downloading reverse dependencies ... downloading bamm_0.5.0.tar.gz ... ok downloading boxly_0.1.1.tar.gz ... ok downloading clinDataReview_1.6.2.tar.gz ... ok downloading clinUtils_0.2.0.tar.gz ... ok downloading connectwidgets_0.2.1.tar.gz ... ok downloading DT_0.33.tar.gz ... ok downloading forestly_0.1.2.tar.gz ... ok downloading gprofiler2_0.2.3.tar.gz ... ok downloading gwpcormapper_0.1.3.tar.gz ... ok downloading kpiwidget_0.1.1.tar.gz ... ok downloading langevitour_0.8.1.tar.gz ... ok downloading leaflet_2.2.2.tar.gz ... ok downloading linevis_1.0.0.tar.gz ... ok downloading plotly_4.11.0.tar.gz ... ok downloading quollr_0.3.7.tar.gz ... ok downloading RagGrid_0.2.0.tar.gz ... ok downloading shinybody_0.1.3.tar.gz ... ok downloading sigmajs_0.1.5.tar.gz ... ok downloading threejs_0.3.4.tar.gz ... ok downloading tsibbletalk_0.1.0.tar.gz ... ok downloading cubble_1.0.0.tar.gz ... ok downloading detourr_0.1.0.tar.gz ... ok downloading echarty_1.6.6.tar.gz ... ok downloading enviGCMS_0.8.0.tar.gz ... ok downloading GGally_2.4.0.tar.gz ... ok downloading govdown_0.10.1.tar.gz ... ok downloading lineupjs_4.6.0.tar.gz ... ok downloading reactable_0.4.4.tar.gz ... ok downloading rgl_1.3.24.tar.gz ... ok downloading SimSurvey_0.1.7.tar.gz ... ok downloading upsetjs_1.11.1.tar.gz ... ok installing dependencies ‘airports’, ‘alphashape3d’, ‘chemometrics’, ‘clinUtils’, ‘crosstalk’, ‘INLA’, ‘INLAspacetime’, ‘inTextSummaryTable’, ‘js’, ‘langevitour’, ‘liminal’, ‘manipulateWidget’, ‘metalite’, ‘metalite.ae’, ‘orientlib’, ‘ozmaps’, ‘patientProfilesVis’, ‘plotlyGeoAssets’, ‘Rdisop’, ‘scagnostics’, ‘sparkline’, ‘tripack’ Warning: packages ‘liminal’, ‘INLA’ are not available for this version of R Versions of these packages for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages also installing the dependencies ‘oz’, ‘som’ begin installing package ‘oz’ begin installing package ‘som’ begin installing package ‘metalite’ begin installing package ‘plotlyGeoAssets’ begin installing package ‘Rdisop’ begin installing package ‘scagnostics’ begin installing package ‘airports’ begin installing package ‘sparkline’ begin installing package ‘orientlib’ begin installing package ‘tripack’ begin installing package ‘alphashape3d’ begin installing package ‘manipulateWidget’ begin installing package ‘js’ begin installing package ‘INLAspacetime’ begin installing package ‘crosstalk’ * installing *source* package ‘oz’ ... ** this is package ‘oz’ version ‘1.0-22’ ** package ‘oz’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 (oz) * installing *source* package ‘plotlyGeoAssets’ ... ** this is package ‘plotlyGeoAssets’ version ‘0.0.2’ ** package ‘plotlyGeoAssets’ 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 ** 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 (plotlyGeoAssets) begin installing package ‘ozmaps’ * installing *source* package ‘airports’ ... ** this is package ‘airports’ version ‘0.1.0’ ** package ‘airports’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (airports) * installing *source* package ‘sparkline’ ... ** this is package ‘sparkline’ version ‘2.0’ ** package ‘sparkline’ 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 (sparkline) * installing *source* package ‘js’ ... ** this is package ‘js’ version ‘1.2.1’ ** package ‘js’ 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 (js) * installing *source* package ‘scagnostics’ ... ** this is package ‘scagnostics’ version ‘0.2-6’ ** package ‘scagnostics’ 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 ** 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 (scagnostics) * installing *source* package ‘metalite’ ... ** this is package ‘metalite’ version ‘0.1.4’ ** package ‘metalite’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (metalite) begin installing package ‘metalite.ae’ * installing *source* package ‘crosstalk’ ... ** this is package ‘crosstalk’ version ‘1.2.2’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (crosstalk) begin installing package ‘clinUtils’ begin installing package ‘langevitour’ * installing *source* package ‘som’ ... ** this is package ‘som’ version ‘0.3-5.2’ ** package ‘som’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLOt7gD/R.INSTALL3c5d1356f1078f/som/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c som.cc -o som.o In file included from tntsupp.h:8, from sub.h:1, from SomParam.h:2, from som.cc:4: tnt/fmat.h: In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘*this.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘double rect_dist(TNT::Region2D >, TNT::Region2D >)’ at SomParam.h:11:19: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘TNT::Subscript find_winner(TNT::DMatrix&, TNT::Subscript, TNT::DMatrix&)’ at som.cc:12:40: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘TNT::Subscript find_winner(TNT::DMatrix&, TNT::Subscript, TNT::DMatrix&)’ at som.cc:16:36: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘void visual(TNT::DMatrix&, TNT::DMatrix&, TNT::DMatrix&, TNT::DMatrix&)’ at som.cc:57:36: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘int update(TNT::DMatrix&, TNT::DMatrix&, TNT::Subscript, double, TNT::DVector&)’ at som.cc:32:24: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘double qerror(TNT::DMatrix&, TNT::DMatrix&, TNT::DMatrix&, TNT::DMatrix&, SomParam&)’ at som.cc:76:38: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘void som_top(TNT::DMatrix&, TNT::DMatrix&, TNT::DMatrix&, SomParam&, SomParam&, double*)’ at som.cc:108:1: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘cord.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘SEXPREC* som_bat(SEXP, SEXP, SEXP, SEXP)’ at som.cc:225:3: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Vis.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘SEXPREC* som_bat(SEXP, SEXP, SEXP, SEXP)’ at som.cc:225:3: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Code.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘SEXPREC* som_bat(SEXP, SEXP, SEXP, SEXP)’ at som.cc:225:3: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Data.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘SEXPREC* som(SEXP, SEXP, SEXP)’ at som.cc:198:3: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Vis.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘SEXPREC* som(SEXP, SEXP, SEXP)’ at som.cc:198:3: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Cord.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘SEXPREC* som(SEXP, SEXP, SEXP)’ at som.cc:198:3: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Code.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ In member function ‘void TNT::Fortran_Matrix::destroy() [with T = double]’, inlined from ‘TNT::Fortran_Matrix::~Fortran_Matrix() [with T = double]’ at tnt/fmat.h:211:16, inlined from ‘SEXPREC* som(SEXP, SEXP, SEXP)’ at som.cc:198:3: tnt/fmat.h:161:9: warning: ‘void operator delete [](void*)’ called on pointer ‘Data.TNT::Fortran_Matrix::col_’ with nonzero offset 8 [-Wfree-nonheap-object] 161 | delete [] (col_); | ^~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o som.so som.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLOt7gD/R.INSTALL3c5d1356f1078f/som/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-som/00new/som/libs ** R ** data ** 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 ** 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 (som) begin installing package ‘chemometrics’ * installing *source* package ‘orientlib’ ... ** this is package ‘orientlib’ version ‘0.10.5’ ** package ‘orientlib’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘rotmatrix’ in package ‘orientlib’ Creating a generic function from function ‘rotvector’ in package ‘orientlib’ Creating a generic function from function ‘eulerzyx’ in package ‘orientlib’ Creating a generic function from function ‘quaternion’ in package ‘orientlib’ Creating a generic function from function ‘skewvector’ in package ‘orientlib’ Creating a generic function from function ‘skewmatrix’ in package ‘orientlib’ Creating a generic function from function ‘eulerzxz’ in package ‘orientlib’ ** 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 (orientlib) * installing *source* package ‘langevitour’ ... ** this is package ‘langevitour’ version ‘0.8.1’ ** package ‘langevitour’ 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 (langevitour) * installing *source* package ‘manipulateWidget’ ... ** this is package ‘manipulateWidget’ version ‘0.11.1’ ** package ‘manipulateWidget’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (manipulateWidget) * installing *source* package ‘alphashape3d’ ... ** this is package ‘alphashape3d’ version ‘1.3.2’ ** package ‘alphashape3d’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1zcZHX/R.INSTALL3c5d24125abc5c/alphashape3d/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c alphashape3d.c -o alphashape3d.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c insideashape.c -o insideashape.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c surfaceNormals.c -o surfaceNormals.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o alphashape3d.so alphashape3d.o init.o insideashape.o surfaceNormals.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1zcZHX/R.INSTALL3c5d24125abc5c/alphashape3d/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-alphashape3d/00new/alphashape3d/libs ** R ** 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 ** 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 (alphashape3d) * installing *source* package ‘tripack’ ... ** this is package ‘tripack’ version ‘1.3-9.3’ ** package ‘tripack’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-1) 15.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpT7HYgL/R.INSTALL3c5d1a4101df6e/tripack/src' gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c dsos.f -o dsos.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c inhull.f -o inhull.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c left.f -o left.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c qsort.f -o qsort.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c tripack.f -o tripack.o tripack.f:3804:72: 3804 | . (YB-YA)*(YC-YA) .GE. 0. | 1 Warning: Obsolescent feature: Statement function at (1) tripack.f:4336:30: 4336 | SUBROUTINE TRLPRT (NCC,LCT,N,X,Y,NROW,NT,LTRI,LOUT, | 1~~ Warning: Unused dummy argument ‘lct’ at (1) [-Wunused-dummy-argument] tripack.f:4336:48: 4336 | SUBROUTINE TRLPRT (NCC,LCT,N,X,Y,NROW,NT,LTRI,LOUT, | 1~~~ Warning: Unused dummy argument ‘ltri’ at (1) [-Wunused-dummy-argument] tripack.f:4336:26: 4336 | SUBROUTINE TRLPRT (NCC,LCT,N,X,Y,NROW,NT,LTRI,LOUT, | 1~~ Warning: Unused dummy argument ‘ncc’ at (1) [-Wunused-dummy-argument] tripack.f:4336:36: 4336 | SUBROUTINE TRLPRT (NCC,LCT,N,X,Y,NROW,NT,LTRI,LOUT, | 1 Warning: Unused dummy argument ‘x’ at (1) [-Wunused-dummy-argument] tripack.f:4336:38: 4336 | SUBROUTINE TRLPRT (NCC,LCT,N,X,Y,NROW,NT,LTRI,LOUT, | 1 Warning: Unused dummy argument ‘y’ at (1) [-Wunused-dummy-argument] tripack.f:5370:47: 5370 | . N,X,Y,LIST,LPTR,LEND,TITLE, | 1~~~~ Warning: Unused dummy argument ‘title’ at (1) [-Wunused-dummy-argument] tripack.f:5890:15: 5890 | INTEGER I, INC, K, LP, LPL, LUN, NA, NABOR(100), NB, | 1 Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable] tripack.f:5833:30: 5833 | SUBROUTINE TRPRNT (NCC,LCC,N,X,Y,LIST,LPTR,LEND,LOUT, | 1~~ Warning: Unused dummy argument ‘lcc’ at (1) [-Wunused-dummy-argument] tripack.f:5833:26: 5833 | SUBROUTINE TRPRNT (NCC,LCC,N,X,Y,LIST,LPTR,LEND,LOUT, | 1~~ Warning: Unused dummy argument ‘ncc’ at (1) [-Wunused-dummy-argument] tripack.f:5833:36: 5833 | SUBROUTINE TRPRNT (NCC,LCC,N,X,Y,LIST,LPTR,LEND,LOUT, | 1 Warning: Unused dummy argument ‘x’ at (1) [-Wunused-dummy-argument] tripack.f:5833:38: 5833 | SUBROUTINE TRPRNT (NCC,LCC,N,X,Y,LIST,LPTR,LEND,LOUT, | 1 Warning: Unused dummy argument ‘y’ at (1) [-Wunused-dummy-argument] tripack.f:2308:14: 2308 | 5 IF (NK .LT. ILAST) THEN | ^ Warning: ‘ilast’ may be used uninitialized [-Wmaybe-uninitialized] tripack.f:2226:25: 2226 | INTEGER I, IFRST, ILAST, J, K, KM1, LCC1, LM1, LP, | ^~~~~ note: ‘ilast’ was declared here tripack.f:2485:72: 2485 | NPTS(L) = NL | ^ Warning: ‘nl’ may be used uninitialized [-Wmaybe-uninitialized] tripack.f:2228:29: 2228 | . NKBAK, NKFOR, NL, NN | ^~ note: ‘nl’ was declared here tripack.f:4936:72: 4936 | NEXT(I0) = NEXTI | ^ Warning: ‘i0’ may be used uninitialized [-Wmaybe-uninitialized] tripack.f:4719:18: 4719 | INTEGER I, I0, J, K, KM1, LCC(1), LP, LPL, NCC, NEXTI, | ^~ note: ‘i0’ was declared here gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c troutp.f -o troutp.o troutp.f:128:5: 128 | 110 FORMAT (1X,10X,'*** N IS OUTSIDE ITS VALID', | 1 Warning: Label 110 at (1) defined but not used [-Wunused-label] troutp.f:61:15: 61 | INTEGER I, INC, K, LP, LPL, LUN, | 1 Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable] troutp.f:1:30: 1 | SUBROUTINE TROUTP (NCC,LCC,N,X,Y,LIST,LPTR,LEND,LOUT, | 1~~ Warning: Unused dummy argument ‘lcc’ at (1) [-Wunused-dummy-argument] troutp.f:1:26: 1 | SUBROUTINE TROUTP (NCC,LCC,N,X,Y,LIST,LPTR,LEND,LOUT, | 1~~ Warning: Unused dummy argument ‘ncc’ at (1) [-Wunused-dummy-argument] troutp.f:1:36: 1 | SUBROUTINE TROUTP (NCC,LCC,N,X,Y,LIST,LPTR,LEND,LOUT, | 1 Warning: Unused dummy argument ‘x’ at (1) [-Wunused-dummy-argument] troutp.f:1:38: 1 | SUBROUTINE TROUTP (NCC,LCC,N,X,Y,LIST,LPTR,LEND,LOUT, | 1 Warning: Unused dummy argument ‘y’ at (1) [-Wunused-dummy-argument] gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c troutq.f -o troutq.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c vleft.f -o vleft.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c voronoi.f -o voronoi.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o tripack.so dsos.o inhull.o init.o left.o qsort.o tripack.o troutp.o troutq.o vleft.o voronoi.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpT7HYgL/R.INSTALL3c5d1a4101df6e/tripack/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-tripack/00new/tripack/libs ** R ** data ** 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 ** 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 (tripack) * installing *source* package ‘metalite.ae’ ... ** this is package ‘metalite.ae’ version ‘0.1.3’ ** package ‘metalite.ae’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (metalite.ae) * installing *source* package ‘chemometrics’ ... ** this is package ‘chemometrics’ version ‘1.4.4’ ** package ‘chemometrics’ 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 (chemometrics) * installing *source* package ‘clinUtils’ ... ** this is package ‘clinUtils’ version ‘0.2.0’ ** package ‘clinUtils’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (clinUtils) begin installing package ‘inTextSummaryTable’ begin installing package ‘patientProfilesVis’ * installing *source* package ‘ozmaps’ ... ** this is package ‘ozmaps’ version ‘0.4.5’ ** package ‘ozmaps’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ozmaps) * installing *source* package ‘INLAspacetime’ ... ** this is package ‘INLAspacetime’ version ‘0.1.12’ ** package ‘INLAspacetime’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpESfwML/R.INSTALL3c5d2079ee756c/INLAspacetime/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c INLAspacetime.c -o INLAspacetime.o In file included from INLAspacetime.c:1: INLAspacetime.h:59:9: warning: ‘iszero’ redefined 59 | #define iszero(x) (((__typeof(x))(x)) == 0) | ^~~~~~ In file included from INLAspacetime.h:45: /usr/include/math.h:1064:12: note: this is the location of the previous definition 1064 | # define iszero(x) (((__typeof (x)) (x)) == 0) | ^~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cgeneric_ar2ss.c -o cgeneric_ar2ss.o In file included from cgeneric_ar2ss.c:29: INLAspacetime.h:59:9: warning: ‘iszero’ redefined 59 | #define iszero(x) (((__typeof(x))(x)) == 0) | ^~~~~~ In file included from INLAspacetime.h:45: /usr/include/math.h:1064:12: note: this is the location of the previous definition 1064 | # define iszero(x) (((__typeof (x)) (x)) == 0) | ^~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cgeneric_barrier.c -o cgeneric_barrier.o In file included from cgeneric_barrier.c:28: INLAspacetime.h:59:9: warning: ‘iszero’ redefined 59 | #define iszero(x) (((__typeof(x))(x)) == 0) | ^~~~~~ In file included from INLAspacetime.h:45: /usr/include/math.h:1064:12: note: this is the location of the previous definition 1064 | # define iszero(x) (((__typeof (x)) (x)) == 0) | ^~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cgeneric_sspde.c -o cgeneric_sspde.o In file included from cgeneric_sspde.c:28: INLAspacetime.h:59:9: warning: ‘iszero’ redefined 59 | #define iszero(x) (((__typeof(x))(x)) == 0) | ^~~~~~ In file included from INLAspacetime.h:45: /usr/include/math.h:1064:12: note: this is the location of the previous definition 1064 | # define iszero(x) (((__typeof (x)) (x)) == 0) | ^~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cgeneric_sstspde.c -o cgeneric_sstspde.o In file included from cgeneric_sstspde.c:28: INLAspacetime.h:59:9: warning: ‘iszero’ redefined 59 | #define iszero(x) (((__typeof(x))(x)) == 0) | ^~~~~~ In file included from INLAspacetime.h:45: /usr/include/math.h:1064:12: note: this is the location of the previous definition 1064 | # define iszero(x) (((__typeof (x)) (x)) == 0) | ^~~~~~ gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o INLAspacetime.so INLAspacetime.o cgeneric_ar2ss.o cgeneric_barrier.o cgeneric_sspde.o cgeneric_sstspde.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpESfwML/R.INSTALL3c5d2079ee756c/INLAspacetime/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-INLAspacetime/00new/INLAspacetime/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (INLAspacetime) * installing *source* package ‘patientProfilesVis’ ... ** this is package ‘patientProfilesVis’ version ‘2.0.9’ ** package ‘patientProfilesVis’ 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 (patientProfilesVis) * installing *source* package ‘inTextSummaryTable’ ... ** this is package ‘inTextSummaryTable’ version ‘3.3.3’ ** package ‘inTextSummaryTable’ 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 (inTextSummaryTable) * installing *source* package ‘Rdisop’ ... ** this is package ‘Rdisop’ version ‘1.68.0’ ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5agrG7/R.INSTALL3c5d02292495a1/Rdisop/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c disop.cpp -o disop.o In file included from ./imslib/src/ims/alphabet.h:8, from disop.cpp:18: ./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(size_type) const’: ./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from disop.cpp:28: ./imslib/src/ims/decomp/decomputils.h: In function ‘std::pair ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)’: ./imslib/src/ims/decomp/decomputils.h:92:60: warning: typedef ‘weight_type’ locally defined but not used [-Wunused-local-typedefs] 92 | typedef typename DecompositionWeights::weight_type weight_type; | ^~~~~~~~~~~ disop.cpp: In function ‘bool isValidMyNitrogenRule(const ims::ComposedElement&, int)’: disop.cpp:106:8: warning: unused variable ‘parityeven’ [-Wunused-variable] 106 | bool parityeven = !parityodd; | ^~~~~~~~~~ disop.cpp: In function ‘SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: disop.cpp:229:50: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 229 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:232:50: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 232 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:240:53: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 240 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) { | ~~~^~~~~~~~~~~~~~~ disop.cpp:240:75: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 240 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) { | ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:192:13: warning: unused variable ‘number_molecules_shown’ [-Wunused-variable] 192 | int number_molecules_shown = 100; | ^~~~~~~~~~~~~~~~~~~~~~ disop.cpp:170:39: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs] 170 | typedef distribution_t::mass_type mass_type; | ^~~~~~~~~ disop.cpp:172:47: warning: typedef ‘nominal_mass_type’ locally defined but not used [-Wunused-local-typedefs] 172 | typedef distribution_t::nominal_mass_type nominal_mass_type; | ^~~~~~~~~~~~~~~~~ disop.cpp:175:42: warning: typedef ‘decomposition_type’ locally defined but not used [-Wunused-local-typedefs] 175 | typedef decompositions_t::value_type decomposition_type; | ^~~~~~~~~~~~~~~~~~ disop.cpp: In function ‘SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)’: disop.cpp:391:53: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 391 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~ disop.cpp:391:75: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 391 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:408:50: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 408 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:411:50: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 411 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:415:53: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 415 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~ disop.cpp:415:75: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 415 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:378:43: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs] 378 | typedef distribution_t::mass_type mass_type; | ^~~~~~~~~ disop.cpp: In function ‘SEXPREC* rlistScores(std::multimap >, int)’: disop.cpp:627:43: warning: typedef ‘scorer_type’ locally defined but not used [-Wunused-local-typedefs] 627 | typedef DistributionProbabilityScorer scorer_type; | ^~~~~~~~~~~ disop.cpp: In function ‘void initializeCHNOPS(alphabet_t&, int)’: disop.cpp:710:39: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs] 710 | typedef alphabet_t::container elements_type; | ^~~~~~~~~~~~~ disop.cpp: In function ‘void initializeAlphabet(SEXP, alphabet_t&, int)’: disop.cpp:815:33: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs] 815 | typedef alphabet_t::container elements_type; | ^~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o In file included from imslib/src/ims/element.cpp:6: ./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(size_type) const’: ./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o In file included from ./imslib/src/ims/composedelement.h:7, from imslib/src/ims/composedelement.cpp:8: ./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(size_type) const’: ./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o In file included from ./imslib/src/ims/alphabet.h:8, from imslib/src/ims/alphabet.cpp:6: ./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(size_type) const’: ./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o In file included from ./imslib/src/ims/alphabet.h:8, from ./imslib/src/ims/distributedalphabet.h:7, from imslib/src/ims/distributedalphabet.cpp:7: ./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(size_type) const’: ./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.cpp: In member function ‘virtual void ims::KeggLigandCompoundsParser::parse(const ims::AbstractMoleculeSequenceParser::sequence_type&)’: imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:39: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 53 | for (; letter_pos < last_pos && | ~~~~~~~~~~~~~~~~~~~~~~^~ 54 | ( std::isalpha(sequence[letter_pos]) && std::isupper(sequence[letter_pos])) || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o In file included from ./imslib/src/ims/alphabet.h:8, from ./imslib/src/ims/decomp/decomputils.h:12, from imslib/src/ims/decomp/realmassdecomposer.cpp:9: ./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(size_type) const’: ./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./imslib/src/ims/decomp/decomputils.h: In function ‘std::pair ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)’: ./imslib/src/ims/decomp/decomputils.h:92:60: warning: typedef ‘weight_type’ locally defined but not used [-Wunused-local-typedefs] 92 | typedef typename DecompositionWeights::weight_type weight_type; | ^~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o In file included from ./imslib/src/ims/alphabet.h:8, from ./imslib/src/ims/characteralphabet.h:6, from imslib/src/ims/characteralphabet.cpp:3: ./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(size_type) const’: ./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o In file included from ./imslib/src/ims/composedelement.h:7, from ./imslib/src/ims/nitrogenrulefilter.h:4, from imslib/src/ims/nitrogenrulefilter.cpp:5: ./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(size_type) const’: ./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp5agrG7/R.INSTALL3c5d02292495a1/Rdisop/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rdisop/00new/Rdisop/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rdisop) checking crosstalk_1.2.2.tar.gz ... checking bamm_0.5.0.tar.gz ... checking boxly_0.1.1.tar.gz ... checking clinDataReview_1.6.2.tar.gz ... checking clinUtils_0.2.0.tar.gz ... checking connectwidgets_0.2.1.tar.gz ... checking DT_0.33.tar.gz ... checking forestly_0.1.2.tar.gz ... checking gprofiler2_0.2.3.tar.gz ... checking gwpcormapper_0.1.3.tar.gz ... checking kpiwidget_0.1.1.tar.gz ... checking langevitour_0.8.1.tar.gz ... checking leaflet_2.2.2.tar.gz ... checking linevis_1.0.0.tar.gz ... checking plotly_4.11.0.tar.gz ... checking quollr_0.3.7.tar.gz ... checking RagGrid_0.2.0.tar.gz ... checking shinybody_0.1.3.tar.gz ... checking sigmajs_0.1.5.tar.gz ... checking threejs_0.3.4.tar.gz ... checking tsibbletalk_0.1.0.tar.gz ... checking cubble_1.0.0.tar.gz ... checking detourr_0.1.0.tar.gz ... checking echarty_1.6.6.tar.gz ... checking enviGCMS_0.8.0.tar.gz ... checking GGally_2.4.0.tar.gz ... checking govdown_0.10.1.tar.gz ... checking lineupjs_4.6.0.tar.gz ... checking reactable_0.4.4.tar.gz ... checking SimSurvey_0.1.7.tar.gz ... checking upsetjs_1.11.1.tar.gz ... checking rgl_1.3.24.tar.gz ... Depends: Package: crosstalk Imports: htmltools (>= 0.3.6), jsonlite, lazyeval, R6 Timings: user system elapsed crosstalk 32.241 3.797 37.967 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 6 25 Check results summary: crosstalk ... OK rdepends_bamm ... OK rdepends_boxly ... OK rdepends_clinDataReview ... OK rdepends_clinUtils ... NOTE * checking Rd cross-references ... NOTE rdepends_connectwidgets ... OK rdepends_cubble ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_detourr ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_DT ... NOTE * checking Rd cross-references ... NOTE rdepends_echarty ... OK rdepends_enviGCMS ... OK rdepends_forestly ... OK rdepends_GGally ... OK rdepends_govdown ... OK rdepends_gprofiler2 ... OK rdepends_gwpcormapper ... OK rdepends_kpiwidget ... OK rdepends_langevitour ... OK rdepends_leaflet ... NOTE * checking Rd cross-references ... NOTE rdepends_lineupjs ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_linevis ... OK rdepends_plotly ... OK rdepends_quollr ... OK rdepends_RagGrid ... OK rdepends_reactable ... OK rdepends_rgl ... OK rdepends_shinybody ... OK rdepends_sigmajs ... OK rdepends_SimSurvey ... OK rdepends_threejs ... OK rdepends_tsibbletalk ... OK rdepends_upsetjs ... OK Check results changes: Package: gprofiler2 Check: CRAN incoming feasibility Old result: NOTE Package: gwpcormapper Check: CRAN incoming feasibility Old result: NOTE