[Bioc-devel] User has issue with importing a BigWig file with rtracklayer despite having a recent openssl and latest R packages
Leonardo Collado Torres
lcollado at jhu.edu
Wed Mar 1 20:33:25 CET 2017
Hi,
I'm trying to figure out what is going wrong in
https://support.bioconductor.org/p/93182/. Mustafa is using recount to
load a bigwig file from the web. The code in recount relies on some
code in derfinder, and the actual importing is done by
rtracklayer::import().
>From looking at the R session information reported by Mustafa I can't
tell what's wrong. He has the correct versions of rtracklayer,
derfinder and recount installed. He also has openssl and pkg-config
installed. At first I thought that he might be missing openssl since
it's not listed as a SystemRequirement in the description file of
rtracklayer/derfinder/recount. I looked back at
https://support.bioconductor.org/p/81267/ and installed the latest
openssl, made it available on my PATH and installed rtracklayer from
SVN source on both R 3.4.0 and 3.3.2. In both situations, the R code
worked for me despite the message "checking for OPENSSL... no" when
installing rtracklayer. It used to be that it would say "yes" instead
of no as you can see at
https://support.bioconductor.org/p/81267/#82142.
So, it doesn't look like it's a version issue with R packages. It's
not a problem with either the latest openssl via homebrew or other
versions https://support.bioconductor.org/p/93182/#93223. I doubt that
it's an issue specific due to his openssl version (in between the
older and newer versions I tested) or his pkg-util version. It's not
an RStudio problem either (version 1.0.136 with both R 3.3.2 and
3.4.0). Could it be an RCurl issue? Could it be that his IP is blocked
by the server hosting the BigWig file?
Anyhow, I don't know what is the source of the problem and have not
been able to reproduce it. Hopefully someone here has an idea of what
is the problem.
Best,
Leo
$ brew install --force openssl
## Edited by .bashrc with the following line:
export PATH="/usr/local/opt/openssl/bin:$PATH"
$ which openssl
/usr/local/opt/openssl/bin/openssl
$ openssl version
OpenSSL 1.0.2k 26 Jan 2017
$ svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rtracklayer
$ R CMD INSTALL rtracklayer
Loading required package: colorout
* installing to library
‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘rtracklayer’ ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... no
...
Then I was able to run without problems
> library(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 37 443 37 73 1
... 24 13 24 2 37 535 37 1028 37 13595
Values : 0 1 0 1 0 1 0 1 0 1
... 1 2 1 0 1 0 1 0 1 0
$chr10
numeric-Rle of length 133797422 with 412887 runs
Lengths: 47132 37 12 37 333 1 3 3 1 1
... 37 479 37 379 37 211 37 2082 37 11003
Values : 0 1 0 1 0 1 2 3 4 5
... 1 0 1 0 1 0 1 0 1 0
$chr11
numeric-Rle of length 135086622 with 700940 runs
Lengths: 74243 37 22178 37 22907 37 699 37
1236 ... 37 66776 37 36834 37 4395 37 17340
Values : 0 1 0 1 0 1 0 1
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 29 7 1 2364 37
... 33 8048 37 172 37 876 37 492 37 47993
Values : 0 1 0 1 2 3 2 1 0 1
... 1 0 1 0 1 0 1 0 1 0
$chr12
numeric-Rle of length 133275309 with 628862 runs
Lengths: 10055 37 4101 37 316 10 1 1 4 21
... 37 13 37 263 37 623 37 4860 37 64715
Values : 0 1 0 1 0 1 2 3 4 5
... 1 0 1 0 1 0 1 0 1 0
...
<89 more elements>
> options(width = 120)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------
setting value
version R Under development (unstable) (2016-10-26 r71594)
system x86_64, darwin13.4.0
ui AQUA
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2017-03-01
Packages ---------------------------------------------------------------------------------------------------------------
package * version date source
Biobase 2.35.1 2017-02-23 Bioconductor
BiocGenerics * 0.21.3 2017-01-12 Bioconductor
BiocParallel 1.9.5 2017-01-24 Bioconductor
Biostrings 2.43.4 2017-02-02 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.4.0)
DelayedArray 0.1.7 2017-02-17 Bioconductor
devtools 1.12.0 2016-12-05 CRAN (R 3.4.0)
digest 0.6.12 2017-01-27 CRAN (R 3.4.0)
GenomeInfoDb * 1.11.9 2017-02-08 Bioconductor
GenomeInfoDbData 0.99.0 2017-02-14 Bioconductor
GenomicAlignments 1.11.9 2017-02-02 Bioconductor
GenomicRanges * 1.27.23 2017-02-25 Bioconductor
IRanges * 2.9.18 2017-02-02 Bioconductor
lattice 0.20-34 2016-09-06 CRAN (R 3.4.0)
Matrix 1.2-8 2017-01-20 CRAN (R 3.4.0)
matrixStats 0.51.0 2016-10-09 CRAN (R 3.4.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.4.0)
RCurl 1.95-4.8 2016-03-01 CRAN (R 3.4.0)
Rsamtools 1.27.12 2017-01-24 Bioconductor
rtracklayer * 1.35.6 2017-03-01 Bioconductor
S4Vectors * 0.13.15 2017-02-14 cran (@0.13.15)
SummarizedExperiment 1.5.7 2017-02-23 Bioconductor
withr 1.0.2 2016-06-20 CRAN (R 3.4.0)
XML 3.98-1.5 2016-11-10 CRAN (R 3.4.0)
XVector 0.15.2 2017-02-02 Bioconductor
zlibbioc 1.21.0 2016-10-23 Bioconductor
I had also just previously tried before updating my openssl:
$ /usr/bin/openssl version
OpenSSL 0.9.8zh 14 Jan 2016
Similarly, everything worked on my system with R 3.3.2 despite the
pkg-config not finding openssl.
$ R CMD INSTALL rtracklayer
Loading required package: colorout
* installing to library
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
* installing *source* package ‘rtracklayer’ ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... no
...
> library(rtracklayer)
> x <- import.bw('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw',as = 'RleList')
> options(width = 120)
> devtools::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 2017-03-01
Packages ---------------------------------------------------------------------------------------------------------------
package * version date source
Biobase 2.34.0 2016-10-18 Bioconductor
BiocGenerics * 0.20.0 2016-10-18 Bioconductor
BiocParallel 1.8.1 2016-10-30 Bioconductor
Biostrings 2.42.1 2016-12-01 Bioconductor
bitops 1.0-6 2013-08-17 cran (@1.0-6)
colorout * 1.1-2 2016-10-19 Github (jalvesaq/colorout at 6d84420)
devtools 1.12.0 2016-06-24 CRAN (R 3.3.0)
digest 0.6.12 2017-01-27 CRAN (R 3.3.2)
GenomeInfoDb * 1.10.3 2017-02-07 Bioconductor
GenomicAlignments 1.10.0 2016-10-18 Bioconductor
GenomicRanges * 1.26.3 2017-02-25 Bioconductor
IRanges * 2.8.1 2016-11-08 Bioconductor
lattice 0.20-34 2016-09-06 CRAN (R 3.3.2)
Matrix 1.2-8 2017-01-20 CRAN (R 3.3.2)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
RCurl 1.95-4.8 2016-03-01 cran (@1.95-4.)
Rsamtools 1.26.1 2016-10-22 Bioconductor
rtracklayer * 1.34.2 2017-03-01 Bioconductor
S4Vectors * 0.12.1 2016-12-01 Bioconductor
SummarizedExperiment 1.4.0 2016-10-18 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)
XVector 0.14.0 2016-10-18 Bioconductor
zlibbioc 1.20.0 2016-10-18 Bioconductor
Back to R 3.4.0 showing the RCurl info:
> library(RCurl)
Loading required package: bitops
> curlVersion()
$age
[1] 3
$version
[1] "7.51.0"
$vesion_num
[1] 471808
$host
[1] "x86_64-apple-darwin16.0"
$features
ipv6 ssl libz ntlm asynchdns spnego largefile ntlm_wb
1 4 8 16 128 256 512 32768
$ssl_version
[1] "SecureTransport"
$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" "rtsp"
[15] "smb" "smbs" "smtp" "smtps" "telnet" "tftp"
$ares
[1] ""
$ares_num
[1] 0
$libidn
[1] ""
> options(width = 120)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------
setting value
version R Under development (unstable) (2016-10-26 r71594)
system x86_64, darwin13.4.0
ui AQUA
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2017-03-01
Packages ---------------------------------------------------------------------------------------------------------------
package * version date source
bitops * 1.0-6 2013-08-17 CRAN (R 3.4.0)
devtools 1.12.0 2016-12-05 CRAN (R 3.4.0)
digest 0.6.12 2017-01-27 CRAN (R 3.4.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.4.0)
RCurl * 1.95-4.8 2016-03-01 CRAN (R 3.4.0)
withr 1.0.2 2016-06-20 CRAN (R 3.4.0)
And now in R 3.3.2:
> library(RCurl)
Loading required package: bitops
> curlVersion()
$age
[1] 3
$version
[1] "7.51.0"
$vesion_num
[1] 471808
$host
[1] "x86_64-apple-darwin16.0"
$features
ipv6 ssl libz ntlm asynchdns spnego largefile ntlm_wb
1 4 8 16 128 256 512 32768
$ssl_version
[1] "SecureTransport"
$ssl_version_num
[1] 0
$libz_version
[1] "1.2.8"
$protocols
[1] "dict" "file" "ftp" "ftps" "gopher" "http" "https" "imap"
[9] "imaps" "ldap" "ldaps" "pop3" "pop3s" "rtsp" "smb" "smbs"
[17] "smtp" "smtps" "telnet" "tftp"
$ares
[1] ""
$ares_num
[1] 0
$libidn
[1] ""
> options(width = 120)
> devtools::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 2017-03-01
Packages ---------------------------------------------------------------------------------------------------------------
package * version date source
bitops * 1.0-6 2013-08-17 cran (@1.0-6)
colorout * 1.1-2 2016-10-19 Github (jalvesaq/colorout at 6d84420)
devtools 1.12.0 2016-06-24 CRAN (R 3.3.0)
digest 0.6.12 2017-01-27 CRAN (R 3.3.2)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
RCurl * 1.95-4.8 2016-03-01 cran (@1.95-4.)
withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
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