############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL geneXtendeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘geneXtendeR’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c annotate.c -o annotate.o annotate.c: In function ‘annotate’: annotate.c:159:79: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 159 | Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld annotate.c:191:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 191 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld annotate.c:199:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 199 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld annotate.c:208:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 208 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld annotate.c:228:83: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 228 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c extract_number.c -o extract_number.o extract_number.c: In function ‘extractnumber’: extract_number.c:72:10: warning: variable ‘n_1’ set but not used [-Wunused-but-set-variable] 72 | long n_1; | ^~~ extract_number.c:66:10: warning: variable ‘j_1’ set but not used [-Wunused-but-set-variable] 66 | long j_1; | ^~~ extract_number.c:54:12: warning: variable ‘pvcfcol5_5’ set but not used [-Wunused-but-set-variable] 54 | char * pvcfcol5_5; | ^~~~~~~~~~ extract_number.c:53:12: warning: variable ‘pvcfcol4_4’ set but not used [-Wunused-but-set-variable] 53 | char * pvcfcol4_4; | ^~~~~~~~~~ extract_number.c:52:12: warning: variable ‘pvcfcol3_3’ set but not used [-Wunused-but-set-variable] 52 | char * pvcfcol3_3; | ^~~~~~~~~~ extract_number.c:51:12: warning: variable ‘pvcfcol2_2’ set but not used [-Wunused-but-set-variable] 51 | char * pvcfcol2_2; | ^~~~~~~~~~ extract_number.c:50:12: warning: variable ‘pvcfcol1_1’ set but not used [-Wunused-but-set-variable] 50 | char * pvcfcol1_1; | ^~~~~~~~~~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c extract_peaks.c -o extract_peaks.o extract_peaks.c: In function ‘extractpeaks’: extract_peaks.c:202:79: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 202 | Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer)); | ~^ ~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-geneXtendeR/00new/geneXtendeR/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 (geneXtendeR)