11-07 r87302) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.1 (1) Debian flang-new version 19.1.1 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘PerRegMod/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PerRegMod’ version ‘4.4.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Regui Slimane ’ New submission Possibly misspelled words in DESCRIPTION: PerRegMod (4:8) The Title field starts with the package name. * 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 ‘PerRegMod’ can be installed ... [4s/4s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Maintainer field differs from that derived from Authors@R Maintainer: ‘Regui Slimane ’ Authors@R: ‘Slimane Regui ’ * 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 ... [6s/6s] OK * checking Rd files ... [0s/0s] 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 examples ... [2s/2s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [26s/26s] ERROR Running ‘test.R’ [26s/26s] Running the tests in ‘tests/test.R’ failed. Complete output: > > #""""""""""""""""""""""""Detecting periodicity > install.packages("expm", repos = "https://cran.r-project.org") Installing package into '/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81' (as 'lib' is unspecified) trying URL 'https://cran.r-project.org/src/contrib/expm_1.0-0.tar.gz' Content type 'application/x-gzip' length 141054 bytes (137 KB) ================================================== downloaded 137 KB * installing *source* package 'expm' ... ** package 'expm' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'Debian clang version 19.1.2 (2)' using Fortran compiler: 'Debian flang-new version 19.1.2 (2)' clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -c R_dgebal.c -o R_dgebal.o clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -c expm-eigen.c -o expm-eigen.o clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -c expm.c -o expm.o clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -c init.c -o init.o clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -c logm-eigen.c -o logm-eigen.o flang-new-19 -fpic -g -O2 -c matexp.f -o matexp.o ./matexp.f:136:7: warning: Reference to the procedure 'dgemm' has an implicit interface that is distinct from another reference: incompatible dummy argument #7: incompatible dummy data object shapes CALL DGEMM( 'N','N',M,M,M, 1.0D0,WSP(IUSED),M, ^ ./matexp.f:115:7: previous reference to 'dgemm' CALL DGEMM( 'N','N',M,M,M,SCALE2,H,M,H,M,0.0D0,WSP(IH2),M ) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ./matexp.f:151:10: warning: Reference to the procedure 'dgemm' has an implicit interface that is distinct from another reference: incompatible dummy argument #7: incompatible dummy data object shapes CALL DGEMM( 'N','N',M,M,M, SCALE,WSP(IQ),M, ^ ./matexp.f:115:7: previous reference to 'dgemm' CALL DGEMM( 'N','N',M,M,M,SCALE2,H,M,H,M,0.0D0,WSP(IH2),M ) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ./matexp.f:155:10: warning: Reference to the procedure 'dgemm' has an implicit interface that is distinct from another reference: incompatible dummy argument #7: incompatible dummy data object shapes CALL DGEMM( 'N','N',M,M,M, SCALE,WSP(IP),M, ^ ./matexp.f:115:7: previous reference to 'dgemm' CALL DGEMM( 'N','N',M,M,M,SCALE2,H,M,H,M,0.0D0,WSP(IH2),M ) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ./matexp.f:176:13: warning: Reference to the procedure 'dgemm' has an implicit interface that is distinct from another reference: incompatible dummy argument #7: incompatible dummy data object shapes CALL DGEMM( 'N','N',M,M,M, 1.0D0,WSP(IGET),M, WSP(IGET),M, ^ ./matexp.f:115:7: previous reference to 'dgemm' CALL DGEMM( 'N','N',M,M,M,SCALE2,H,M,H,M,0.0D0,WSP(IH2),M ) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -c matexp_MH09.c -o matexp_MH09.o clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -c matpow.c -o matpow.o flang-new-19 -fpic -g -O2 -c matrexp.f -o matrexp.o ./matrexp.f:302:7: warning: Reference to the procedure 'dcopy' has an implicit interface that is distinct from another reference: incompatible dummy argument #2: incompatible dummy data object shapes call dcopy(m, f,1, r, 1) ^^^^^^^^^^^^^^^^^^^^^^^^^^ ./matrexp.f:259:7: previous reference to 'dcopy' call dcopy(m2, x,1, xx,1) ^^^^^^^^^^^^^^^^^^^^^^^^^ ./matrexp.f:303:7: warning: Reference to the procedure 'dcopy' has an implicit interface that is distinct from another reference: incompatible dummy argument #2: incompatible dummy data object shapes call dcopy(m, r,1, rcgs,1) ^^^^^^^^^^^^^^^^^^^^^^^^^^ ./matrexp.f:259:7: previous reference to 'dcopy' call dcopy(m2, x,1, xx,1) ^^^^^^^^^^^^^^^^^^^^^^^^^ ./matrexp.f:304:7: warning: Reference to the procedure 'dcopy' has an implicit interface that is distinct from another reference: incompatible dummy argument #2: incompatible dummy data object shapes call dcopy(m, r,1, p, 1) ^^^^^^^^^^^^^^^^^^^^^^^^^^ ./matrexp.f:259:7: previous reference to 'dcopy' call dcopy(m2, x,1, xx,1) ^^^^^^^^^^^^^^^^^^^^^^^^^ ./matrexp.f:305:7: warning: Reference to the procedure 'dcopy' has an implicit interface that is distinct from another reference: incompatible dummy argument #2: incompatible dummy data object shapes call dcopy(m, r,1, u, 1) ^^^^^^^^^^^^^^^^^^^^^^^^^^ ./matrexp.f:259:7: previous reference to 'dcopy' call dcopy(m2, x,1, xx,1) ^^^^^^^^^^^^^^^^^^^^^^^^^ ./matrexp.f:312:7: warning: Reference to the procedure 'dcopy' has an implicit interface that is distinct from another reference: incompatible dummy argument #2: incompatible dummy data object shapes call dcopy(m, r,1, rbar,1) ^^^^^^^^^^^^^^^^^^^^^^^^^^ ./matrexp.f:259:7: previous reference to 'dcopy' call dcopy(m2, x,1, xx,1) ^^^^^^^^^^^^^^^^^^^^^^^^^ flang-new-19 -fpic -g -O2 -c matrexpO.f -o matrexpO.o flang-new-19 -fpic -g -O2 -c mexp-common.f -o mexp-common.o clang-19 -shared -L/home/hornik/tmp/R-d-clang-19/lib -Wl,-O1 -o expm.so R_dgebal.o expm-eigen.o expm.o init.o logm-eigen.o matexp.o matexp_MH09.o matpow.o matrexp.o matrexpO.o mexp-common.o -llapack -L/home/hornik/tmp/R-d-clang-19/lib -lRblas -L/usr/lib/llvm-19/lib -lFortranRuntime -lFortranDecimal -lm -L/usr/lib/llvm-19/lib -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R-d-clang-19/lib -lR Error in file(filename, "r", encoding = encoding) : cannot open the connection Calls: local ... eval.parent -> eval -> eval -> eval -> eval -> source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file 'startup.Rs': No such file or directory Execution halted make: *** [/home/hornik/tmp/R-d-clang-19/share/make/shlib.mk:24: symbols.rds] Error 1 installing to /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/00LOCK-expm/00new/expm/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (expm) The downloaded source packages are in '/tmp/Rtmp2jEIVa/working_dir/RtmpXeG37x/downloaded_packages' > install.packages("sn", repos = "https://cran.r-project.org") Installing package into '/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81' (as 'lib' is unspecified) trying URL 'https://cran.r-project.org/src/contrib/sn_2.1.1.tar.gz' Content type 'application/x-gzip' length 827061 bytes (807 KB) ================================================== downloaded 807 KB * installing *source* package 'sn' ... ** package 'sn' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sn) The downloaded source packages are in '/tmp/Rtmp2jEIVa/working_dir/RtmpXeG37x/downloaded_packages' > install.packages("readxl", repos = "https://cran.r-project.org") Installing package into '/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81' (as 'lib' is unspecified) trying URL 'https://cran.r-project.org/src/contrib/readxl_1.4.3.tar.gz' Content type 'application/x-gzip' length 2093488 bytes (2.0 MB) ================================================== downloaded 2.0 MB * installing *source* package 'readxl' ... ** package 'readxl' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'Debian clang version 19.1.2 (2)' using C++ compiler: 'Debian clang version 19.1.2 (2)' clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -Iunix -I. -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include' -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c cpp11.cpp -o cpp11.o In file included from cpp11.cpp:5: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/declarations.hpp:13: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11.hpp:3: /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :5:9: note: previous definition is here 5 | #define R_NO_REMAP 1 | ^ In file included from cpp11.cpp:5: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/declarations.hpp:13: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11.hpp:3: /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -Iunix -I. -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include' -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c XlsWorkBook.cpp -o XlsWorkBook.o In file included from XlsWorkBook.cpp:1: In file included from ./XlsWorkBook.h:3: In file included from ./ColSpec.h:3: In file included from ./utils.h:3: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/protect.hpp:10: /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :5:9: note: previous definition is here 5 | #define R_NO_REMAP 1 | ^ In file included from XlsWorkBook.cpp:1: In file included from ./XlsWorkBook.h:3: In file included from ./ColSpec.h:3: In file included from ./utils.h:3: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/protect.hpp:10: /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -Iunix -I. -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include' -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c XlsxWorkBook.cpp -o XlsxWorkBook.o In file included from XlsxWorkBook.cpp:1: In file included from ./XlsxWorkBook.h:3: In file included from ./ColSpec.h:3: In file included from ./utils.h:3: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/protect.hpp:10: /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :5:9: note: previous definition is here 5 | #define R_NO_REMAP 1 | ^ In file included from XlsxWorkBook.cpp:1: In file included from ./XlsxWorkBook.h:3: In file included from ./ColSpec.h:3: In file included from ./utils.h:3: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/protect.hpp:10: /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -Iunix -I. -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include' -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c zip.cpp -o zip.o In file included from zip.cpp:5: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/function.hpp:9: /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :5:9: note: previous definition is here 5 | #define R_NO_REMAP 1 | ^ In file included from zip.cpp:5: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/function.hpp:9: /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -Iunix -I. -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include' -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c Read.cpp -o Read.o In file included from Read.cpp:1: In file included from ./SheetView.h:4: In file included from ./CellLimits.h:3: In file included from ./XlsCell.h:3: In file included from ./ColSpec.h:3: In file included from ./utils.h:3: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/protect.hpp:10: /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :5:9: note: previous definition is here 5 | #define R_NO_REMAP 1 | ^ In file included from Read.cpp:1: In file included from ./SheetView.h:4: In file included from ./CellLimits.h:3: In file included from ./XlsCell.h:3: In file included from ./ColSpec.h:3: In file included from ./utils.h:3: In file included from /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/protect.hpp:10: /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -Iunix -I. -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include' -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c cran.c -o cran.o clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -Iunix -I. -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include' -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c libxls/xlstool.c -o libxls/xlstool.o clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -Iunix -I. -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include' -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c libxls/endian.c -o libxls/endian.o clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -Iunix -I. -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include' -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c libxls/ole.c -o libxls/ole.o clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -Iunix -I. -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include' -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c libxls/xls.c -o libxls/xls.o clang-19 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -Iunix -I. -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/cpp11/include' -I'/tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c libxls/locale.c -o libxls/locale.o clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-19/lib -Wl,-O1 -o readxl.so cpp11.o XlsWorkBook.o XlsxWorkBook.o zip.o Read.o cran.o libxls/xlstool.o libxls/endian.o libxls/ole.o libxls/xls.o libxls/locale.o -L/home/hornik/tmp/R-d-clang-19/lib -lR Error in file(filename, "r", encoding = encoding) : cannot open the connection Calls: local ... eval.parent -> eval -> eval -> eval -> eval -> source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file 'startup.Rs': No such file or directory Execution halted make: *** [/home/hornik/tmp/R-d-clang-19/share/make/shlib.mk:24: symbols.rds] Error 1 installing to /tmp/Rtmp2jEIVa/RLIBS_7d7184a7dfa81/00LOCK-readxl/00new/readxl/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (readxl) The downloaded source packages are in '/tmp/Rtmp2jEIVa/working_dir/RtmpXeG37x/downloaded_packages' > > #install.packages("expm") > #install.packages("sn") > #install.packages("readxl") > > > library(PerRegMod) > library(expm) Loading required package: Matrix Attaching package: 'expm' The following object is masked from 'package:Matrix': expm > library(readxl) > library(sn)# for skew normal density Loading required package: stats4 Attaching package: 'sn' The following object is masked from 'package:stats': sd > > n=200 > s=2 > x1=rnorm(n,0,1) > x2=rnorm(n,0,2) > x3=rnorm(n,0,3) > x4=rnorm(n,0,2.7) > y=rnorm(n,0,2.5) > x=list(x1,x2,x3,x4) > model=lm(y~x1+x2+x3+x4) > z=model$residuals > check_periodicity(x,y,s) Chi-squared test for detecting periodicity of coefficients Chi-squared statistic: 13.39751 on df= 6 , p-value: 0.0371401945326278> > ####""""""""""""""""""""""""" LSE method > set.seed(4) > s=2 > n=200 > m=n/s > p=3 > mu=c(2,6) > beta1=c(3,5) > beta2=c(1,2.5) > beta3=c(-2,1) > x1=runif(n,0,5) > x2=runif(n,0,10) > x3=runif(n,0,15) > y=rep(0,n) > for (i in 1:s) { + q=seq(i,n,s) + y[q]=mu[i] + beta1[i] * x1[q] + beta2[i] * x2[q] + beta3[i] * x3[q] + rnorm(m,0,1) + } > x=list(x1,x2,x3) > lm_per(x,y,s) Residuals: 0% 25% 50% 75% 100% -2.549633 -0.626857 0.024333 0.639637 2.920669 Coefficients: intercept x...1... X...2... X...3... sd s= 1 2.0178 3.0710 1.0052 -2.04169 0.96313 s= 2 5.7531 5.1528 2.4795 0.98718 0.97588 Root mean square error: 0.9499377> > > ##""""""""""""""""""""""" AE > set.seed(4) > s=2 > n=200 > m=n/s > p=3 > mu=c(2,6) > beta1=c(3,5) > beta2=c(1,2.5) > beta3=c(-2,1) > x1=runif(n,0,5) > x2=runif(n,0,10) > x3=runif(n,0,15) > y=rep(0,n) > for (i in 1:s) { + q=seq(i,n,s) + y[q]=mu[i] + beta1[i] * x1[q] + beta2[i] * x2[q] + beta3[i] * x3[q] + rsn(m,alpha = 10) + } > x=list(x1,x2,x3) > lm_per_AE(x,y,s) Residuals: 0% 25% 50% 75% 100% -0.47063 0.14000 0.48720 0.92105 2.65079 Coefficients: intercept x...1... X...2... X...3... SD s= 1 2.1250 2.9693 0.98514 -1.96983 0.46734 s= 2 6.2427 4.9575 2.51490 0.99866 0.38663 Root mean square error: 0.8224663> > ######"""""""""""""""""""""""""" real data examples > #####" > #Data <- system.file("data", "weather_data_casablanca-settat.xlsx", package = "PerRegMod") > #load("~/PerRegMod_4.4.1/PerRegMod/data/weather_data_casablanca_settat.RData") > #Data=weather_data_casablanca_settat > > #file_path <- system.file("data", "weather_data_casablanca_settat.xlsx", package = "PerRegMod") > #Data <- readxl::read_excel(file_path) > #file_path <- system.file("inst/extdata", "weather_data_casablanca_settat.xlsx", package = "PerRegMod") > #Data <- readxl::read_excel(file_path) > Data=read_xlsx("~/PerRegMod_4.4.1/PerRegMod/inst/extdata/weather_data_casablanca_settat.xlsx") Error: `path` does not exist: '~/PerRegMod_4.4.1/PerRegMod/inst/extdata/weather_data_casablanca_settat.xlsx' Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs