############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL casper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘casper’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c casper.cpp -o casper.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c cstat.cpp -o cstat.o cstat.cpp: In function ‘void free_vector(float*, int, int)’: cstat.cpp:1111:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 4)))’ and NULL [-Waddress] 1111 | if( (v+nl) != NULL ) free((char *) (v+nl)); | ^ cstat.cpp: In function ‘void free_dvector(double*, int, int)’: cstat.cpp:1117:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 8)))’ and NULL [-Waddress] 1117 | if( (v+nl) != NULL ) free((char *) (v+nl)); | ^ cstat.cpp: In function ‘void free_ivector(int*, int, int)’: cstat.cpp:1123:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 4)))’ and NULL [-Waddress] 1123 | if( (v+nl) != NULL ) free((char *) (v+nl)); | ^ cstat.cpp: In function ‘void free_dmatrix(double**, int, int, int, int)’: cstat.cpp:1131:47: warning: comparing the result of pointer addition ‘((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 8)))’ and NULL [-Waddress] 1131 | for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL ) | ^ cstat.cpp:1133:21: warning: comparing the result of pointer addition ‘(m + ((sizetype)(((long unsigned int)nrl) * 8)))’ and NULL [-Waddress] 1133 | if( (m+nrl) != NULL ) free((char *) (m+nrl)); | ^ cstat.cpp: In function ‘void free_imatrix(int**, int, int, int, int)’: cstat.cpp:1141:47: warning: comparing the result of pointer addition ‘((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 4)))’ and NULL [-Waddress] 1141 | for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL ) | ^ cstat.cpp:1143:21: warning: comparing the result of pointer addition ‘(m + ((sizetype)(((long unsigned int)nrl) * 8)))’ and NULL [-Waddress] 1143 | if( (m+nrl) != NULL ) free((char *) (m+nrl)); | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c dataframe.cpp -o dataframe.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c discretedf.cpp -o discretedf.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c dropVariant.cpp -o dropVariant.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c exon.cpp -o exon.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c fragFunc.c -o fragFunc.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fragment.cpp -o fragment.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c functions.c -o functions.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c hash.c -o hash.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c join_exons.c -o join_exons.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c makeIslands.c -o makeIslands.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c model.cpp -o model.o In file included from /usr/include/stdio.h:980, from model.cpp:1: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char* Model::toString()’ at model.cpp:147:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 overlaps destination object ‘’ [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c model_cmp.cpp -o model_cmp.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c pathCounts.c -o pathCounts.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c procBam.c -o procBam.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c rcasper.cpp -o rcasper.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c seppel.cpp -o seppel.o seppel.cpp: In member function ‘void Seppel::exploreUnif(int, std::set*)’: seppel.cpp:484:9: warning: array subscript -1 is outside array bounds of ‘void [24]’ [-Warray-bounds=] 484 | delete [] possiblemodels; | ^~~~~~~~~~~~~~~~~~~~~~~~ seppel.cpp:402:55: note: at offset -8 into object of size 24 allocated by ‘operator new’ 402 | vector* possiblemodels = new vector(); | ^ seppel.cpp:484:19: warning: ‘void operator delete [](void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 484 | delete [] possiblemodels; | ^~~~~~~~~~~~~~ seppel.cpp:402:55: note: returned from ‘void* operator new(std::size_t)’ 402 | vector* possiblemodels = new vector(); | ^ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c simReads.c -o simReads.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c simReadsfunc.c -o simReadsfunc.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c smartmodeldist.cpp -o smartmodeldist.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c uniqQname.c -o uniqQname.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c variant.cpp -o variant.o In file included from /usr/include/stdio.h:980, from variant.cpp:1: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void Variant::toString(char*)’ at variant.cpp:164:45: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 overlaps destination object ‘str’ [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ variant.cpp: In member function ‘void Variant::toString(char*)’: variant.cpp:156:30: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 156 | void Variant::toString(char *str) | ~~~~~~^~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c variant_cmp.cpp -o variant_cmp.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o casper.so casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-casper/00new/casper/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘transcripts’ in package ‘casper’ ** 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 (casper)