############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL oligo ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘oligo’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c DABG.c -o DABG.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c ParserGzXYS.c -o ParserGzXYS.o ParserGzXYS.c: In function ‘gzcountLines’: ParserGzXYS.c:18:17: warning: passing argument 1 of ‘gzeof’ from incompatible pointer type [-Wincompatible-pointer-types] 18 | while (!gzeof(file)){ | ^~~~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from ParserGzXYS.c:4: /usr/include/zlib.h:1595:27: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1595 | ZEXTERN int ZEXPORT gzeof OF((gzFile file)); | ^~ ParserGzXYS.c:19:12: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 19 | gzgets(file, buffer, 1000); | ^~~~ | | | struct gzFile_s ** In file included from ParserGzXYS.c:4: /usr/include/zlib.h:1492:24: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1492 | ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); | ^~~~~~ ParserGzXYS.c: In function ‘gzxys_header_field’: ParserGzXYS.c:46:6: warning: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 46 | fp = gzopen(currentFile, "rb"); | ^ ParserGzXYS.c:50:10: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 50 | gzgets(fp, buffer, LINEMAX); | ^~ | | | struct gzFile_s ** In file included from ParserGzXYS.c:4: /usr/include/zlib.h:1492:24: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1492 | ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); | ^~~~~~ ParserGzXYS.c:51:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 51 | gzclose(fp); | ^~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from ParserGzXYS.c:4: /usr/include/zlib.h:1631:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1631 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ ParserGzXYS.c: In function ‘R_read_gzxys_files’: ParserGzXYS.c:134:6: warning: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 134 | fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb"); | ^ ParserGzXYS.c:138:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 138 | gzclose(fp); | ^~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from ParserGzXYS.c:4: /usr/include/zlib.h:1631:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1631 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c ParserXYS.c -o ParserXYS.o ParserXYS.c: In function ‘xys_header_field’: ParserXYS.c:145:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 145 | fgets(buffer, LINEMAX, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ParserXYS.c: In function ‘R_read_xys_header’: ParserXYS.c:320:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 320 | fgets(buffer, LINEMAX, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c baseProfile.c -o baseProfile.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c basecontent.c -o basecontent.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c mas5calls.c -o mas5calls.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rma2.c -o rma2.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c trimmed.c -o trimmed.o gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-oligo/00new/oligo/libs ** R ** inst ** byte-compile and prepare package for lazy loading Note: in method for ‘pm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" Note: in method for ‘mm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" ** 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 (oligo)