Question: error message relating to png file when running maQualityPlots
0
gravatar for Yanqing Hu
6.7 years ago by
Yanqing Hu20
Yanqing Hu20 wrote:
Thanks, Jim and Dan! To Jim: Yes, I tried capabilities and there are TRUEs under png as well as jpeg, so changing dev to other format didn't work. I also noticed that there's a FALSE under X11. Another post https://stat.ethz.ch/pipermail/bioconductor/2006-August/014161.html mentioned that png needs X11 to be running. But seems now MAC doesn't support X11 any more. To Dan: Yes, I was running the code from the beginning of that chapter. AnnBuilder is indeed obsolete, but the book mentioned that the data set beta 7 can alternatively be loaded from the data package beta7, which is what I did and it was successful. So I guess the problem may be related to the maQualityPlots function and the MAC system themselves. >>> Dan Tenenbaum 01/03/13 12:50 PM >>> On Thu, Jan 3, 2013 at 8:37 AM, James W. MacDonald wrote: > I don't remember if Macs come ready to do png graphics or not, and a quick > google doesn't clear it up for me. In general, png is supported on the mac. > So the first step I would take is to > ensure that you have the capability to do so. Try typing > > capabilities() > > at an R prompt and see if there is a TRUE under png. If not, you can set the > dev argument of maQualityPlots() to a device for which you have > capabilities. If there is a TRUE under png, then you will need to furnish > the actual code you are running (or better yet, a reproducible example, > which implies that I or anybody else can try and replicate what you have > done). > Yes, a reproducible example would be great. I am guessing that you are working your way through this code: http://www.bioconductor.org/help/publications/books/bioinformatics- and-computational-biology-solutions/chapter-code/TwoColorPre.R This uses packages which are obsolete so it's not surprising that you are getting errors. Dan > Best, > > Jim > > > On 1/3/2013 11:15 AM, Yanqing Hu [guest] wrote: >> >> I'm using Rstudio on my Mac. When I ran the code maQualityPlots(beta7) in >> Chapter 4 of Bioinformatics and Computational Biology Solutions Using R and >> Bioconductor, I got the mesasge "Error in plot.new() : could not open file >> 'diagPlot.6Hs.195.1.png'". Does anyone know how to fix this problem? Thanks >> a lot! >> >> -- output of sessionInfo(): >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-redhat-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods >> [7] base >> >> other attached packages: >> [1] vsn_3.26.0 arrayQuality_1.36.0 beta7_1.0.4 >> [4] marray_1.36.0 cluster_1.14.2 BiocInstaller_1.8.2 >> [7] affycomp_1.34.0 affyPLM_1.34.0 preprocessCore_1.20.0 >> [10] gcrma_2.30.0 hgu133acdf_2.11.0 hgu95av2cdf_2.11.0 >> [13] AnnotationDbi_1.20.0 affydata_1.11.17 affy_1.36.0 >> [16] Biobase_2.18.0 BiocGenerics_0.4.0 class_7.3-5 >> [19] limma_3.14.3 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.26.0 Biostrings_2.26.1 DBI_0.2-5 >> [4] grid_2.15.1 gridBase_0.4-5 hexbin_1.26.0 >> [7] IRanges_1.16.2 lattice_0.20-10 parallel_2.15.1 >> [10] RColorBrewer_1.0-5 RSQLite_0.11.2 splines_2.15.1 >> [13] stats4_2.15.1 tools_2.15.1 zlibbioc_1.4.0 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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ADD COMMENTlink modified 6.7 years ago by Dan Tenenbaum8.2k • written 6.7 years ago by Yanqing Hu20
Answer: error message relating to png file when running maQualityPlots
0
gravatar for Dan Tenenbaum
6.7 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
On Thu, Jan 3, 2013 at 11:50 AM, Yanqing Hu <yanqing.hu at="" mail.wvu.edu=""> wrote: > Thanks, Jim and Dan! > > > To Jim: Yes, I tried capabilities and there are TRUEs under png as well as jpeg, so changing dev to other format didn't work. I also noticed that there's a FALSE under X11. Another post > https://stat.ethz.ch/pipermail/bioconductor/2006-August/014161.html > mentioned that png needs X11 to be running. But seems now MAC doesn't support X11 any more. > X11 is supported on Mac systems. If you are running Lion or newer, you have to install XQuartz though: http://xquartz.macosforge.org/landing/ BTW, your sessionInfo() says you are on a Red Hat Linux machine! > > > > To Dan: Yes, I was running the code from the beginning of that chapter. AnnBuilder is indeed obsolete, but the book mentioned that the data set beta 7 can alternatively be loaded from the data package beta7, which is what I did and it was successful. So I guess the problem may be related to the maQualityPlots function and the MAC system themselves. > There is a lot of code in that file, it might be best if you post the exact lines of code that cause the error. Thanks, Dan > > > > > >>>> Dan Tenenbaum 01/03/13 12:50 PM >>> > On Thu, Jan 3, 2013 at 8:37 AM, James W. MacDonald wrote: >> I don't remember if Macs come ready to do png graphics or not, and a quick >> google doesn't clear it up for me. > > In general, png is supported on the mac. > >> So the first step I would take is to >> ensure that you have the capability to do so. Try typing >> >> capabilities() >> >> at an R prompt and see if there is a TRUE under png. If not, you can set the >> dev argument of maQualityPlots() to a device for which you have >> capabilities. If there is a TRUE under png, then you will need to furnish >> the actual code you are running (or better yet, a reproducible example, >> which implies that I or anybody else can try and replicate what you have >> done). >> > > Yes, a reproducible example would be great. I am guessing that you are > working your way through this code: > > http://www.bioconductor.org/help/publications/books/bioinformatics- and-computational-biology-solutions/chapter-code/TwoColorPre.R > > This uses packages which are obsolete so it's not surprising that you > are getting errors. > > Dan > > >> Best, >> >> Jim >> >> >> On 1/3/2013 11:15 AM, Yanqing Hu [guest] wrote: >>> >>> I'm using Rstudio on my Mac. When I ran the code maQualityPlots(beta7) in >>> Chapter 4 of Bioinformatics and Computational Biology Solutions Using R and >>> Bioconductor, I got the mesasge "Error in plot.new() : could not open file >>> 'diagPlot.6Hs.195.1.png'". Does anyone know how to fix this problem? Thanks >>> a lot! >>> >>> -- output of sessionInfo(): >>> >>> R version 2.15.1 (2012-06-22) >>> Platform: x86_64-redhat-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods >>> [7] base >>> >>> other attached packages: >>> [1] vsn_3.26.0 arrayQuality_1.36.0 beta7_1.0.4 >>> [4] marray_1.36.0 cluster_1.14.2 BiocInstaller_1.8.2 >>> [7] affycomp_1.34.0 affyPLM_1.34.0 preprocessCore_1.20.0 >>> [10] gcrma_2.30.0 hgu133acdf_2.11.0 hgu95av2cdf_2.11.0 >>> [13] AnnotationDbi_1.20.0 affydata_1.11.17 affy_1.36.0 >>> [16] Biobase_2.18.0 BiocGenerics_0.4.0 class_7.3-5 >>> [19] limma_3.14.3 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.26.0 Biostrings_2.26.1 DBI_0.2-5 >>> [4] grid_2.15.1 gridBase_0.4-5 hexbin_1.26.0 >>> [7] IRanges_1.16.2 lattice_0.20-10 parallel_2.15.1 >>> [10] RColorBrewer_1.0-5 RSQLite_0.11.2 splines_2.15.1 >>> [13] stats4_2.15.1 tools_2.15.1 zlibbioc_1.4.0 >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD COMMENTlink written 6.7 years ago by Dan Tenenbaum8.2k
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