On 07/26/2011 07:14 AM, Ivan Gregoretti wrote:
Great. The subversion compiles without problems.
For those who usually don't install from SVN, this is how it's done:
1)
Become root
Not usually necessary. Just cd to some location on your file system, svn
co ... and then R CMD INSTALL rtracklayer. You might sudo R CMD INSTALL
rtracklayer if you were updating a system-wide installation (but then
you probably wouldn't want to be installing from svn).
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
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--
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
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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