Great. The subversion compiles without problems. For those who usually don't install from SVN, this is how it's done:
1) Become root 2) cd to the R-devel directory 3) Knowing that the user and password for this SVN are readonly and readonly, do: svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rtracklayer 4) R CMD INSTALL rtracklayer Thank you Hervé. Ivan 2011/7/26 Hervé Pagès <hpa...@fhcrc.org>: > Hi Ivan, > > On 11-07-25 09:41 PM, Ivan Gregoretti wrote: >> >> Can somebody give me a hint as to what is failing in my attempt to >> compile rtracklayer? > > A recent change in IRanges breaks rtracklayer < 1.13.10. This problem > is fixed in rtracklayer 1.13.10 but an error in the vignette prevents > the package from propagating. You should be able to install the package > from svn if you need it now. > >> >> The error message is uninformative: make: *** [chain_io.o] Error 1 > > The informative messages are on the previous lines: > > 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 > > Cheers, > H. > >> >> 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 > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing