[archi]

I think I need libcurl (version 7.14.0 or higher) as I'm working on linux but can't figure out how to do that. Can someone please suggest something asap.
thanks in advance

[archi]

Thanks a lot everyone. I have successfully installed ShortRead package on my system.

[maubp]

Can you explain how you solved the remaining problems? That would help anyone else reading this thread in future (e.g. from a Google search with the error message).

[archi]

Yes,sure.
after installing libxml,the main problem was having libcurl on my system.As I'm working on linux,libcurl has to be explicitly installed and I did that using Ubuntu software center.After that type source("http://bioconductor.org/biocLite.R")
biocLite("ShortRead")
and it gets installed.

[Simon Anders]

You should add that you have not only installed the curl library but also the header files, which are required to compile other stuff (such as Bioconductor packages) using the library. Therefore, it is important to chose the 'dev 'package ('libcurl-dev', not only 'libcurl' and 'libxml2-dev', not only 'libxml2') when installing system libraries that an R package needs.

[archi]

Now I'm getting following error in using readFastq function:

readFastq("home/linux/sratoolkit.2.34-2-centos_linux64/bin",pattern="SRR039194_1.fastq")
Error: Input/Output
no input files found
dirPath: home/linux/sratoolkit.2.34-2-centos_linux64/bin
pattern: SRR039194_1.fastq

any suggestions on how to go about?
please respond asap.
thanks in advance!

[archi]

now I'm getting the following errors in using the readFastq function
readFastq("home/linux/sratoolkit.2.34-2-centos_linux64/bin",pattern="SRR039194_1.fastq")
Error: Input/Output
no input files found
dirPath: home/linux/sratoolkit.2.34-2-centos_linux64/bin
pattern: SRR039194_1.fastq

any suggestions on how to fix this?
please reply asap
thanks!