Hi Leonardo,

I thank you about your guidances. But i still have problematic through import BigWig file or any Project as  project = 'SRP009615'.

Despite that i check the version of "rtracelayer" that is (1.34.2 for bioc-release), furthermore i have been tried to apply all commands which is (bioc-devel mailing list   "https://stat.ethz.ch/pipermail/bioc-devel/2016-May/009336.html, ")

like the following

+ as = 'RleList'

2- url <- unshorten_url('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw')

3-  url_http <- 'http://content-na.drive.amazonaws.com/cdproxy/templink/i_aQAPZJkJ9d9lN1NO5DJJtlbpvAdgbNuc1SkqSTHFouFiZq5'

4-bw <- BigWigFile(url)

5- x <- import.bw(url, as = 'RleList') ; x <- import.bw(bw, as = 'RleList')

6- download.file('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw,

+ destfile = 'DRR000897.bw', method = 'curl', extra = '-L')

HERE it told me i don't have 'curl'

that processed the same my case but until this moment i couldn't to fix that problem which said me 

[[[2017-02-28 16:59:34 loadCoverage: loading BigWig file http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw
Too many pushAbortHandlers, can only handle 11
 Show Traceback
Error in seqinfo(con) : UCSC library operation failed]]]

i will be very thankful to guide me what is the optimal solution concerning this problem.

thanks

Mustafa.

Hi Mustafa,

This is not going to be a satisfying answer, but at least we know by now that workaround exists for your situation.

Basically, the issue you are reporting is not a recount or derfinder issue, but an rtracklayer one. For some reason, 

library('rtracklayer')
x <- import.bw('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw',as = 'RleList')

does not work for you in Bioc 3.4 with the latest packages installed as well as recent pkg-config, openssl and a working RCurl. recount::expressed_regions() tries by default to access the BigWig files from the web and does so by using some functions in derfinder, which in turn rely on rtracklayer::import.bw(). However, recount::expressed_regions() can access the data on a local disk which removes the web issues. This is not the default behavior because it involves downloading the BigWig files even if you are interested in a small portion of the genome. The following should then work for you:

library('recount')
regions <- expressed_regions('DRP000366', 'chrY', cutoff = 5L,
    maxClusterGap = 3000L, outdir = 'DRP000366')

instead of the default

regions <- expressed_regions('DRP000366', 'chrY', cutoff = 5L,
    maxClusterGap = 3000L, outdir = NULL)

When specifying outdir = 'DRP000366', recount::expressed_regions()will check if the data exists and if it's missing (which would be the case normally), then it will use recount::download_study() to download the necessary files. Similarly, use outdir = 'DRP000366' when using recount::coverage_matrix().

Another option also exists, which is using SciServer Compute to access the files via a R Jupyter Notebook, run the computations on SciServer, save your files (I assume that you plan to run recount::coverage_matrix() next), then download them to your computer. Most of this is described in the recount vignette at http://bioconductor.org/packages/release/bioc/vignettes/recount/inst/doc/recount-quickstart.html#accessing-recount-via-sciserver.

If you are interested in accessing the BigWig files from the web, please post a new question using the rtracklayer tag. Basically, with the output of:

library('rtracklayer')
x <- import.bw('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw',as = 'RleList')
options(width = 120)
devtools::session_info()

I have reported most of this already at the bioc-devel mailing list https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010518.html and have run out of ideas on what could be the source of the problem behind your rtracklayer issue.

Best,
Leonardo