downloading reverse dependencies ... downloading ajv_1.0.0.tar.gz ... ok downloading animint2_2025.1.28.tar.gz ... ok downloading CirceR_1.3.3.tar.gz ... ok downloading cmmr_1.0.3.tar.gz ... ok downloading CodelistGenerator_3.4.0.tar.gz ... ok downloading CohortGenerator_0.11.2.tar.gz ... ok downloading CropScapeR_1.1.5.tar.gz ... ok downloading DIZutils_0.1.3.tar.gz ... ok downloading FAOSTAT_2.4.0.tar.gz ... ok downloading gpboost_1.5.6.tar.gz ... ok downloading haploR_4.0.7.tar.gz ... ok downloading kerastuneR_0.1.0.7.tar.gz ... ok downloading LDAvis_0.3.2.tar.gz ... ok downloading LightningR_1.0.2.tar.gz ... ok downloading lipidmapsR_1.0.4.tar.gz ... ok downloading ltertools_1.2.0.tar.gz ... ok downloading mitre_1.0.0.tar.gz ... ok downloading mojson_0.1.tar.gz ... ok downloading PhageCocktail_1.0.3.tar.gz ... ok downloading PubChemR_2.1.4.tar.gz ... ok downloading pubmed.mineR_1.0.21.tar.gz ... ok downloading pxR_0.42.7.tar.gz ... ok downloading R4CouchDB_0.7.5.tar.gz ... ok downloading rbiouml_1.11.tar.gz ... ok downloading RedditExtractoR_3.0.9.tar.gz ... ok downloading restimizeapi_1.0.0.tar.gz ... ok downloading rfigshare_0.3.8.tar.gz ... ok downloading Rgff_0.1.6.tar.gz ... ok downloading ropensecretsapi_1.0.1.tar.gz ... ok downloading RSDA_3.2.1.tar.gz ... ok downloading RXKCD_1.9.2.tar.gz ... ok downloading rYoutheria_1.0.3.tar.gz ... ok downloading SignacX_2.2.5.tar.gz ... ok downloading switchr_0.14.8.tar.gz ... ok downloading tsmp_0.4.15.tar.gz ... ok downloading wilson_2.4.2.tar.gz ... ok downloading CodeDepends_0.6.6.tar.gz ... ok downloading exams_2.4-1.tar.gz ... ok downloading leaflet_2.2.2.tar.gz ... ok installing dependencies ‘CirceR’, ‘compareDF’, ‘DIZtools’, ‘Eunomia’, ‘ggplot2movies’, ‘ggpolypath’, ‘gistr’, ‘keras3’, ‘lme4’, ‘log4r’, ‘mallet’, ‘ResultModelManager’, ‘RJSONIO’, ‘RPresto’, ‘smerc’, ‘tfdatasets’, ‘tidyjson’, ‘tth’, ‘visOmopResults’ also installing the dependencies ‘CommonDataModel’, ‘cleaR’, ‘dotty’ begin installing package ‘CommonDataModel’ begin installing package ‘cleaR’ begin installing package ‘dotty’ begin installing package ‘gistr’ begin installing package ‘ggplot2movies’ begin installing package ‘visOmopResults’ begin installing package ‘ResultModelManager’ begin installing package ‘tidyjson’ begin installing package ‘RPresto’ begin installing package ‘tfdatasets’ begin installing package ‘mallet’ begin installing package ‘compareDF’ begin installing package ‘smerc’ begin installing package ‘ggpolypath’ begin installing package ‘log4r’ begin installing package ‘tth’ begin installing package ‘RJSONIO’ begin installing package ‘lme4’ * installing *source* package ‘cleaR’ ... ** this is package ‘cleaR’ version ‘0.0.4’ ** package ‘cleaR’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cleaR) begin installing package ‘DIZtools’ * installing *source* package ‘dotty’ ... ** this is package ‘dotty’ version ‘0.1.0’ ** package ‘dotty’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dotty) begin installing package ‘keras3’ * installing *source* package ‘log4r’ ... ** this is package ‘log4r’ version ‘0.4.4’ ** package ‘log4r’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfQqyBq/R.INSTALL26883e63161635/log4r/src' gcc-14 -std=gnu23 -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 log4r.c -o log4r.o gcc-14 -std=gnu23 -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 logfmt.c -o logfmt.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o log4r.so log4r.o logfmt.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfQqyBq/R.INSTALL26883e63161635/log4r/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-log4r/00new/log4r/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 (log4r) * installing *source* package ‘ggplot2movies’ ... ** this is package ‘ggplot2movies’ version ‘0.0.1’ ** package ‘ggplot2movies’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (ggplot2movies) * installing *source* package ‘mallet’ ... ** this is package ‘mallet’ version ‘1.3.0’ ** package ‘mallet’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mallet) * installing *source* package ‘DIZtools’ ... ** this is package ‘DIZtools’ version ‘1.0.2’ ** package ‘DIZtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DIZtools) * installing *source* package ‘ggpolypath’ ... ** this is package ‘ggpolypath’ version ‘0.3.0’ ** package ‘ggpolypath’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggpolypath) * installing *source* package ‘compareDF’ ... ** this is package ‘compareDF’ version ‘2.3.5’ ** package ‘compareDF’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (compareDF) * installing *source* package ‘gistr’ ... ** this is package ‘gistr’ version ‘0.9.0’ ** package ‘gistr’ 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 (gistr) * installing *source* package ‘CommonDataModel’ ... ** this is package ‘CommonDataModel’ version ‘1.0.1’ ** package ‘CommonDataModel’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CommonDataModel) begin installing package ‘Eunomia’ * installing *source* package ‘tth’ ... ** this is package ‘tth’ version ‘4.16-0’ ** package ‘tth’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpwgdzQv/R.INSTALL26884229b75360/tth/src' gcc-14 -std=gnu17 -w -o tth tth.c gcc-14 -std=gnu17 -w -o ttm ttm.c make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpwgdzQv/R.INSTALL26884229b75360/tth/src' installing via 'install.libs.R' to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-tth/00new/tth ** R ** 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 (tth) * installing *source* package ‘visOmopResults’ ... ** this is package ‘visOmopResults’ version ‘1.0.2’ ** package ‘visOmopResults’ 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 (visOmopResults) * installing *source* package ‘tidyjson’ ... ** this is package ‘tidyjson’ version ‘0.3.2’ ** package ‘tidyjson’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tidyjson) * installing *source* package ‘RPresto’ ... ** this is package ‘RPresto’ version ‘1.4.7’ ** package ‘RPresto’ 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 (RPresto) * installing *source* package ‘Eunomia’ ... ** this is package ‘Eunomia’ version ‘2.0.0’ ** package ‘Eunomia’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Eunomia) * installing *source* package ‘ResultModelManager’ ... ** this is package ‘ResultModelManager’ version ‘0.5.11’ ** package ‘ResultModelManager’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading R6Class ConnectionHandler: finalize() method is public, but it should be private as of R6 2.4.0. This code will continue to work, but in a future version of R6, finalize() will be required to be private. R6Class DataMigrationManager: finalize() method is public, but it should be private as of R6 2.4.0. This code will continue to work, but in a future version of R6, finalize() will be required to be private. R6Class QueryNamespace: finalize() method is public, but it should be private as of R6 2.4.0. This code will continue to work, but in a future version of R6, finalize() will be required to be private. ** 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 (ResultModelManager) * installing *source* package ‘RJSONIO’ ... ** this is package ‘RJSONIO’ version ‘1.3-1.11’ ** using staged installation Trying to find libjson.h header file checking for gcc... gcc-14 -std=gnu23 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 -std=gnu23 accepts -g... yes checking for gcc-14 -std=gnu23 option to enable C11 features... none needed USE_LOCAL = "" Minor Version: 6 Using local libjson code. Copying files from src/libjson/Source /home/hornik/tmp/scratch/Rtmpm2Pgew/R.INSTALL26884161b5a605/RJSONIO JSONAllocator.cpp JSONChildren.cpp JSONDebug.cpp JSONIterators.cpp JSONMemory.cpp JSONNode.cpp JSONNode_Mutex.cpp JSONPreparse.cpp JSONStream.cpp JSONValidator.cpp JSONWorker.cpp JSONWriter.cpp internalJSONNode.cpp libjson.cpp configure: creating ./config.status config.status: creating src/Makevars config.status: creating tools/cleanup ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpm2Pgew/R.INSTALL26884161b5a605/RJSONIO/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ConvertUTF.c -o ConvertUTF.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONAllocator.cpp -o JSONAllocator.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONChildren.cpp -o JSONChildren.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONDebug.cpp -o JSONDebug.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONIterators.cpp -o JSONIterators.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONMemory.cpp -o JSONMemory.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONNode.cpp -o JSONNode.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONNode_Mutex.cpp -o JSONNode_Mutex.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONPreparse.cpp -o JSONPreparse.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONStream.cpp -o JSONStream.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONValidator.cpp -o JSONValidator.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONWorker.cpp -o JSONWorker.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c JSONWriter.cpp -o JSONWriter.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c JSON_parser.c -o JSON_parser.o JSON_parser.c: In function ‘parse_parse_buffer’: JSON_parser.c:487:25: warning: unused variable ‘ok’ [-Wunused-variable] 487 | int ok = sscanf(jc->parse_buffer, "%lf", &tmp); | ^~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RJSON.c -o RJSON.o RJSON.c: In function ‘R_readFromJSON’: RJSON.c:83:25: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic] 83 | conf.callback = (JSON_parser_callback) R_ExternalPtrAddr(VECTOR_ELT(data, 0)); | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -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 g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c internalJSONNode.cpp -o internalJSONNode.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c libjson.cpp -o libjson.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rlibjson.c -o rlibjson.o rlibjson.c: In function ‘processJSONNode’: rlibjson.c:164:19: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic] 164 | fun = (SEXPStringRoutine) R_ExternalPtrAddr(r_stringCall); | ^ rlibjson.c:169:19: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic] 169 | fun = (StringRoutine) R_ExternalPtrAddr(r_stringCall); | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_READ_PRIORITY=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rparser.c -o rparser.o rparser.c: In function ‘R_json_parser_init_from_con’: rparser.c:152:18: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 152 | callback = R_ExternalPtrAddr(cbCall); | ^ g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o RJSONIO.so ConvertUTF.o JSONAllocator.o JSONChildren.o JSONDebug.o JSONIterators.o JSONMemory.o JSONNode.o JSONNode_Mutex.o JSONPreparse.o JSONStream.o JSONValidator.o JSONWorker.o JSONWriter.o JSON_parser.o RJSON.o init.o internalJSONNode.o libjson.o rlibjson.o rparser.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpm2Pgew/R.INSTALL26884161b5a605/RJSONIO/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RJSONIO/00new/RJSONIO/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 (RJSONIO) begin installing package ‘CirceR’ * installing *source* package ‘CirceR’ ... ** this is package ‘CirceR’ version ‘1.3.3’ ** package ‘CirceR’ 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 ** 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 (CirceR) * installing *source* package ‘tfdatasets’ ... ** this is package ‘tfdatasets’ version ‘2.17.0’ ** package ‘tfdatasets’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tfdatasets) * installing *source* package ‘smerc’ ... ** this is package ‘smerc’ version ‘1.8.4’ ** package ‘smerc’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8Xo9hq/R.INSTALL26883914075652/smerc/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/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++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c distance_functions.cpp -o distance_functions.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c noc_cpp.cpp -o noc_cpp.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c optimized_statistics.cpp -o optimized_statistics.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scsg2_cpp.cpp -o scsg2_cpp.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o smerc.so RcppExports.o distance_functions.o noc_cpp.o optimized_statistics.o scsg2_cpp.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp8Xo9hq/R.INSTALL26883914075652/smerc/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-smerc/00new/smerc/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 (smerc) * installing *source* package ‘keras3’ ... ** this is package ‘keras3’ version ‘1.3.0’ ** package ‘keras3’ 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 (keras3) * installing *source* package ‘lme4’ ... ** this is package ‘lme4’ version ‘1.1-37’ ** package ‘lme4’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzLH8qF/R.INSTALL26884618b352cb/lme4/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/tmp/R-d-gcc-14/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -pedantic -mtune=native -c external.cpp -o external.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/tmp/R-d-gcc-14/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -pedantic -mtune=native -c glmFamily.cpp -o glmFamily.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/tmp/R-d-gcc-14/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -pedantic -mtune=native -c optimizer.cpp -o optimizer.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/tmp/R-d-gcc-14/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -pedantic -mtune=native -c predModule.cpp -o predModule.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/tmp/R-d-gcc-14/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -pedantic -mtune=native -c respModule.cpp -o respModule.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o lme4.so external.o glmFamily.o optimizer.o predModule.o respModule.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzLH8qF/R.INSTALL26884618b352cb/lme4/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-lme4/00new/lme4/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lme4) checking RJSONIO_1.3-1.11.tar.gz ... checking ajv_1.0.0.tar.gz ... checking animint2_2025.1.28.tar.gz ... checking CirceR_1.3.3.tar.gz ... checking cmmr_1.0.3.tar.gz ... checking CodelistGenerator_3.4.0.tar.gz ... checking CohortGenerator_0.11.2.tar.gz ... checking CropScapeR_1.1.5.tar.gz ... checking DIZutils_0.1.3.tar.gz ... checking FAOSTAT_2.4.0.tar.gz ... checking gpboost_1.5.6.tar.gz ... checking haploR_4.0.7.tar.gz ... checking kerastuneR_0.1.0.7.tar.gz ... checking LDAvis_0.3.2.tar.gz ... checking LightningR_1.0.2.tar.gz ... checking lipidmapsR_1.0.4.tar.gz ... checking ltertools_1.2.0.tar.gz ... checking mitre_1.0.0.tar.gz ... checking mojson_0.1.tar.gz ... checking PhageCocktail_1.0.3.tar.gz ... checking PubChemR_2.1.4.tar.gz ... checking pubmed.mineR_1.0.21.tar.gz ... checking pxR_0.42.7.tar.gz ... checking R4CouchDB_0.7.5.tar.gz ... checking rbiouml_1.11.tar.gz ... checking RedditExtractoR_3.0.9.tar.gz ... checking restimizeapi_1.0.0.tar.gz ... checking rfigshare_0.3.8.tar.gz ... checking rYoutheria_1.0.3.tar.gz ... checking wilson_2.4.2.tar.gz ... checking ropensecretsapi_1.0.1.tar.gz ... checking tsmp_0.4.15.tar.gz ... checking RXKCD_1.9.2.tar.gz ... checking CodeDepends_0.6.6.tar.gz ... checking Rgff_0.1.6.tar.gz ... checking leaflet_2.2.2.tar.gz ... checking switchr_0.14.8.tar.gz ... checking SignacX_2.2.5.tar.gz ... checking RSDA_3.2.1.tar.gz ... checking exams_2.4-1.tar.gz ... Depends: Package: RJSONIO Imports: methods Timings: user system elapsed RJSONIO 42.265 6.146 51.138 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 5 34 Check results summary: RJSONIO ... NOTE * checking CRAN incoming feasibility ... [7s/9s] NOTE rdepends_ajv ... OK rdepends_animint2 ... OK rdepends_CirceR ... OK rdepends_cmmr ... OK rdepends_CodeDepends ... OK rdepends_CodelistGenerator ... OK rdepends_CohortGenerator ... OK rdepends_CropScapeR ... OK rdepends_DIZutils ... OK rdepends_exams ... OK rdepends_FAOSTAT ... OK rdepends_gpboost ... OK rdepends_haploR ... OK rdepends_kerastuneR ... OK rdepends_LDAvis ... OK rdepends_leaflet ... NOTE * checking Rd cross-references ... NOTE rdepends_LightningR ... NOTE * checking Rd cross-references ... NOTE rdepends_lipidmapsR ... OK rdepends_ltertools ... OK rdepends_mitre ... OK rdepends_mojson ... OK rdepends_PhageCocktail ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_PubChemR ... OK rdepends_pubmed.mineR ... OK rdepends_pxR ... OK rdepends_R4CouchDB ... OK rdepends_rbiouml ... OK rdepends_RedditExtractoR ... OK rdepends_restimizeapi ... OK rdepends_rfigshare ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_Rgff ... OK rdepends_ropensecretsapi ... OK rdepends_RSDA ... OK rdepends_RXKCD ... OK rdepends_rYoutheria ... OK rdepends_SignacX ... OK rdepends_switchr ... OK rdepends_tsmp ... NOTE * checking C++ specification ... NOTE rdepends_wilson ... OK