Thanks Henrik Answers in-line below, and full output at end.
> -----Original Message----- > From: aroma-affymetrix@googlegroups.com [mailto:aroma- > affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson > Sent: January-18-12 9:04 AM > To: aroma-affymetrix@googlegroups.com > Subject: Re: [aroma.affymetrix] ChromosomeExplorer producing zero byte png > files > > On Wed, Jan 18, 2012 at 1:36 AM, Henrik Bengtsson > <henrik.bengts...@aroma-project.org> wrote: > > Hi, > > > > the loading of the Cairo package is misleading here, since it is > > actually not utilizing it. (In the next version of aroma.core, the > > Cairo package will not be loaded unless really needed). Instead, > > > >>> print(pngDev) > >> function (...) > >> pngTyped(..., type = "cairo") > >> <environment: 0x103f64b88> > > > > tells me that it here in the end uses png(..., type="cairo"), because > > internally pngTyped <- function(...) png(...); To confirm, start a > > fresh R session and check if the following gives you an empty PNG > > file? > > > > png("foo.png", type="cairo"); plot(1:10); dev.off(); In a fresh R session: > png("foo.png", type="cairo"); plot(1:10); dev.off(); null device 1 libpng warning: Application built with libpng-1.2.26 but running with 1.5.2 Outcome: Produced zero byte png file. > > > > If so, what about type="cairo-png"? Your reply will help me update > > findPngDevice() such that it will find a working PNG device (these > > problems are indeed why it was created in the first place; it is hard > > to find a cross-platform working driver). > png("bar.png", type="cairo-png"); plot(1:10); dev.off(); null device 1 Outcome: 8 kb plot file produced. No libpng warning. > > So, if it turn out you really have problems with your built in > png(..., type="cairo") device, before trying fix it/rebuild R, could > you please verify that the updated R.utils 1.9.11 and aroma.core 2.4.3 > manage to detect the problem and find another working device for you? > As usual, update via: > > source("http://aroma-project.org/hbLite.R";); > hbLite("aroma.affymetrix"); > > and then retry: > > library("aroma.core"); > pngDev <- findPngDevice(transparent=FALSE); > pngDev("foo.png"); plot(1:10); dev.off(); > > Does it work? It could be that when you do the above you get the > warning, then it more or less halts for 10secs (while waiting to see > if that zero file grows; this delay occurs only once per R session), > before it returns a working PNG device. After updating: > pngDev <- findPngDevice(transparent=FALSE); libpng warning: Application built with libpng-1.2.26 but running with 1.5.2 > pngDev("foo3.png"); plot(1:10); dev.off(); null device 1 Outcome: foo3.png - a 16 kb file with plot. No libpng warning on running the plot, though the warning was seen with the findPngDevice() command. I also ran these updates for my current aroma pipeline analysis and now ChromosomeExplorer is producing valid png plots. Many thanks! So is there anything else left to do here? Is this "fixed" now (for some sense of the concept of fixed)? Should I submit any kind of problem report to the grDevices maintainers? Steve > > /Henrik > > > > > /Henrik > > > > On Tue, Jan 17, 2012 at 9:09 PM, Steven McKinney <smckin...@bccrc.ca> > wrote: > >> Hi Henrik > >> > >> If I just load the Cairo library and do a PNG plot, the plot appears > >> in the png file alright (8 kb file). I also don't notice the message > >> about "libpng warning: Application built with libpng-1.2.41 but running > with 1.5.7" > >> > >> So there appears to be something amiss in aroma.affymetrix > >> in its interface to Cairo devices. Does this provide any clues? > >> I have not gone through the aroma source to understand > >> how aroma interacts with Cairo. > >> > >> Steve > >> > >> R version 2.14.1 (2011-12-22) > >> Copyright (C) 2011 The R Foundation for Statistical Computing > >> ISBN 3-900051-07-0 > >> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) > >> > >> R is free software and comes with ABSOLUTELY NO WARRANTY. > >> You are welcome to redistribute it under certain conditions. > >> Type 'license()' or 'licence()' for distribution details. > >> > >> Natural language support but running in an English locale > >> > >> R is a collaborative project with many contributors. > >> Type 'contributors()' for more information and > >> 'citation()' on how to cite R or R packages in publications. > >> > >> Type 'demo()' for some demos, 'help()' for on-line help, or > >> 'help.start()' for an HTML browser interface to help. > >> Type 'q()' to quit R. > >> > >>> .help.ESS <- help > >>> options(STERM='iESS', editor='emacsclient') > >>> require("Cairo") > >> Loading required package: Cairo > >>> CairoPNG("foo.png", width=840, height=640); plot(1:10); dev.off(); > >> null device > >> 1 > >>> > >> > >> > >> > >> > >> Steven McKinney > >> > >> ________________________________________ > >> From: Steven McKinney > >> Sent: January 17, 2012 8:59 PM > >> To: aroma-affymetrix@googlegroups.com > >> Subject: RE: [aroma.affymetrix] ChromosomeExplorer producing zero byte > png files > >> > >> Hi Henrik, > >> > >> Running the commands you provided, I get an empty foo.png. > >> > >>> print(pngDev) > >> function (...) > >> pngTyped(..., type = "cairo") > >> <environment: 0x103f64b88> > >>> > >> > >> Full output below. > >> > >> This is looking like a Cairo problem. > >> > >> > >> R version 2.14.1 (2011-12-22) > >> Copyright (C) 2011 The R Foundation for Statistical Computing > >> ISBN 3-900051-07-0 > >> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) > >> > >> R is free software and comes with ABSOLUTELY NO WARRANTY. > >> You are welcome to redistribute it under certain conditions. > >> Type 'license()' or 'licence()' for distribution details. > >> > >> Natural language support but running in an English locale > >> > >> R is a collaborative project with many contributors. > >> Type 'contributors()' for more information and > >> 'citation()' on how to cite R or R packages in publications. > >> > >> Type 'demo()' for some demos, 'help()' for on-line help, or > >> 'help.start()' for an HTML browser interface to help. > >> Type 'q()' to quit R. > >> > >>> .help.ESS <- help > >>> options(STERM='iESS', editor='emacsclient') > >>> library("aroma.core") > >> Loading required package: R.methodsS3 > >> R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 > for help. > >> Loading required package: R.oo > >> R.oo v1.8.3 (2011-11-01) successfully loaded. See ?R.oo for help. > >> > >> Attaching package: ‘R.oo’ > >> > >> The following object(s) are masked from ‘package:R.methodsS3’: > >> > >> throw.default > >> > >> The following object(s) are masked from ‘package:methods’: > >> > >> getClass, getClasses, getMethods > >> > >> The following object(s) are masked from ‘package:base’: > >> > >> attach, detach, environment, gc, load, save > >> > >> Loading required package: R.utils > >> R.utils v1.9.9 (2012-01-11) successfully loaded. See ?R.utils for help. > >> > >> Attaching package: ‘R.utils’ > >> > >> The following object(s) are masked from ‘package:utils’: > >> > >> timestamp > >> > >> The following object(s) are masked from ‘package:base’: > >> > >> cat, commandArgs, getOption, inherits, isOpen, lapply, parse, > >> remove, warnings > >> > >> Loading required package: R.cache > >> R.cache v0.5.2 (2011-10-05) successfully loaded. See ?R.cache for help. > >> > >> Loading required package: R.filesets > >> Loading required package: digest > >> R.filesets v1.1.4 (2011-11-19) successfully loaded. See ?R.filesets for > help. > >> > >> Attaching package: ‘R.filesets’ > >> > >> The following object(s) are masked from ‘package:R.cache’: > >> > >> getChecksum > >> > >> The following object(s) are masked from ‘package:base’: > >> > >> append, readLines, sapply > >> > >> Loading required package: R.rsp > >> R.rsp v0.7.1 (2011-11-28) successfully loaded. See ?R.rsp for help. > >> Type browseRsp() to open the RSP main menu in your browser. > >> > >> Attaching package: ‘R.rsp’ > >> > >> The following object(s) are masked from ‘package:R.filesets’: > >> > >> getHeader > >> > >> The following object(s) are masked from ‘package:base’: > >> > >> flush, restart, stop, write > >> > >> Loading required package: matrixStats > >> matrixStats v0.4.3 (2011-12-11) successfully loaded. See ?matrixStats > for help. > >> Loading required package: aroma.light > >> aroma.light v1.22.0 (2011-10-31) successfully loaded. See ?aroma.light > for help. > >> aroma.core v2.4.2 (2012-01-14) successfully loaded. See ?aroma.core for > help. > >> > >> Attaching package: ‘aroma.core’ > >> > >> The following object(s) are masked from ‘package:base’: > >> > >> .Machine, append, apply, colMeans, colSums, library, require, > >> sapply > >> > >>> pngDev <- findPngDevice(transparent=FALSE) > >> Loading required package: Cairo > >> libpng warning: Application built with libpng-1.2.41 but running with > 1.5.7 > >>> pngDev("foo.png", width=840, height=640); plot(1:10); dev.off(); > >> libpng warning: Application built with libpng-1.2.41 but running with > 1.5.7 > >> null device > >> 1 > >>> print(pngDev) > >> function (...) > >> pngTyped(..., type = "cairo") > >> <environment: 0x103f64b88> > >>> > >>> sessionInfo() > >> R version 2.14.1 (2011-12-22) > >> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) > >> > >> locale: > >> [1] en_CA/en_CA/en_CA/C/en_CA/en_CA > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] Cairo_1.5-1 aroma.core_2.4.2 aroma.light_1.22.0 > matrixStats_0.4.3 > >> [5] R.rsp_0.7.1 R.filesets_1.1.4 digest_0.5.1 > R.cache_0.5.2 > >> [9] R.utils_1.9.9 R.oo_1.8.3 R.methodsS3_1.2.1 > >>> > >> > >> -- > >> When reporting problems on aroma.affymetrix, make sure 1) to run the > latest version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > >> > >> > >> You received this message because you are subscribed to the Google > Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. > >> To post to this group, send email to aroma-affymetrix@googlegroups.com > >> To unsubscribe and other options, go to http://www.aroma- > project.org/forum/ > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ R version 2.14.1 Patched (2012-01-11 r58090) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [R.app GUI 1.44 (5997) x86_64-apple-darwin9.8.0] [History restored from /Users/stevenmckinney/.Rhistory] > sessionInfo() R version 2.14.1 Patched (2012-01-11 r58090) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base > png("foo.png", type="cairo"); plot(1:10); dev.off(); null device 1 libpng warning: Application built with libpng-1.2.26 but running with 1.5.2 > ?png starting httpd help server ... done > getwd() [1] "/Users/stevenmckinney" > png("foo2.png", type="cairo"); plot(1:10); dev.off(); null device 1 libpng warning: Application built with libpng-1.2.26 but running with 1.5.2 > ## both produced zero byte png files. > > > png("bar.png", type="cairo-png"); plot(1:10); dev.off(); null device 1 > ## 8 kb plot file produced > source("http://aroma-project.org/hbLite.R";); > hbLite("aroma.affymetrix"); Using repository: http://www.braju.com/R/repos Identified packages to be processed: utils, R.methodsS3, methods, R.oo, R.utils, digest, R.utils, R.cache, R.filesets, R.rsp, matrixStats, aroma.light, affxparser, RColorBrewer, R.huge, aroma.core, aroma.light, aroma.apd, R.rsp, MASS, splines, aroma.affymetrix Installing external packages... Packages: utils, methods, digest, R.utils, R.rsp, aroma.light, affxparser, RColorBrewer, MASS, splines Updating packages: utils, methods, digest, R.utils, R.rsp, aroma.light, affxparser, RColorBrewer, MASS, splines 01/10. utils: not available. 02/10. methods: not available. 03/10. digest: v0.5.1, i.e. up to date. 04/10. R.utils: not available. 05/10. R.rsp: not available. 06/10. aroma.light: not available. 07/10. affxparser: not available. 08/10. RColorBrewer: v1.0-5, i.e. up to date. 09/10. MASS: v7.3-16, i.e. up to date. 10/10. splines: not available. Installing external packages...done Installing braju.com packages... Packages: R.methodsS3, R.oo, R.utils, R.cache, R.filesets, matrixStats, R.huge, aroma.core, aroma.light, aroma.apd, R.rsp, aroma.affymetrix Detected R option pkgType="mac.binary.leopard" (or similar), which is not available. Enforcing installation from source instead for packages: R.methodsS3, R.oo, R.utils, R.cache, R.filesets, matrixStats, R.huge, aroma.core, aroma.light, aroma.apd, R.rsp, aroma.affymetrix Updating packages: R.methodsS3, R.oo, R.utils, R.cache, R.filesets, matrixStats, R.huge, aroma.core, aroma.light, aroma.apd, R.rsp, aroma.affymetrix 01/12. R.methodsS3: v1.2.1, i.e. up to date. 02/12. R.oo: v1.8.3, i.e. up to date. 03/12. R.utils: v1.9.9, but v1.9.11 is available, i.e. out of date. Updating: trying URL 'http://www.braju.com/R/repos/R.utils_1.9.11.tar.gz' Content type 'application/x-tar' length 264179 bytes (257 Kb) opened URL ================================================== downloaded 257 Kb * installing *source* package ‘R.utils’ ... ** R ** inst ** preparing package for lazy loading Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function inherits to inherits.default, which was defined in environment base. Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function cat to cat.default, which was defined in environment base. Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function remove to remove.default, which was defined in environment base. Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function parse to parse.default, which was defined in environment base. Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function lapply to lapply.default, which was defined in environment base. Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function getOption to getOption.default, which was defined in environment base. Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function timestamp to timestamp.default, which was defined in environment base. Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function warnings to warnings.default, which was defined in environment base. Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function isOpen to isOpen.default, which was defined in environment base. ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded * DONE (R.utils) The downloaded packages are in ‘/private/var/folders/-I/-IwfookDG3Wu7O0-CiOMZE+++TI/-Tmp-/RtmpIbAZ6e/downloaded_packages’ 04/12. R.cache: v0.5.2, but v0.6.0 is available, i.e. out of date. Updating: trying URL 'http://www.braju.com/R/repos/R.cache_0.6.0.tar.gz' Content type 'application/x-tar' length 22720 bytes (22 Kb) opened URL ================================================== downloaded 22 Kb * installing *source* package ‘R.cache’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded * DONE (R.cache) The downloaded packages are in ‘/private/var/folders/-I/-IwfookDG3Wu7O0-CiOMZE+++TI/-Tmp-/RtmpIbAZ6e/downloaded_packages’ 05/12. R.filesets: v1.1.4, i.e. up to date. 06/12. matrixStats: v0.4.3, i.e. up to date. 07/12. R.huge: v0.3.0, i.e. up to date. 08/12. aroma.core: v2.4.2, but v2.4.3 is available, i.e. out of date. Updating: trying URL 'http://www.braju.com/R/repos/aroma.core_2.4.3.tar.gz' Content type 'application/x-tar' length 335397 bytes (327 Kb) opened URL ================================================== downloaded 327 Kb * installing *source* package ‘aroma.core’ ... ** R ** inst ** preparing package for lazy loading Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function colSums to colSums.default, which was defined in environment base. Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function colMeans to colMeans.default, which was defined in environment base. Warning in setGenericS3.default(name, envir = envir, validators = validators) : Renamed the preexisting function apply to apply.default, which was defined in environment base. ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded * DONE (aroma.core) The downloaded packages are in ‘/private/var/folders/-I/-IwfookDG3Wu7O0-CiOMZE+++TI/-Tmp-/RtmpIbAZ6e/downloaded_packages’ 09/12. aroma.light: v1.22.0, i.e. up to date. 10/12. aroma.apd: v0.2.0, i.e. up to date. 11/12. R.rsp: v0.7.1, i.e. up to date. 12/12. aroma.affymetrix: v2.4.0, i.e. up to date. Installing braju.com packages...done Warning message: In hbLite("aroma.affymetrix") : Detected R option pkgType="mac.binary.leopard" (or similar), which is not available. Enforcing installation from source instead for packages: R.methodsS3, R.oo, R.utils, R.cache, R.filesets, matrixStats, R.huge, aroma.core, aroma.light, aroma.apd, R.rsp, aroma.affymetrix > > > > library("aroma.core"); Loading required package: R.methodsS3 R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help. Loading required package: R.oo R.oo v1.8.3 (2011-11-01) successfully loaded. See ?R.oo for help. Attaching package: ‘R.oo’ The following object(s) are masked from ‘package:R.methodsS3’: throw.default The following object(s) are masked from ‘package:methods’: getClass, getClasses, getMethods The following object(s) are masked from ‘package:base’: attach, detach, environment, gc, load, save Loading required package: R.utils R.utils v1.9.11 (2012-01-17) successfully loaded. See ?R.utils for help. Attaching package: ‘R.utils’ The following object(s) are masked _by_ ‘.GlobalEnv’: installPackages The following object(s) are masked from ‘package:utils’: timestamp The following object(s) are masked from ‘package:base’: cat, commandArgs, getOption, inherits, isOpen, lapply, parse, remove, warnings Loading required package: R.cache R.cache v0.6.0 (2011-12-30) successfully loaded. See ?R.cache for help. Loading required package: R.filesets Loading required package: digest R.filesets v1.1.4 (2011-11-19) successfully loaded. See ?R.filesets for help. Attaching package: ‘R.filesets’ The following object(s) are masked from ‘package:R.cache’: getChecksum The following object(s) are masked from ‘package:base’: append, readLines, sapply Loading required package: R.rsp R.rsp v0.7.1 (2011-11-28) successfully loaded. See ?R.rsp for help. Type browseRsp() to open the RSP main menu in your browser. Attaching package: ‘R.rsp’ The following object(s) are masked from ‘package:R.filesets’: getHeader The following object(s) are masked from ‘package:base’: flush, restart, stop, write Loading required package: matrixStats matrixStats v0.4.3 (2011-12-11) successfully loaded. See ?matrixStats for help. Loading required package: aroma.light aroma.light v1.22.0 (2011-10-31) successfully loaded. See ?aroma.light for help. aroma.core v2.4.3 (2012-01-17) successfully loaded. See ?aroma.core for help. Attaching package: ‘aroma.core’ The following object(s) are masked from ‘package:base’: .Machine, append, apply, colMeans, colSums, library, require, sapply > pngDev <- findPngDevice(transparent=FALSE); libpng warning: Application built with libpng-1.2.26 but running with 1.5.2 > pngDev("foo3.png"); plot(1:10); dev.off(); null device 1 > ### foo3.png is a 16 kb file with plot > > > sessionInfo() R version 2.14.1 Patched (2012-01-11 r58090) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.core_2.4.3 aroma.light_1.22.0 matrixStats_0.4.3 R.rsp_0.7.1 [5] R.filesets_1.1.4 digest_0.5.1 R.cache_0.6.0 R.utils_1.9.11 [9] R.oo_1.8.3 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] Cairo_1.5-1 tools_2.14.1 > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
