############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL garfield ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘garfield’ ... ** 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’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c garfield_init.c -o garfield_init.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 garfield_perm.cpp -o garfield_perm.o garfield_perm.cpp: In function ‘void batchfeep(std::vector >&, std::vector >&, const std::vector&, const std::vector&, int, int, bool, int, double, int, std::vector)’: garfield_perm.cpp:306:29: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘long int’ [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ~^ ~~~ | | | | char* long int | %ld garfield_perm.cpp:306:32: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘int’ [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ~^ ~~~~~~ | | | | char* int | %d garfield_perm.cpp:306:38: warning: format ‘%s’ expects argument of type ‘char*’, but argument 4 has type ‘double’ [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | char* double | %f garfield_perm.cpp:306:41: warning: unknown conversion type character ‘\x09’ in format [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ^~ garfield_perm.cpp:306:46: warning: format ‘%s’ expects argument of type ‘char*’, but argument 5 has type ‘int’ [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ~^ ~~~~~~ | | | | char* int | %d garfield_perm.cpp:306:83: warning: format ‘%s’ expects argument of type ‘char*’, but argument 6 has type ‘double’ [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | char* double | %f garfield_perm.cpp: In function ‘int garfield_perm(char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**)’: garfield_perm.cpp:356:27: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘int’ [-Wformat=] 356 | Rprintf("%s",nannot); | ~^ ~~~~~~ | | | | | int | char* | %d 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 garfield_prep.cpp -o garfield_prep.o garfield_prep.cpp:144:28: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 144 | struct Enumerator : public iterator { | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from garfield_prep.cpp:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ garfield_prep.cpp:225:37: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 225 | struct TagsOutputIterator1 : public iterator { | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ garfield_prep.cpp:234:37: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 234 | struct TagsOutputIterator2 : public iterator { | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ garfield_prep.cpp:245:38: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 245 | struct TagRefOutputIterator : public iterator { | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ garfield_prep.cpp:273:37: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 273 | struct PrintOutputIterator : public iterator { | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o garfield.so garfield_init.o garfield_perm.o garfield_prep.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-garfield/00new/garfield/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 (garfield)