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

Martin Morgan mtmorgan at fhcrc.org
Tue Jul 26 17:35:11 CEST 2011


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<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
>>
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at 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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