[Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1)

Hervé Pagès hpages at fhcrc.org
Tue Jul 26 10:12:11 CEST 2011 

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 at 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: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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