Can somebody give me a hint as to what is failing in my attempt to compile rtracklayer?
The error message is uninformative: make: *** [chain_io.o] Error 1 Thank you, Ivan ********************************************************************** > source("http://bioconductor.org/biocLite.R") BioC_mirror = http://bioconductor.org Change using chooseBioCmirror(). > biocLite("rtracklayer") Using R version 2.14.0 (R-devel), biocinstall version 2.9.3. Installing Bioconductor version 2.9 packages: [1] "rtracklayer" Please wait... trying URL 'http://bioconductor.org/packages/2.9/bioc/src/contrib/rtracklayer_1.13.7.tar.gz' Content type 'application/x-gzip' length 1538270 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb * installing *source* package 'rtracklayer' ... checking for gcc... gcc 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking sys/file.h usability... yes checking sys/file.h presence... yes checking for sys/file.h... yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking termios.h usability... yes checking termios.h presence... yes checking for termios.h... yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for off_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking for uid_t in sys/types.h... yes checking vfork.h usability... no checking vfork.h presence... no checking for vfork.h... no checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking whether time.h and sys/time.h may both be included... yes checking for sys/time.h... (cached) yes checking for unistd.h... (cached) yes checking for alarm... yes checking for working mktime... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for bzero... yes checking for dup2... yes checking for getcwd... yes checking for gethostbyname... yes checking for gettimeofday... yes checking for memmove... yes checking for memset... yes checking for mkdir... yes checking for regcomp... yes checking for select... yes checking for socket... yes checking for sqrt... no checking for strcasecmp... yes checking for strchr... yes checking for strcspn... yes checking for strdup... yes checking for strerror... yes checking for strrchr... yes checking for strspn... yes checking for strstr... yes checking for uname... yes configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -I"/usr/local/lib64/R/library/IRanges/include" -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -I"/usr/local/lib64/R/library/IRanges/include" -fpic -g -O2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -I"/usr/local/lib64/R/library/IRanges/include" -fpic -g -O2 -c bigWig.c -o bigWig.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -I"/usr/local/lib64/R/library/IRanges/include" -fpic -g -O2 -c chain_io.c -o chain_io.o chain_io.c: In function 'read_chain_file': chain_io.c:77:50: error: 'IntAE' has no member named 'nelt' chain_io.c:82:47: error: 'CharAE' has no member named 'nelt' chain_io.c:96:60: error: 'IntAE' has no member named 'nelt' chain_io.c:98:52: error: 'IntAE' has no member named 'nelt' chain_io.c:112:54: error: 'IntAE' has no member named 'nelt' make: *** [chain_io.o] Error 1 ERROR: compilation failed for package 'rtracklayer' * removing '/usr/local/lib64/R/library/rtracklayer' The downloaded packages are in '/tmp/RtmpvVYzlB/downloaded_packages' Updating HTML index of packages in '.Library' Making packages.html ... done Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'rtracklayer' had non-zero exit status > sessionInfo() R version 2.14.0 Under development (unstable) (2011-04-14 r55450) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.14.0 _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing