[BioC] qrqc with error message of "unable to start device PNG" and "unable to open connection to X11 display"?
Sang Chul Choi
schoi at cornell.edu
Thu May 31 15:29:04 CEST 2012
Hi,
Thank you for the helpful replies.
The command line that causes the problem is:
makeReport(fq.file, outputDir=bwadir)
from qrqc package.
I do not know what parts in makeReport of qrqc R package cause the problem. Appended are outputs of capabilities() run at the head and compute nodes. A session info at the compute is also following that.
I do not have access to the head node to run makeReport command of qrqc because the command takes too much memory and would cause problems that could affect other users. So, I have to use a compute node. Clearly, the compute nodes capabilities() shows that png cannot be produced. Thank you for the command. It was helpful.
I am not sure whether I have options. What I want to have from my raw RNA-seq data is to plot "per-base sequence quality," one that is shown at
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
I will appreciate if there are other ways.
Thank you,
SangChul
I also tried to install cairo. But, it has the following errors when I ran an install command:
> install.packages("Cairo")
===================================================
checking for FreeType support in cairo... yes
checking whether FreeType needs additional flags... yes
checking whether pkg-config knows about fontconfig or freetype2... no
checking whether fontconfig/freetype2 location can be guessed... no
configure: error: Cannot find fontconfig/freetype2 although cairo claims to support it. Please check your cairo installation and/or update cairo if necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly.
ERROR: configuration failed for package 'Cairo'
At the head node:
===================================================
> capabilities()
jpeg png tiff tcltk X11 aqua http/ftp sockets
TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE
libxml fifo cledit iconv NLS profmem cairo
TRUE TRUE TRUE TRUE TRUE FALSE FALSE
At the compute node:
===================================================
> capabilities()
jpeg png tiff tcltk X11 aqua http/ftp sockets
FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE
libxml fifo cledit iconv NLS profmem cairo
TRUE TRUE TRUE TRUE TRUE FALSE FALSE
> sessionInfo()
R Under development (unstable) (2012-04-01 r58897)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
[3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
[5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] qrqc_1.10.0 testthat_0.6 Rsamtools_1.8.5
[4] GenomicRanges_1.8.6 xtable_1.7-0 brew_1.0-6
[7] biovizBase_1.4.2 Biostrings_2.24.1 IRanges_1.14.3
[10] BiocGenerics_0.2.0 ggplot2_0.9.1 reshape_0.8.4
[13] plyr_1.7.1
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.18.1 Biobase_2.16.0 biomaRt_2.12.0
[4] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2
[7] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4
[10] digest_0.5.2 evaluate_0.4.2 GenomicFeatures_1.8.1
[13] grid_2.16.0 Hmisc_3.9-3 labeling_0.1
[16] lattice_0.20-6 MASS_7.3-18 memoise_0.1
[19] munsell_0.3 proto_0.3-9.2 RColorBrewer_1.0-5
[22] RCurl_1.91-1 reshape2_1.2.1 RSQLite_0.11.1
[25] rtracklayer_1.16.1 scales_0.2.1 stats4_2.16.0
[28] stringr_0.6 tools_2.16.0 XML_3.9-4
[31] zlibbioc_1.2.0
On May 30, 2012, at 12:06 PM, Dan Tenenbaum wrote:
> Hi SangChul and Jim,
>
> On Wed, May 30, 2012 at 6:22 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
>> Hi SangChul,
>>
>>
>> On 5/29/2012 4:46 PM, Sang Chul Choi wrote:
>>>
>>> Hi,
>>>
>>> I am trying to use qrqc Bioc package in a linux machine used as a compute
>>> node. I have the following error:
>>>
>>> ====================
>>> Error in X11(paste("png::", filename, sep = ""), g$width, g$height,
>>> pointsize, :
>>> unable to start device PNG
>>> In addition: Warning message:
>>> In grDevices::png(..., width = width, height = height, res = dpi, :
>>> unable to open connection to X11 display ''
>>> ====================
>>>
>>> I have googled for an answer and bumped into following mailing list posts:
>>>
>>> https://stat.ethz.ch/pipermail/r-help/2008-March/155943.html
>>> https://stat.ethz.ch/pipermail/r-help/2008-February/155021.html
>>> https://stat.ethz.ch/pipermail/r-help/2008-February/155023.html
>>>
>>> It is not obvious what I should do. I will appreciate your answers.
>>
>>
>> The simple answer is to run the code on the head rather than a compute node.
>> In my experience, compute nodes usually don't have 'GUI-type' software
>> installed (X11, png, etc), as it is not common for people to need that sort
>> of thing.
>>
>
> If Jim's suggestion to run the relevant computations on your Windows
> machine does not work out, you can go back on the Linux machine and
> start R. What is the output of the
> capabilities()
> command?
> And
> sessionInfo()
> for that matter?
>
> Can you tell what the exact command is that causes the error?
> Do you need your files to be in png format?
>
> If you install the Cairo package:
> biocLite("Cairo")
>
> Does qrqc then work?
> Is it practical to use bitmap() to generate your png?
>
> What Linux distribution are you on? You may want to install Xvfb which
> should solve the problem, though it can be sort of tricky, according
> to this somewhat dated page for Ubuntu.
> http://blog.martin-lyness.com/archives/installing-xvfb-on-ubuntu-9-10-karmic-koala
>
> Dan
>
>
>
>
>> Best,
>>
>> Jim
>>
>>
>>
>>>
>>> Thank you,
>>>
>>> SangChul
>>> _______________________________________________
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>>
>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>>
>>
>> _______________________________________________
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