Error through importing (project = 'SRP009615') or even to download any BigWig File
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@mustafa-abuelqumsan-12460
Last seen 5.2 years ago
France/Marseille

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

1- x <- import.bw('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw',

+ 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.

 

recount Tutorial • 3.9k views
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0
Entering edit mode

Hi Mustafa,

Can you add the full session information output please?

Thanks,

Leonardo

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Entering edit mode

Hi Mustafa,

I can't reproduce your problem with recount 1.0.12 and rtracklayer 1.34.2. The thing that comes to mind from the bioc-devel mailing list thread you linked to is the openssl. In any case, please post the full session information.

## Un-evaluated code

library('rtracklayer')
library('devtools')
library('recount')

## Try importing a bigwig file with rtracklayer
x <- import.bw('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw',as = 'RleList')
x

## From http://bioconductor.org/packages/release/bioc/vignettes/recount/inst/doc/recount-quickstart.html#define-expressed-regions
## Define expressed regions for study SRP009615, only for chromosome Y
regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L, 
    maxClusterGap = 3000L)
regions

## Reproducibility information
Sys.time()
proc.time()
options(width = 120)
session_info()

## Evaluated code

> library('rtracklayer')
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
> library('devtools')
> library('recount')
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> ## Try importing a bigwig file with rtracklayer
> x <- import.bw('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw',as = 'RleList')
> x
RleList of length 94
$chr1
numeric-Rle of length 248956422 with 1249470 runs
Lengths: 13378 37 366 37 25 ... 535 37 1028 37 13595
Values : 0 1 0 1 0 ... 0 1 0 1 0
$chr10
numeric-Rle of length 133797422 with 412887 runs
Lengths: 47132 37 12 37 333 ... 211 37 2082 37 11003
Values : 0 1 0 1 0 ... 0 1 0 1 0
$chr11
numeric-Rle of length 135086622 with 700940 runs
Lengths: 74243 37 22178 37 22907 ... 37 4395 37 17340
Values : 0 1 0 1 0 ... 1 0 1 0
$chr11_KI270721v1_random
numeric-Rle of length 100316 with 363 runs
Lengths: 2593 37 17 7 1 ... 876 37 492 37 47993
Values : 0 1 0 1 2 ... 0 1 0 1 0
$chr12
numeric-Rle of length 133275309 with 628862 runs
Lengths: 10055 37 4101 37 316 ... 623 37 4860 37 64715
Values : 0 1 0 1 0 ... 0 1 0 1 0
...
<89 more elements>
>
> ## From http://bioconductor.org/packages/release/bioc/vignettes/recount/inst/doc/recount-quickstart.html#define-expressed-regions
> ## Define expressed regions for study SRP009615, only for chromosome Y
> regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
+ maxClusterGap = 3000L)
2017-02-28 13:35:58 loadCoverage: loading BigWig file http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw
2017-02-28 13:35:59 loadCoverage: applying the cutoff to the merged data
2017-02-28 13:35:59 filterData: originally there were 57227415 rows, now there are 57227415 rows. Meaning that 0 percent was filtered.
2017-02-28 13:35:59 findRegions: identifying potential segments
2017-02-28 13:35:59 findRegions: segmenting information
2017-02-28 13:35:59 .getSegmentsRle: segmenting with cutoff(s) 5
2017-02-28 13:35:59 findRegions: identifying candidate regions
2017-02-28 13:35:59 findRegions: identifying region clusters
> regions
GRanges object with 808 ranges and 6 metadata columns:
seqnames ranges strand | value area
<Rle> <IRanges> <Rle> | <numeric> <numeric>
1 chrY [2929794, 2929829] * | 14.7265009482702 530.154034137726
2 chrY [2956678, 2956701] * | 12.8106340567271 307.45521736145
3 chrY [2977203, 2977227] * | 5.34908433914185 133.727108478546
4 chrY [2977957, 2977994] * | 6.46976616508082 245.851114273071
5 chrY [2978850, 2978871] * | 5.7976552139629 127.548414707184
... ... ... ... . ... ...
804 chrY [26614511, 26614546] * | 7.28189378314548 262.148176193237
805 chrY [26614548, 26614553] * | 5.48768202463786 32.9260921478271
806 chrY [26614779, 26614808] * | 6.64339276949565 199.301783084869
807 chrY [26626808, 26626848] * | 12.6038152648181 516.756425857544
808 chrY [26626971, 26627028] * | 14.1673366941255 821.705528259277
indexStart indexEnd cluster clusterL
<integer> <integer> <Rle> <Rle>
1 2929794 2929829 1 36
2 2956678 2956701 2 24
3 2977203 2977227 3 2750
4 2977957 2977994 3 2750
5 2978850 2978871 3 2750
... ... ... ... ...
804 26614511 26614546 224 298
805 26614548 26614553 224 298
806 26614779 26614808 224 298
807 26626808 26626848 225 221
808 26626971 26627028 225 221
-------
seqinfo: 1 sequence from an unspecified genome
>
> ## Reproducibility information
> Sys.time()
[1] "2017-02-28 13:36:00 EST"
> proc.time()
user system elapsed
20.312 2.162 34.487
> options(width = 120)
> session_info()
Session info -----------------------------------------------------------------------------------------------------------
setting value
version R version 3.3.2 RC (2016-10-26 r71594)
system x86_64, darwin13.4.0
ui X11
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2017-02-28
Packages ---------------------------------------------------------------------------------------------------------------
package * version date source
acepack 1.4.1 2016-10-29 CRAN (R 3.3.0)
AnnotationDbi 1.36.2 2017-01-30 Bioconductor
assertthat 0.1 2013-12-06 cran (@0.1)
backports 1.0.5 2017-01-18 CRAN (R 3.3.2)
base64enc 0.1-3 2015-07-28 cran (@0.1-3)
Biobase * 2.34.0 2016-10-18 Bioconductor
BiocGenerics * 0.20.0 2016-10-18 Bioconductor
BiocParallel 1.8.1 2016-10-30 Bioconductor
biomaRt 2.30.0 2016-10-18 Bioconductor
Biostrings 2.42.1 2016-12-01 Bioconductor
bitops 1.0-6 2013-08-17 cran (@1.0-6)
BSgenome 1.42.0 2016-10-18 Bioconductor
bumphunter 1.14.0 2016-10-18 Bioconductor
checkmate 1.8.2 2016-11-02 CRAN (R 3.3.1)
cluster 2.0.5 2016-10-08 CRAN (R 3.3.2)
codetools 0.2-15 2016-10-05 CRAN (R 3.3.2)
colorout * 1.1-2 2016-10-19 Github (jalvesaq/colorout@6d84420)
colorspace 1.3-2 2016-12-14 CRAN (R 3.3.2)
data.table 1.10.4 2017-02-01 CRAN (R 3.3.2)
DBI 0.5-1 2016-09-10 cran (@0.5-1)
derfinder 1.8.0 2016-10-18 Bioconductor
derfinderHelper 1.8.0 2016-10-18 Bioconductor
devtools * 1.12.0 2016-06-24 CRAN (R 3.3.0)
digest 0.6.12 2017-01-27 CRAN (R 3.3.2)
doRNG 1.6 2014-03-07 CRAN (R 3.3.0)
downloader 0.4 2015-07-09 CRAN (R 3.3.0)
foreach 1.4.3 2015-10-13 CRAN (R 3.3.0)
foreign 0.8-67 2016-09-13 CRAN (R 3.3.2)
Formula 1.2-1 2015-04-07 CRAN (R 3.3.0)
GenomeInfoDb * 1.10.3 2017-02-07 Bioconductor
GenomicAlignments 1.10.0 2016-10-18 Bioconductor
GenomicFeatures 1.26.3 2017-02-22 Bioconductor
GenomicFiles 1.10.3 2016-10-21 Bioconductor
GenomicRanges * 1.26.3 2017-02-25 Bioconductor
GEOquery 2.40.0 2016-10-18 Bioconductor
ggplot2 2.2.1 2016-12-30 CRAN (R 3.3.2)
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
Hmisc 4.0-2 2016-12-31 CRAN (R 3.3.2)
htmlTable 1.9 2017-01-26 CRAN (R 3.3.2)
htmltools 0.3.5 2016-03-21 cran (@0.3.5)
htmlwidgets 0.8 2016-11-09 CRAN (R 3.3.2)
httr 1.2.1 2016-07-03 CRAN (R 3.3.0)
IRanges * 2.8.1 2016-11-08 Bioconductor
iterators 1.0.8 2015-10-13 CRAN (R 3.3.0)
jsonlite 1.3 2017-02-28 CRAN (R 3.3.2)
knitr 1.15.1 2016-11-22 CRAN (R 3.3.2)
lattice 0.20-34 2016-09-06 CRAN (R 3.3.2)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
lazyeval 0.2.0 2016-06-12 cran (@0.2.0)
locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.0)
magrittr 1.5 2014-11-22 cran (@1.5)
Matrix 1.2-8 2017-01-20 CRAN (R 3.3.2)
matrixStats 0.51.0 2016-10-09 CRAN (R 3.3.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
munsell 0.4.3 2016-02-13 cran (@0.4.3)
nnet 7.3-12 2016-02-02 CRAN (R 3.3.2)
pkgmaker 0.22 2014-05-14 CRAN (R 3.3.0)
plyr 1.8.4 2016-06-08 cran (@1.8.4)
qvalue 2.6.0 2016-10-18 Bioconductor
R6 2.2.0 2016-10-05 CRAN (R 3.3.0)
RColorBrewer 1.1-2 2014-12-07 cran (@1.1-2)
Rcpp 0.12.9 2017-01-14 CRAN (R 3.3.2)
RCurl 1.95-4.8 2016-03-01 cran (@1.95-4.)
recount * 1.0.12 2017-02-23 Bioconductor
registry 0.3 2015-07-08 CRAN (R 3.3.0)
rentrez 1.0.4 2016-10-26 CRAN (R 3.3.0)
reshape2 1.4.2 2016-10-22 CRAN (R 3.3.0)
rngtools 1.2.4 2014-03-06 CRAN (R 3.3.0)
rpart 4.1-10 2015-06-29 CRAN (R 3.3.2)
Rsamtools 1.26.1 2016-10-22 Bioconductor
RSQLite 1.1-2 2017-01-08 CRAN (R 3.3.2)
rtracklayer * 1.34.2 2017-02-19 Bioconductor
S4Vectors * 0.12.1 2016-12-01 Bioconductor
scales 0.4.1 2016-11-09 CRAN (R 3.3.2)
stringi 1.1.2 2016-10-01 cran (@1.1.2)
stringr 1.2.0 2017-02-18 CRAN (R 3.3.2)
SummarizedExperiment * 1.4.0 2016-10-18 Bioconductor
survival 2.40-1 2016-10-30 CRAN (R 3.3.0)
tibble 1.2 2016-08-26 cran (@1.2)
VariantAnnotation 1.20.2 2016-12-01 Bioconductor
withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
XML 3.98-1.5 2016-11-10 CRAN (R 3.3.2)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
XVector 0.14.0 2016-10-18 Bioconductor
zlibbioc 1.20.0 2016-10-18 Bioconductor

Best,

Leonardo

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0
Entering edit mode

Hi Mustafa,

I saw that you posted the session information as a new question at my session information regarding " Error through importing (project = 'SRP009615') or even to download any BigWig File". In the future, please use the "add reply" button on the original thread. Otherwise it makes it hard for anyone else in the future to follow the set question, replies and comments to understand the solution to the problem if they encounter the same error you reported. 

I know that the character limit is a bit annoying, but you can add long output like the session information in a gist https://gist.github.com/ and then post the gist link in the reply (using "text" formatting). If you do so, the website will automatically show the contents of your gist, just like it did with mine in my previous reply.

As for the actual error, your first screenshot shows a different error (or part of it, I can't see it all). I think that the error is related to the openssl system dependency in rtracklayer. I'll ask about it in bioc-devel and will get back to you.

Best,

Leonardo

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Entering edit mode

Mustafa,

Please add in a reply your openssl and pkg-util versions by running in your terminal (not the R one, but the unix one):

openssl version
pkg-config --version

 

Here is the output in two machines I have access to:

$ openssl version
OpenSSL 0.9.8zh 14 Jan 2016
$ pkg-config --version
0.29.1


$ openssl version
OpenSSL 1.0.1e-fips 11 Feb 2013
$ pkg-config --version
0.23

Best,

Leonardo

 

 

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Hi Leonardo,

This is my configuration for openssl.


root@Dell-CG1XF82:~# openssl version OpenSSL 1.0.2g 1 Mar 2016 root@Dell-CG1XF82:~# pkg-config --version 0.29.1 root@Dell-CG1XF82:~#



Best,

Mustafa.

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<script src="&lt;a href=" elqumsan="" a03e5f207774abca772b6bec2138a604"="">elqumsan/a03e5f207774abca772b6bec2138a604"></script>

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Hi Leonardo,

unlimited thanks for yours instruction to put my session information here, Because of it have a bit annoying limit. 

> regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
+ maxClusterGap = 3000L)
2017-03-01 17:33:25 loadCoverage: loading BigWig file http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw
unable to parse last-modified string [Sun, 24 Jul 2016 18:26:52 GMT]Error in seqinfo(con) : UCSC library operation failed
> session_info()
Session info ---------------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.3.2 (2016-10-31)
system x86_64, linux-gnu
ui RStudio (1.0.136)
language en_US
collate en_US.UTF-8
tz Europe/Paris
date 2017-03-01
Packages -------------------------------------------------------------------------------------------------------------------------------
package * version date source
acepack 1.4.1 2016-10-29 CRAN (R 3.3.2)
annotate 1.52.1 2017-02-23 Bioconductor
AnnotationDbi 1.36.2 2017-02-24 Bioconductor
assertthat 0.1 2013-12-06 CRAN (R 3.3.2)
backports 1.0.5 2017-01-18 CRAN (R 3.3.2)
base64enc 0.1-3 2015-07-28 CRAN (R 3.3.2)
bibtex 0.4.0 2014-12-31 CRAN (R 3.3.2)
Biobase * 2.34.0 2017-02-24 Bioconductor
BiocGenerics * 0.20.0 2017-02-24 Bioconductor
BiocParallel 1.8.1 2017-02-24 Bioconductor
biomaRt 2.30.0 2017-02-24 Bioconductor
Biostrings 2.42.1 2017-02-24 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.3.2)
BSgenome 1.42.0 2017-02-24 Bioconductor
bumphunter 1.14.0 2017-02-24 Bioconductor
checkmate 1.8.2 2016-11-02 CRAN (R 3.3.2)
cluster 2.0.5 2016-10-08 CRAN (R 3.3.2)
codetools 0.2-15 2016-10-05 CRAN (R 3.3.1)
colorspace 1.3-2 2016-12-14 CRAN (R 3.3.2)
data.table 1.10.4 2017-02-01 CRAN (R 3.3.2)
DBI 0.5-1 2016-09-10 CRAN (R 3.3.2)
DEFormats 1.2.0 2017-02-27 Bioconductor
derfinder 1.8.0 2017-02-24 Bioconductor
derfinderHelper 1.8.0 2017-02-24 Bioconductor
DESeq2 * 1.14.1 2017-02-23 Bioconductor
devtools * 1.12.0 2016-12-05 CRAN (R 3.3.2)
digest 0.6.12 2017-01-27 CRAN (R 3.3.2)
doRNG 1.6 2014-03-07 CRAN (R 3.3.2)
downloader 0.4 2015-07-09 CRAN (R 3.3.2)
DT * 0.2 2016-08-09 CRAN (R 3.3.2)
edgeR 3.16.5 2017-02-27 Bioconductor
evaluate 0.10 2016-10-11 CRAN (R 3.3.2)
foreach 1.4.3 2015-10-13 CRAN (R 3.3.2)
foreign 0.8-67 2016-09-13 CRAN (R 3.3.1)
Formula 1.2-1 2015-04-07 CRAN (R 3.3.2)
genefilter 1.56.0 2017-02-23 Bioconductor
geneplotter 1.52.0 2017-02-23 Bioconductor
GenomeInfoDb * 1.10.3 2017-02-24 Bioconductor
GenomicAlignments 1.10.0 2017-02-24 Bioconductor
GenomicFeatures 1.26.3 2017-02-24 Bioconductor
GenomicFiles 1.10.3 2017-02-24 Bioconductor
GenomicRanges * 1.26.2 2017-02-24 Bioconductor
GEOquery 2.40.0 2017-02-24 Bioconductor
ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.3.2)
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.2)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.2)
highr 0.6 2016-05-09 CRAN (R 3.3.2)
Hmisc 4.0-2 2016-12-31 CRAN (R 3.3.2)
htmlTable 1.9 2017-01-26 CRAN (R 3.3.2)
htmltools 0.3.5 2016-03-21 CRAN (R 3.3.2)
htmlwidgets 0.8 2016-11-09 CRAN (R 3.3.2)
httr 1.2.1 2016-07-03 CRAN (R 3.3.2)
IRanges * 2.8.1 2017-02-24 Bioconductor
iterators 1.0.8 2015-10-13 CRAN (R 3.3.2)
jsonlite 1.2 2016-12-31 CRAN (R 3.3.2)
knitcitations 1.0.7 2015-10-28 CRAN (R 3.3.2)
knitr * 1.15.1 2016-11-22 CRAN (R 3.3.2)
knitrBootstrap 1.0.0 2015-12-16 CRAN (R 3.3.2)
labeling 0.3 2014-08-23 CRAN (R 3.3.2)
lattice 0.20-34 2016-09-06 CRAN (R 3.3.1)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.2)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.2)
limma 3.30.11 2017-02-24 Bioconductor
locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.2)
lubridate 1.6.0 2016-09-13 CRAN (R 3.3.2)
magrittr 1.5 2014-11-22 CRAN (R 3.3.2)
markdown 0.7.7 2015-04-22 CRAN (R 3.3.2)
Matrix 1.2-8 2017-01-20 CRAN (R 3.3.2)
matrixStats 0.51.0 2016-10-09 CRAN (R 3.3.2)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.2)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.2)
nnet 7.3-12 2016-02-02 CRAN (R 3.2.5)
pheatmap * 1.0.8 2015-12-11 CRAN (R 3.3.2)
pkgmaker 0.22 2014-05-14 CRAN (R 3.3.2)
plyr 1.8.4 2016-06-08 CRAN (R 3.3.2)
qvalue 2.6.0 2017-02-24 Bioconductor
R6 2.2.0 2016-10-05 CRAN (R 3.3.2)
RColorBrewer * 1.1-2 2014-12-07 CRAN (R 3.3.2)
Rcpp 0.12.9 2017-01-14 CRAN (R 3.3.2)
RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.2)
recount * 1.0.12 2017-02-24 Bioconductor
RefManageR 0.13.1 2016-11-13 CRAN (R 3.3.2)
regionReport * 1.8.0 2017-02-27 Bioconductor
registry 0.3 2015-07-08 CRAN (R 3.3.2)
rentrez 1.0.4 2016-10-26 CRAN (R 3.3.2)
reshape2 1.4.2 2016-10-22 CRAN (R 3.3.2)
RJSONIO 1.3-0 2014-07-28 CRAN (R 3.3.2)
rmarkdown 1.3 2016-12-21 CRAN (R 3.3.2)
rngtools 1.2.4 2014-03-06 CRAN (R 3.3.2)
rpart 4.1-10 2015-06-29 CRAN (R 3.2.1)
rprojroot 1.2 2017-01-16 CRAN (R 3.3.2)
Rsamtools 1.26.1 2017-02-24 Bioconductor
RSQLite 1.1-2 2017-01-08 CRAN (R 3.3.2)
rstudioapi 0.6 2016-06-27 CRAN (R 3.3.2)
rtracklayer 1.34.2 2017-02-24 Bioconductor
S4Vectors * 0.12.1 2017-02-24 Bioconductor
scales 0.4.1 2016-11-09 CRAN (R 3.3.2)
stringi 1.1.2 2016-10-01 CRAN (R 3.3.2)
stringr 1.2.0 2017-02-18 CRAN (R 3.3.2)
SummarizedExperiment * 1.4.0 2017-02-24 Bioconductor
survival 2.40-1 2016-10-30 CRAN (R 3.3.2)
tibble 1.2 2016-08-26 CRAN (R 3.3.2)
VariantAnnotation 1.20.2 2017-02-24 Bioconductor
withr 1.0.2 2016-06-20 CRAN (R 3.3.2)
XML 3.98-1.5 2016-11-10 CRAN (R 3.3.2)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.2)
XVector 0.14.0 2017-02-24 Bioconductor
yaml 2.1.14 2016-11-12 CRAN (R 3.3.2)
zlibbioc 1.20.0 2017-02-24 Bioconductor
>

Best.

Mustafa.

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Entering edit mode

Hi Mustafa,

If you go to your browser and enter http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw, can you download the bigwig file to your computer? Maybe the server with the bigwig files is blocking your access. It's just a thought.

Best,

Leonardo

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Also, what happens if you type in R the following code?

library('RCurl')
curlVersion()
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Hi Leonardo,

I really appreciated your efforts in order to i finally arrived to the good solution. but when i run your last code which is  

> library('RCurl')
> curlVersion()
$age
[1] 3
$version
[1] "7.47.0"
$vesion_num
[1] 470784
$host
[1] "x86_64-pc-linux-gnu"
$features
ipv6 ssl libz ntlm asynchdns spnego largefile idn tlsauth_srp ntlm_wb
1 4 8 16 128 256 512 1024 16384 32768
$ssl_version
[1] "OpenSSL/1.0.2g"
$ssl_version_num
[1] 0
$libz_version
[1] "1.2.8"
$protocols
[1] "dict" "file" "ftp" "ftps" "gopher" "http" "https" "imap" "imaps" "ldap" "ldaps" "pop3" "pop3s" "rtmp"
[15] "rtsp" "smb" "smbs" "smtp" "smtps" "telnet" "tftp"
$ares
[1] ""
$ares_num
[1] 0
$libidn
[1] "1.32"
>

Thanks a lot Leonardo.

Best.

Mustafa

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Hi Leonardo,

I tried  to download that specified file which is you tell me to download it from the link

 http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw

But also when i attempt read that file locally from my computer i faced furthermore it another error message which is 

getwd()
list.files()
bigwig <- file.path("/home/abuelqumsan/Dropbox/Mustafa_Abu_Al-Qumsan_demande_Dispense_master_2015-06/scientific/discussion_notes", "DRR000897.bw" )
regions <- expressed_regions('bigwig', 'chrY', cutoff = 5L,
    maxClusterGap = 3000L)

i getting this another error message

Error: nrow(url_table) > 0 is not TRUE

now i frustrating and i don't know what and how i would continuing with "recount' whereas i need to continue to conduct my project which is new and followed stage to your great work .

Thank you so much Leonardo.

Best.

Mustafa.

 

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Yeah, that's not going to work. You are passing a path to a bigwig file to the "project" argument in expressed_regions(). Please check the help page of expressed_regions() and in particular check the "outdir" argument. You already had an issue of being frustrated by not following instructions and having a mix of Bioc 3.3 and 3.4 (current release) packages, which we discussed via email. Your last comment is basically a new question, so in the future please post it as one. Imagine that a new user is running into the specific problem from your last comment. If they started reading this thread they wouldn't see how it's related to their problem, unless they read everything.

Ok, so your IP is not blocked since you can download the bigwig files. recount is coded so that it can use files already downloaded following a specific file structure. I recommend using the function download_study(), which will create the particular file structure needed. Otherwise, you have to manually mimic the portion DRP000366/bw/DRR000897.bw of http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw.

library('recount')
## Note the default of the "outdir" argument in download_study() is the "project"
download_study('DRP000366', type = 'phenotype')
download_study('DRP000366', type = 'mean')
## Check that the files are there
dir('DRP000366', include.dirs = TRUE, recursive = TRUE)
## Use the outdir argument in expressed_regions() to use the local data
regions <- expressed_regions('DRP000366', 'chrY', cutoff = 5L,
    maxClusterGap = 3000L, outdir = 'DRP000366')
options(width = 120)
devtools::session_info()
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Hi Mustafa,

recount versions 1.0.15 and 1.1.22 now provide a more informative error in case that the 'project' argument is invalid. Details at https://github.com/leekgroup/recount/commit/ab9ca78a7ddc44247f5fbc7101b6dbdc039485ce and https://github.com/Bioconductor-mirror/recount/commit/9227ec760258eb61f57a91d7c099b7c15c942247.

Best,

Leonardo

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Entering edit mode
@lcolladotor
Last seen 4 weeks ago
United States

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

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