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

Ivan Gregoretti ivangreg at gmail.com
Tue Jul 26 16:14:48 CEST 2011 

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 <hpages at 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 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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