downloading reverse dependencies ... downloading apng_1.1.tar.gz ... ok downloading bnstruct_1.0.15.tar.gz ... ok downloading caTools_1.18.3.tar.gz ... ok downloading cherry_0.6-14.tar.gz ... ok downloading dgpsi_2.4.0.tar.gz ... ok downloading GENEAread_2.0.10.tar.gz ... ok downloading geozoo_0.5.1.tar.gz ... ok downloading gepaf_0.1.1.tar.gz ... ok downloading GGIRread_1.0.1.tar.gz ... ok downloading ggmap_4.0.0.tar.gz ... ok downloading gt_0.11.0.tar.gz ... ok downloading IgorR_0.9.0.tar.gz ... ok downloading mapsapi_0.5.4.tar.gz ... ok downloading multiCA_1.1.tar.gz ... ok downloading oro.nifti_0.11.4.tar.gz ... ok downloading osrmr_0.1.36.tar.gz ... ok downloading R4CouchDB_0.7.5.tar.gz ... ok downloading rattle_5.5.1.tar.gz ... ok downloading RCurl_1.98-1.16.tar.gz ... ok downloading ryandexdirect_3.6.2.tar.gz ... ok downloading sysid_1.0.4.tar.gz ... ok downloading CorrectOverloadedPeaks_1.3.3.tar.gz ... ok downloading gtExtras_0.5.0.tar.gz ... ok downloading pkgload_1.4.0.tar.gz ... ok downloading XML_3.99-0.17.tar.gz ... ok installing dependencies ‘arulesViz’, ‘bitops’, ‘cairoDevice’, ‘cba’, ‘clhs’, ‘descr’, ‘googleAnalyticsR’, ‘katex’, ‘mmap’, ‘pmml’, ‘RGtk2’, ‘tframe’, ‘xcms’ Warning: packages ‘cairoDevice’, ‘RGtk2’ 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 ‘BiocBaseUtils’, ‘MultiAssayExperiment’, ‘AnnotationFilter’, ‘PSMatch’, ‘vsn’, ‘MALDIquant’, ‘mzID’, ‘QFeatures’, ‘measurementProtocol’, ‘MSnbase’, ‘mzR’, ‘ProtGenerics’, ‘MassSpecWavelet’, ‘MsCoreUtils’, ‘MsFeatures’, ‘MsExperiment’, ‘Spectra’, ‘MetaboCoreUtils’ begin installing package ‘BiocBaseUtils’ begin installing package ‘AnnotationFilter’ begin installing package ‘MALDIquant’ begin installing package ‘vsn’ begin installing package ‘measurementProtocol’ begin installing package ‘ProtGenerics’ begin installing package ‘MassSpecWavelet’ begin installing package ‘MsCoreUtils’ begin installing package ‘clhs’ begin installing package ‘mmap’ begin installing package ‘katex’ begin installing package ‘pmml’ begin installing package ‘arulesViz’ begin installing package ‘cba’ begin installing package ‘descr’ begin installing package ‘tframe’ begin installing package ‘bitops’ * installing *source* package ‘BiocBaseUtils’ ... ** package ‘BiocBaseUtils’ 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 (BiocBaseUtils) begin installing package ‘MultiAssayExperiment’ * installing *source* package ‘measurementProtocol’ ... ** package ‘measurementProtocol’ 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 ** 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 (measurementProtocol) begin installing package ‘googleAnalyticsR’ * installing *source* package ‘tframe’ ... ** package ‘tframe’ 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 (tframe) * installing *source* package ‘bitops’ ... ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpsCWQWs/R.INSTALL5ca60471d6208/bitops/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bit-ops.c -o bit-ops.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cksum.c -o cksum.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o bitops.so bit-ops.o cksum.o init.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpsCWQWs/R.INSTALL5ca60471d6208/bitops/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-bitops/00new/bitops/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 (bitops) * installing *source* package ‘katex’ ... ** package ‘katex’ 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 (katex) * installing *source* package ‘MassSpecWavelet’ ... ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpxg2AeT/R.INSTALL5ca531895490a/MassSpecWavelet/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c find_local_maximum.c -o find_local_maximum.o find_local_maximum.c: In function ‘localMaximumSlidingWindow’: find_local_maximum.c:471:17: warning: ‘kmax’ may be used uninitialized [-Wmaybe-uninitialized] 471 | outi[kmax] = 1; | ^ find_local_maximum.c:461:13: note: ‘kmax’ was declared here 461 | int kmax; | ^~~~ find_local_maximum.c:493:17: warning: ‘kmax’ may be used uninitialized [-Wmaybe-uninitialized] 493 | outi[kmax] = 1; | ^ find_local_maximum.c:479:13: note: ‘kmax’ was declared here 479 | int kmax; | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o MassSpecWavelet.so find_local_maximum.o init.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpxg2AeT/R.INSTALL5ca531895490a/MassSpecWavelet/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-MassSpecWavelet/00new/MassSpecWavelet/libs ** 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 ** 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 (MassSpecWavelet) * installing *source* package ‘ProtGenerics’ ... ** package ‘ProtGenerics’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘smooth’ in package ‘ProtGenerics’ ** 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 (ProtGenerics) begin installing package ‘mzID’ begin installing package ‘mzR’ * installing *source* package ‘descr’ ... ** package ‘descr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0nGZBt/R.INSTALL5ca6440fe095f/descr/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c descr.c -o descr.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o descr.so descr.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0nGZBt/R.INSTALL5ca6440fe095f/descr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-descr/00new/descr/libs ** 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 ** 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 (descr) * installing *source* package ‘MALDIquant’ ... ** package ‘MALDIquant’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpE2CtLN/R.INSTALL5ca46760d524b/MALDIquant/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c colMedians.c -o colMedians.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c localMaxima.c -o localMaxima.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lowerConvexHull.c -o lowerConvexHull.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c morphologicalFilters.c -o morphologicalFilters.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c snip.c -o snip.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o MALDIquant.so colMedians.o init.o localMaxima.o lowerConvexHull.o morphologicalFilters.o snip.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpE2CtLN/R.INSTALL5ca46760d524b/MALDIquant/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-MALDIquant/00new/MALDIquant/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘approxfun’ from package ‘stats’ in package ‘MALDIquant’ ** 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 (MALDIquant) * installing *source* package ‘cba’ ... ** package ‘cba’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpvAqR00/R.INSTALL5ca5c72552141/cba/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c arrayIndex.c -o arrayIndex.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ccfkms.c -o ccfkms.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cluster.c -o cluster.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c coding.c -o coding.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dll.c -o dll.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gknn.c -o gknn.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c greedy.c -o greedy.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c interpolate.c -o interpolate.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c optimal.c -o optimal.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c proximus.c -o proximus.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rock.c -o rock.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sdists.c -o sdists.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stress.c -o stress.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o cba.so arrayIndex.o ccfkms.o cluster.o coding.o dll.o gknn.o greedy.o interpolate.o optimal.o proximus.o rock.o sdists.o stress.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpvAqR00/R.INSTALL5ca5c72552141/cba/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-cba/00new/cba/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 (cba) * installing *source* package ‘mmap’ ... ** package ‘mmap’ successfully unpacked and MD5 sums checked ** using staged installation checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for gcc... gcc-14 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc-14 accepts -g... yes checking for gcc-14 option to enable C11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking alignment of char... 1 checking alignment of int... 4 checking alignment of short... 2 checking alignment of long... 8 checking alignment of double... 8 checking for madvise... yes checking for strnlen... yes configure: creating ./config.status config.status: creating src/config.h ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfUnRPe/R.INSTALL5ca585c673544/mmap/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c endian.c -o endian.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mmap.c -o mmap.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c strings.c -o strings.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c types.c -o types.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o mmap.so endian.o init.o mmap.o strings.o types.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfUnRPe/R.INSTALL5ca585c673544/mmap/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mmap/00new/mmap/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 (mmap) * installing *source* package ‘MsCoreUtils’ ... ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpu1q3l5/R.INSTALL5ca4f3a1d2d31/MsCoreUtils/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c between.c -o between.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c closest.c -o closest.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c impNeighbourAvg.c -o impNeighbourAvg.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -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-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c join.c -o join.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c localMaxima.c -o localMaxima.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lowerConvexHull.c -o lowerConvexHull.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c maxi.c -o maxi.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c morphologicalFilters.c -o morphologicalFilters.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c snip.c -o snip.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sumi.c -o sumi.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c which.c -o which.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o MsCoreUtils.so between.o closest.o impNeighbourAvg.o init.o join.o localMaxima.o lowerConvexHull.o maxi.o morphologicalFilters.o snip.o sumi.o which.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpu1q3l5/R.INSTALL5ca4f3a1d2d31/MsCoreUtils/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-MsCoreUtils/00new/MsCoreUtils/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 (MsCoreUtils) begin installing package ‘MsFeatures’ begin installing package ‘MetaboCoreUtils’ * installing *source* package ‘mzID’ ... ** 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 (mzID) * installing *source* package ‘vsn’ ... ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpcNJ6Rv/R.INSTALL5ca3bbb1dcf0/vsn/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vsn.c -o vsn.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vsn2.c -o vsn2.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o vsn.so init.o vsn.o vsn2.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpcNJ6Rv/R.INSTALL5ca3bbb1dcf0/vsn/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-vsn/00new/vsn/libs ** 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 ** 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 (vsn) * installing *source* package ‘googleAnalyticsR’ ... ** package ‘googleAnalyticsR’ 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 ** 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 (googleAnalyticsR) * installing *source* package ‘pmml’ ... ** package ‘pmml’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (pmml) * installing *source* package ‘arulesViz’ ... ** package ‘arulesViz’ 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 (arulesViz) * installing *source* package ‘AnnotationFilter’ ... ** 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 (AnnotationFilter) * installing *source* package ‘MetaboCoreUtils’ ... ** 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 (MetaboCoreUtils) begin installing package ‘Spectra’ * installing *source* package ‘MsFeatures’ ... ** 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 (MsFeatures) * installing *source* package ‘Spectra’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘entropy’ in package ‘Spectra’ ** 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 (Spectra) * installing *source* package ‘MultiAssayExperiment’ ... ** package ‘MultiAssayExperiment’ 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 (MultiAssayExperiment) begin installing package ‘QFeatures’ * installing *source* package ‘clhs’ ... ** package ‘clhs’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpObWb8j/R.INSTALL5ca4c1291b263/clhs/src' g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c CppLHS.cpp -o CppLHS.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o clhs.so CppLHS.o RcppExports.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpObWb8j/R.INSTALL5ca4c1291b263/clhs/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-clhs/00new/clhs/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 (clhs) * installing *source* package ‘QFeatures’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘sweep’ in package ‘QFeatures’ ** 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 (QFeatures) begin installing package ‘PSMatch’ begin installing package ‘MsExperiment’ * installing *source* package ‘PSMatch’ ... ** 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 (PSMatch) * installing *source* package ‘MsExperiment’ ... ** 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 (MsExperiment) * installing *source* package ‘mzR’ ... ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFwT0TP/R.INSTALL5d02f41c4dc11/mzR/src' rm -f RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppPwiz.cpp -o RcppPwiz.o In file included from pwiz/data/msdata/Reader.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:30, from RcppPwiz.h:12, from RcppPwiz.cpp:1: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RcppPwiz.cpp: In member function ‘Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector)’: RcppPwiz.cpp:407:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 407 | if (current_scan < 1 || current_scan > n_scans) { | ~~~~~~~~~~~~~^~~~~~~~~ RcppPwiz.cpp:408:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 408 | Rprintf("Index whichScan out of bounds [1 ... %d].\n", n_scans); | ~^ ~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld RcppPwiz.cpp: In member function ‘Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)’: RcppPwiz.cpp:853:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 853 | } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) { | ~~~~~~~~~~~^~~~~~~~~~~~~ RcppPwiz.cpp:854:55: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 854 | Rprintf("Index whichChrom out of bounds [0 ... %d].\n", (clp->size())-1); | ~^ ~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld RcppPwiz.cpp:863:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 863 | for (int i = 0; i < pairs.size(); i++) { | ~~^~~~~~~~~~~~~~ RcppPwiz.cpp: In member function ‘Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector, double, double, double)’: RcppPwiz.cpp:1014:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1014 | for (int i = 0; i < scanNumbers.size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~ RcppPwiz.cpp:1020:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1020 | for (int k=0; k < pairs.size(); k++) | ~~^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppPwizModule.cpp -o RcppPwizModule.o In file included from pwiz/data/msdata/Reader.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:30, from RcppPwiz.h:12, from RcppPwizModule.cpp:2: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppIdent.cpp -o RcppIdent.o RcppIdent.cpp: In member function ‘Rcpp::DataFrame RcppIdent::getScore()’: RcppIdent.cpp:293:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 293 | for (size_t j = 0; j < nCvParams; j++) { | ~~^~~~~~~~~~~ RcppIdent.cpp: In member function ‘Rcpp::List RcppIdent::getPara()’: RcppIdent.cpp:382:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 382 | for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RcppIdent.cpp:388:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 388 | for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppIdentModule.cpp -o RcppIdentModule.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o In file included from ./boost/checked_delete.hpp:15, from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27, from ./boost/smart_ptr/detail/shared_count.hpp:27, from ./boost/smart_ptr/shared_ptr.hpp:17, from ./boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = pwiz::data::MemoryIndex::Impl]’: ./boost/smart_ptr/detail/shared_count.hpp:154:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::MemoryIndex::Impl]’ 154 | boost::checked_delete( p ); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ ./boost/smart_ptr/shared_ptr.hpp:279:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, shared_count&) [with T = pwiz::data::MemoryIndex::Impl; Y = pwiz::data::MemoryIndex::Impl]’ 279 | boost::detail::shared_count( p ).swap( pn ); | ^~~~~~~~~~~~~~~~~ ./boost/smart_ptr/shared_ptr.hpp:373:44: required from ‘boost::shared_ptr::shared_ptr(Y*) [with Y = pwiz::data::MemoryIndex::Impl; T = pwiz::data::MemoryIndex::Impl]’ 373 | boost::detail::sp_pointer_construct( this, p, pn ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ pwiz/data/common/MemoryIndex.cpp:73:44: required from here 73 | PWIZ_API_DECL MemoryIndex::MemoryIndex() : impl_(new Impl) {} | ^~~~~~~~~~~~~~~ ./boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type ‘pwiz::data::MemoryIndex::Impl’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 36 | delete x; | ^~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o pwiz/data/common/CVTranslator.cpp: In function ‘bool pwiz::data::shouldIgnore(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)’: pwiz/data/common/CVTranslator.cpp:145:53: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 145 | return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:147:40: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 147 | key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:148:40: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 148 | key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o In file included from pwiz/data/common/cv.cpp:26876: pwiz/data/common/cv.inl: In function ‘const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)’: pwiz/data/common/cv.inl:103:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 103 | for (int o=0;o struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from pwiz/data/common/Index.hpp:27, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ./boost/checked_delete.hpp:15, from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27, from ./boost/smart_ptr/detail/shared_count.hpp:27, from ./boost/smart_ptr/shared_ptr.hpp:17, from ./boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30: ./boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = pwiz::data::BinaryIndexStream::Impl]’: ./boost/smart_ptr/detail/shared_count.hpp:154:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl]’ 154 | boost::checked_delete( p ); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ ./boost/smart_ptr/shared_ptr.hpp:279:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, shared_count&) [with T = pwiz::data::BinaryIndexStream::Impl; Y = pwiz::data::BinaryIndexStream::Impl]’ 279 | boost::detail::shared_count( p ).swap( pn ); | ^~~~~~~~~~~~~~~~~ ./boost/smart_ptr/shared_ptr.hpp:373:44: required from ‘boost::shared_ptr::shared_ptr(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl; T = pwiz::data::BinaryIndexStream::Impl]’ 373 | boost::detail::sp_pointer_construct( this, p, pn ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ pwiz/data/common/BinaryIndexStream.cpp:417:82: required from here 417 | PWIZ_API_DECL BinaryIndexStream::BinaryIndexStream(shared_ptr isPtr) : impl_(new Impl(isPtr)) {} | ^~~~~~~~~~~~~~~~~~~~~~ ./boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type ‘pwiz::data::BinaryIndexStream::Impl’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 36 | delete x; | ^~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o In file included from pwiz/data/msdata/mz5/../Reader.hpp:29, from pwiz/data/msdata/mz5/../MSDataFile.hpp:30, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o In file included from pwiz/data/msdata/mz5/../Reader.hpp:29, from pwiz/data/msdata/mz5/../MSDataFile.hpp:30, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28, from pwiz/data/msdata/mz5/Connection_mz5.hpp:28, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o In file included from pwiz/data/msdata/mz5/../Reader.hpp:29, from pwiz/data/msdata/mz5/../MSDataFile.hpp:30, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28, from pwiz/data/msdata/mz5/Connection_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:25: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o In file included from pwiz/data/msdata/mz5/../Reader.hpp:29, from pwiz/data/msdata/mz5/../MSDataFile.hpp:30, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28, from pwiz/data/msdata/mz5/Connection_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/mz5/../SpectrumListBase.hpp:30, from pwiz/data/msdata/mz5/../SpectrumList_mz5.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:27: ./boost/container_hash/hash.hpp: At global scope: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from pwiz/data/msdata/mz5/../../common/cv.hpp:35, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:27: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o In file included from pwiz/data/msdata/mz5/../Reader.hpp:29, from pwiz/data/msdata/mz5/../MSDataFile.hpp:30, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28, from pwiz/data/msdata/mz5/Connection_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o In file included from pwiz/data/msdata/Reader.hpp:29, from pwiz/data/msdata/DefaultReaderList.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:29: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:30: ./boost/container_hash/hash.hpp: At global scope: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from ./pwiz/utility/misc/Exception.hpp:28, from ./pwiz/utility/misc/Std.hpp:28, from pwiz/data/msdata/DefaultReaderList.cpp:26: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o In file included from pwiz/data/msdata/mz5/../Reader.hpp:29, from pwiz/data/msdata/mz5/../MSDataFile.hpp:30, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28, from pwiz/data/msdata/mz5/Connection_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:28: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:28: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:29, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o In file included from pwiz/data/msdata/Reader.hpp:29, from pwiz/data/msdata/Reader.cpp:26: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o In file included from pwiz/data/msdata/mz5/../Reader.hpp:29, from pwiz/data/msdata/mz5/../MSDataFile.hpp:30, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28, from pwiz/data/msdata/Serializer_mz5.hpp:32, from pwiz/data/msdata/Serializer_mz5.cpp:28: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mz5.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:29: ./boost/container_hash/hash.hpp: At global scope: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from ./pwiz/utility/misc/Exception.hpp:28, from ./pwiz/utility/misc/Std.hpp:28, from pwiz/data/msdata/Serializer_mz5.cpp:26: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/Serializer_MGF.cpp:26: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:26: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/SpectrumListBase.cpp -o pwiz/data/msdata/SpectrumListBase.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumListBase.cpp:25: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ./boost/thread/thread_only.hpp:17, from ./boost/thread/thread.hpp:12, from ./boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_MGF.cpp:29: ./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’: ./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 61 | if (size struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ./boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from ./boost/smart_ptr/detail/yield_k.hpp:23, from ./boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from ./boost/smart_ptr/detail/spinlock.hpp:42, from ./boost/smart_ptr/detail/spinlock_pool.hpp:25, from ./boost/smart_ptr/shared_ptr.hpp:29, from ./boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:30: ./boost/config/pragma_message.hpp:24:34: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ ./boost/bind.hpp:36:1: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from ./boost/thread/thread_only.hpp:17, from ./boost/thread/thread.hpp:12, from ./boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mzML.cpp:32: ./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’: ./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 61 | if (size struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ./boost/thread/thread_only.hpp:17, from ./boost/thread/thread.hpp:12, from ./boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_MSn.cpp:31: ./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’: ./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 61 | if (size struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from ./pwiz/utility/misc/Exception.hpp:28, from ./pwiz/utility/misc/Std.hpp:28, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from pwiz/data/msdata/mz5/../Reader.hpp:29, from pwiz/data/msdata/mz5/../MSDataFile.hpp:30, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28, from pwiz/data/msdata/mz5/Connection_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.hpp:31: ./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’: ./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./boost/thread/thread_only.hpp:17, from ./boost/thread/thread.hpp:12, from ./boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mz5.cpp:29: ./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’: ./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 61 | if (size(byteBuffer, byteCount,compressed); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: ‘byteCount’ was declared here 131 | size_t byteCount; | ^~~~~~~~~ pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: ‘byteBuffer’ may be used uninitialized [-Wmaybe-uninitialized] 302 | filterArray(byteBuffer, byteCount,compressed); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: ‘byteBuffer’ was declared here 132 | const void* byteBuffer; | ^~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o pwiz/data/msdata/MSData.cpp: In member function ‘virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const’: pwiz/data/msdata/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type] 1115 | } | ^ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ./boost/thread/thread_only.hpp:17, from ./boost/thread/thread.hpp:12, from ./boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mzXML.cpp:30: ./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’: ./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 61 | if (size >, const pwiz::msdata::MSData&, bool)’: pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type ‘struct pwiz::msdata::SpectrumList_mzXML::index_not_found’ by value [-Wcatch-value=] 84 | } catch (index_not_found e){ | ^ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o pwiz/data/msdata/IO.cpp: In function ‘void pwiz::msdata::IO::writeBinaryDataArray(pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&)’: pwiz/data/msdata/IO.cpp:1657:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1657 | if (usedConfig.byteOrder == BinaryDataEncoder::ByteOrder_BigEndian) | ^~ pwiz/data/msdata/IO.cpp:1660:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1660 | bool zlib = false; // Handle numpress+zlib | ^~~~ pwiz/data/msdata/IO.cpp: In member function ‘virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)’: pwiz/data/msdata/IO.cpp:2132:35: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2132 | else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/IO.cpp: In member function ‘virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)’: pwiz/data/msdata/IO.cpp:2836:31: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2836 | else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o In file included from ./boost/functional/hash.hpp:6, from pwiz/data/msdata/SpectrumListBase.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ./boost/thread/thread_only.hpp:17, from ./boost/thread/thread.hpp:12, from ./boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_BTDX.cpp:30: ./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’: ./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 61 | if (size struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o pwiz/data/msdata/MSNumpress.cpp: In function ‘void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)’: pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 114 | } else if (init == mask) { | ~~~~~^~~~~~~ In file included from /usr/include/c++/14/iostream:41, from pwiz/data/msdata/MSNumpress.cpp:27: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)’ at pwiz/data/msdata/MSNumpress.cpp:403:33: /usr/include/c++/14/ostream:210:25: warning: ‘extrapol’ may be used uninitialized [-Wmaybe-uninitialized] 210 | { return _M_insert(__n); } | ~~~~~~~~~^~~~~ pwiz/data/msdata/MSNumpress.cpp: In function ‘size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)’: pwiz/data/msdata/MSNumpress.cpp:346:15: note: ‘extrapol’ was declared here 346 | long long extrapol; | ^~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)’ at pwiz/data/msdata/MSNumpress.cpp:404:26: /usr/include/c++/14/ostream:210:25: warning: ‘y’ may be used uninitialized [-Wmaybe-uninitialized] 210 | { return _M_insert(__n); } | ~~~~~~~~~^~~~~ pwiz/data/msdata/MSNumpress.cpp: In function ‘size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)’: pwiz/data/msdata/MSNumpress.cpp:347:15: note: ‘y’ was declared here 347 | long long y; | ^ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o In file included from ./boost/functional/hash.hpp:6, from ./boost/multi_index/detail/hash_index_args.hpp:17, from ./boost/multi_index/hashed_index_fwd.hpp:16, from ./boost/multi_index/hashed_index.hpp:43, from ./pwiz/utility/misc/mru_list.hpp:26, from pwiz/data/msdata/MemoryMRUCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.hpp:28, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ./pwiz/utility/misc/BinaryData.hpp:30, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o In file included from ./boost/functional/hash.hpp:6, from ./pwiz/data/msdata/SpectrumListBase.hpp:30, from ./pwiz/data/msdata/SpectrumListWrapper.hpp:28, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:27: ./boost/container_hash/hash.hpp:131:33: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from ./pwiz/utility/misc/Exception.hpp:28, from ./pwiz/utility/misc/Std.hpp:28, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ./boost/thread/thread_only.hpp:17, from ./boost/thread/thread.hpp:12, from ./boost/thread.hpp:13, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:31: ./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’: ./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 61 | if (size >*)’: pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: ‘pwiz::identdata::{anonymous}::Handler_protXML::strict’ will be initialized after [-Wreorder] 478 | bool strict; | ^~~~~~ pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning: ‘int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides’ [-Wreorder] 85 | int nPeptides; | ^~~~~~~~~ pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning: when initialized here [-Wreorder] 91 | Handler_protXML(IdentData& mzid, | ^~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o pwiz/data/identdata/Serializer_pepXML.cpp: In member function ‘void pwiz::identdata::{anonymous}::HandlerSearchSummary::translateParameters()’: pwiz/data/identdata/Serializer_pepXML.cpp:1100:23: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1100 | const string& decoyPrefix = getValueOrDefault(kvPairs, "decoyprefix", ""); | ^~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1100:54: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"decoyprefix"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1100 | const string& decoyPrefix = getValueOrDefault(kvPairs, "decoyprefix", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1111:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1111 | const string& parentToleranceUnits = getValueOrDefault(kvPairs, "tolu", ""); | ^~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1111:75: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"tolu"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1111 | const string& parentToleranceUnits = getValueOrDefault(kvPairs, "tolu", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1122:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1122 | const string& fragmentToleranceUnits = getValueOrDefault(kvPairs, "itolu", ""); | ^~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1122:77: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"itolu"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1122 | const string& fragmentToleranceUnits = getValueOrDefault(kvPairs, "itolu", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1133:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1133 | const string& instrument = getValueOrDefault(kvPairs, "instrument", ""); | ^~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1133:65: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"instrument"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1133 | const string& instrument = getValueOrDefault(kvPairs, "instrument", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1158:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1158 | const string& precursorMzTolerance = getValueOrDefault(kvPairs, "config: precursormztolerance", ""); | ^~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1158:75: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"config: precursormztolerance"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1158 | const string& precursorMzTolerance = getValueOrDefault(kvPairs, "config: precursormztolerance", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1159:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1159 | const string& precursorMzToleranceUnits = getValueOrDefault(kvPairs, "config: precursormztoleranceunits", ""); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1159:80: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"config: precursormztoleranceunits"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1159 | const string& precursorMzToleranceUnits = getValueOrDefault(kvPairs, "config: precursormztoleranceunits", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1160:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1160 | const string& precursorMzToleranceRule = getValueOrDefault(kvPairs, "config: precursormztolerancerule", ""); | ^~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1160:79: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"config: precursormztolerancerule"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1160 | const string& precursorMzToleranceRule = getValueOrDefault(kvPairs, "config: precursormztolerancerule", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1170:39: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1170 | const string& avgPrecursorMzTolerance = getValueOrDefault(kvPairs, "config: avgprecursormztolerance", ""); | ^~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1170:82: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"config: avgprecursormztolerance"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1170 | const string& avgPrecursorMzTolerance = getValueOrDefault(kvPairs, "config: avgprecursormztolerance", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1171:39: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1171 | const string& monoPrecursorMzTolerance = getValueOrDefault(kvPairs, "config: monoprecursormztolerance", ""); | ^~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1171:83: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"config: monoprecursormztolerance"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1171 | const string& monoPrecursorMzTolerance = getValueOrDefault(kvPairs, "config: monoprecursormztolerance", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1186:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1186 | const string& fragmentMzTolerance = getValueOrDefault(kvPairs, "config: fragmentmztolerance", ""); | ^~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1186:74: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"config: fragmentmztolerance"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1186 | const string& fragmentMzTolerance = getValueOrDefault(kvPairs, "config: fragmentmztolerance", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1187:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1187 | const string& fragmentMzToleranceUnits = getValueOrDefault(kvPairs, "config: fragmentmztoleranceunits", ""); | ^~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1187:79: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"config: fragmentmztoleranceunits"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1187 | const string& fragmentMzToleranceUnits = getValueOrDefault(kvPairs, "config: fragmentmztoleranceunits", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1202:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1202 | const string& fragmentationRule = getValueOrDefault(kvPairs, "config: fragmentationrule", "cid"); | ^~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1202:72: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"config: fragmentationrule"), std::allocator()), std::__cxx11::basic_string(((const char*)"cid"), std::allocator()))’ 1202 | const string& fragmentationRule = getValueOrDefault(kvPairs, "config: fragmentationrule", "cid"); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1211:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1211 | const string& parentErrorMinus = getValueOrDefault(kvPairs, "spectrum, parent monoisotopic mass error minus", ""); | ^~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1211:71: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"spectrum, parent monoisotopic mass error minus"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1211 | const string& parentErrorMinus = getValueOrDefault(kvPairs, "spectrum, parent monoisotopic mass error minus", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1212:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1212 | const string& parentErrorPlus = getValueOrDefault(kvPairs, "spectrum, parent monoisotopic mass error plus", ""); | ^~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1212:70: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"spectrum, parent monoisotopic mass error plus"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1212 | const string& parentErrorPlus = getValueOrDefault(kvPairs, "spectrum, parent monoisotopic mass error plus", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1213:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1213 | const string& parentErrorUnits = getValueOrDefault(kvPairs, "spectrum, parent monoisotopic mass error units", ""); | ^~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1213:71: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"spectrum, parent monoisotopic mass error units"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1213 | const string& parentErrorUnits = getValueOrDefault(kvPairs, "spectrum, parent monoisotopic mass error units", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1218:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1218 | const string& fragmentError = getValueOrDefault(kvPairs, "spectrum, fragment monoisotopic mass error", ""); | ^~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1218:68: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"spectrum, fragment monoisotopic mass error"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1218 | const string& fragmentError = getValueOrDefault(kvPairs, "spectrum, fragment monoisotopic mass error", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1219:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1219 | const string& fragmentErrorUnits = getValueOrDefault(kvPairs, "spectrum, fragment monoisotopic mass error units", ""); | ^~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1219:73: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"spectrum, fragment monoisotopic mass error units"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1219 | const string& fragmentErrorUnits = getValueOrDefault(kvPairs, "spectrum, fragment monoisotopic mass error units", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1269:35: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1269 | const string& decoyPrefix = getValueOrDefault(kvPairs, "decoy_prefix", ""); | ^~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:1269:66: note: the temporary was destroyed at the end of the full expression ‘pwiz::identdata::{anonymous}::HandlerSearchSummary::getValueOrDefault(kvPairs, std::__cxx11::basic_string(((const char*)"decoy_prefix"), std::allocator()), std::__cxx11::basic_string(((const char*)""), std::allocator()))’ 1269 | const string& decoyPrefix = getValueOrDefault(kvPairs, "decoy_prefix", ""); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp: In function ‘void pwiz::identdata::{anonymous}::write_spectrum_queries(pwiz::minimxml::XMLWriter&, const pwiz::identdata::IdentData&, const std::string&, const pwiz::util::IterationListenerRegistry*)’: pwiz/data/identdata/Serializer_pepXML.cpp:801:52: warning: ‘lastSpectrumIndex’ may be used uninitialized [-Wmaybe-uninitialized] 801 | if (sii.chargeState != lastChargeState || spectrumIndex != lastSpectrumIndex) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp:775:26: note: ‘lastSpectrumIndex’ was declared here 775 | int lastChargeState, lastSpectrumIndex; | ^~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o pwiz/data/identdata/References.cpp: In function ‘void pwiz::identdata::References::resolve(std::vector >&, pwiz::identdata::IdentData&)’: pwiz/data/identdata/References.cpp:148:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 148 | else if (dynamic_cast(c.get())) | ^ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o pwiz/data/proteome/Modification.cpp:89:5: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 89 | auto_ptr formula_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ./boost/smart_ptr/detail/sp_counted_impl.hpp:35, from ./boost/smart_ptr/detail/shared_count.hpp:27, from ./boost/smart_ptr/shared_ptr.hpp:17, from ./boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o pwiz/utility/minimxml/SAXParser.cpp: In function ‘void pwiz::minimxml::SAXParser::parse(std::istream&, Handler&)’: pwiz/utility/minimxml/SAXParser.cpp:543:61: warning: offset ‘1’ outside bounds of constant string [-Warray-bounds=] 543 | Handler::Status status = wrangler.endElement(buffer.c_str()+1, position); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: ‘inCDATA’ may be used uninitialized [-Wmaybe-uninitialized] 549 | if (inCDATA) | ^~ pwiz/utility/minimxml/SAXParser.cpp:501:14: note: ‘inCDATA’ was declared here 501 | bool inCDATA; | ^~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o pwiz/utility/misc/IntegerSet.cpp: In member function ‘bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const’: pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 307 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o pwiz/utility/misc/BinaryData.cpp:303: warning: ignoring ‘#pragma managed ’ [-Wunknown-pragmas] 303 | #pragma managed(push, off) pwiz/utility/misc/BinaryData.cpp:475: warning: ignoring ‘#pragma managed ’ [-Wunknown-pragmas] 475 | #pragma managed(pop) g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o In file included from ./boost/thread/thread_only.hpp:17, from ./boost/thread/thread.hpp:12, from ./boost/thread.hpp:13, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:77: ./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’: ./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 61 | if (size struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/locale:41, from ./boost/iostreams/detail/config/codecvt.hpp:63, from ./boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o In file included from ./boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: ./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’: ./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 61 | if (size struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 131 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from ./boost/thread/exceptions.hpp:20, from ./boost/thread/pthread/thread_data.hpp:10: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o mzR.so RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o -lpthread /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/lib/libhdf5_cpp.a /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFwT0TP/R.INSTALL5d02f41c4dc11/mzR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mzR/00new/mzR/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 (mzR) begin installing package ‘MSnbase’ * installing *source* package ‘MSnbase’ ... ** package ‘MSnbase’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpbgr2yS/R.INSTALL5da0a36e2ae96/MSnbase/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Spectrum1_class.c -o Spectrum1_class.o Spectrum1_class.c:8:13: warning: ‘_new_Spectrum1’ defined but not used [-Wunused-function] 8 | static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt, | ^~~~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Spectrum2_class.c -o Spectrum2_class.o Spectrum2_class.c:9:13: warning: ‘_new_Spectrum2’ defined but not used [-Wunused-function] 9 | static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt, | ^~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utils.c -o utils.o utils.c: In function ‘compar_double_dd_for_stable_asc_order’: utils.c:92:15: warning: unused variable ‘ret’ [-Wunused-variable] 92 | int i1, i2, ret; | ^~~ utils.c: In function ‘compar_double_dd_for_stable_desc_order’: utils.c:107:15: warning: unused variable ‘ret’ [-Wunused-variable] 107 | int i1, i2, ret; | ^~~ utils.c: In function ‘compar_double_asc_order’: utils.c:123:18: warning: unused variable ‘ret’ [-Wunused-variable] 123 | double d1, d2, ret; | ^~~ utils.c: In function ‘compar_double_desc_order’: utils.c:133:18: warning: unused variable ‘ret’ [-Wunused-variable] 133 | double d1, d2, ret; | ^~~ utils.c: At top level: utils.c:131:12: warning: ‘compar_double_desc_order’ defined but not used [-Wunused-function] 131 | static int compar_double_desc_order(const void *p1, const void *p2) | ^~~~~~~~~~~~~~~~~~~~~~~~ utils.c:121:12: warning: ‘compar_double_asc_order’ defined but not used [-Wunused-function] 121 | static int compar_double_asc_order(const void *p1, const void *p2) | ^~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpbgr2yS/R.INSTALL5da0a36e2ae96/MSnbase/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-MSnbase/00new/MSnbase/libs ** R ** data *** moving datasets to lazyload DB Creating a new generic function for ‘trimws’ in package ‘MSnbase’ in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra” in method for ‘plotMzDelta’ with signature ‘"mzRramp"’: no definition for class “mzRramp” ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘trimws’ in package ‘MSnbase’ in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra” in method for ‘plotMzDelta’ with signature ‘"mzRramp"’: no definition for class “mzRramp” ** 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 (MSnbase) begin installing package ‘xcms’ * installing *source* package ‘xcms’ ... ** package ‘xcms’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQPdWpK/R.INSTALL5db1671f1fc92/xcms/src' rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c massifquant/Tracker.cpp -o massifquant/Tracker.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c massifquant/SegProc.cpp -o massifquant/SegProc.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c obiwarp/mat.cpp -o obiwarp/mat.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c obiwarp/vec.cpp -o obiwarp/vec.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o obiwarp/xcms_dynprog.cpp: In member function ‘void DynProg::find_path(VEC::MatF&, VEC::VecF&, int, float, float, int, float)’: obiwarp/xcms_dynprog.cpp:1113:9: warning: variable ‘bestscore’ set but not used [-Wunused-but-set-variable] 1113 | float bestscore; | ^~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c xcms_obiwarp.cpp -o xcms_obiwarp.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fastMatch.c -o fastMatch.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mzClust_hclust.c -o mzClust_hclust.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mzROI.c -o mzROI.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util.c -o util.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c xcms.c -o xcms.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c binners.c -o binners.o binners.c: In function ‘_breaks_on_binSize’: binners.c:357:7: warning: unused variable ‘idx’ [-Wunused-variable] 357 | int idx = 0; | ^~~ g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpQPdWpK/R.INSTALL5db1671f1fc92/xcms/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-xcms/00new/xcms/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘group’ in package ‘xcms’ Creating a new generic function for ‘sigma’ in package ‘xcms’ ** 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 (xcms) checking bitops_1.0-9.tar.gz ... checking apng_1.1.tar.gz ... checking bnstruct_1.0.15.tar.gz ... checking caTools_1.18.3.tar.gz ... checking cherry_0.6-14.tar.gz ... checking GENEAread_2.0.10.tar.gz ... checking dgpsi_2.4.0.tar.gz ... checking geozoo_0.5.1.tar.gz ... checking GGIRread_1.0.1.tar.gz ... checking gepaf_0.1.1.tar.gz ... checking gt_0.11.0.tar.gz ... checking ggmap_4.0.0.tar.gz ... checking mapsapi_0.5.4.tar.gz ... checking IgorR_0.9.0.tar.gz ... checking multiCA_1.1.tar.gz ... checking oro.nifti_0.11.4.tar.gz ... checking osrmr_0.1.36.tar.gz ... checking R4CouchDB_0.7.5.tar.gz ... checking rattle_5.5.1.tar.gz ... checking RCurl_1.98-1.16.tar.gz ... checking ryandexdirect_3.6.2.tar.gz ... checking sysid_1.0.4.tar.gz ... checking CorrectOverloadedPeaks_1.3.3.tar.gz ... checking gtExtras_0.5.0.tar.gz ... checking pkgload_1.4.0.tar.gz ... checking XML_3.99-0.17.tar.gz ... Depends: Timings: user system elapsed bitops 22.219 3.289 27 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 5 20 Check results summary: bitops ... OK rdepends_apng ... OK rdepends_bnstruct ... OK rdepends_caTools ... OK rdepends_cherry ... NOTE * checking Rd cross-references ... NOTE rdepends_CorrectOverloadedPeaks ... OK rdepends_dgpsi ... OK rdepends_GENEAread ... OK rdepends_geozoo ... OK rdepends_gepaf ... OK rdepends_GGIRread ... OK rdepends_ggmap ... NOTE * checking Rd cross-references ... NOTE rdepends_gt ... OK rdepends_gtExtras ... OK rdepends_IgorR ... NOTE * checking R code for possible problems ... [4s/4s] NOTE rdepends_mapsapi ... OK rdepends_multiCA ... OK rdepends_oro.nifti ... OK rdepends_osrmr ... OK rdepends_pkgload ... OK rdepends_R4CouchDB ... OK rdepends_rattle ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_RCurl ... OK rdepends_ryandexdirect ... OK rdepends_sysid ... NOTE * checking for non-standard things in the check directory ... NOTE rdepends_XML ... OK