Question: flowQ on WinXP: Error in matrix for dimnames
0
gravatar for Karin Breuer
9.1 years ago by
Karin Breuer20
Karin Breuer20 wrote:
Hello everybody, I am trying to get flowQ running on Windows XP 2002 Professional SP3 (ImageMagic 6.6.3). It's running fine on Linux, but for some reason I get the following error when trying to reproduce the code for basic functions from the vignette (both for R2.10.1 and R2.11.1) - it does create the correct output files, though: Error in matrix(c(dims, newDims), ncol = 2, byrow = TRUE, dimnames = list(ft, : length of 'dimnames' [1] not equal to array extent See below for full output and sessionInfo. I am quite stuck right now and would appreciate any thoughts on this. Many thanks! Karin PS: Also, is there a way to prevent flowQ to use the default "convert" command on a Windows system which hasn't ImageMagic installed? It totally tries to reformat the file system. ------------------------------------------------------------ > library(flowQ) > options(width=70) > binaryAggregator() Binary quality score passing the requirements > discreteAggregator(2) Discrete quality score not passing the requirements with state warn > factorAggregator(factor("a", levels=letters[1:3])) Factorized quality score passing the requirements of value=a > stringAggregator("test", passed=FALSE) Textual quality score not passing the requirements of value=test > numericAggregator(20) Numeric quality score passing the requirements of value=20 > rangeAggregator(10, 0, 100) Range quality score passing the requirements of value=10 > aggregatorList(bin=binaryAggregator(FALSE), disc=discreteAggregator(1)) List of 2 aggregators > tmp <- tempdir() > fn <- file.path(tmp, "test.jpg") > jpeg(file=fn) > plot(1:3) > dev.off() null device 1 > idir <- file.path(tmp, "images") > g <- qaGraph(fn, imageDir=idir) '\\sharename\home\homename' CMD.EXE was started with the above path as the current directory. UNC paths are not supported. Defaulting to Windows directory. Error in matrix(c(dims, newDims), ncol = 2, byrow = TRUE, dimnames = list(ft, : length of 'dimnames' [1] not equal to array extent > g Error: object 'g' not found > qaGraph(imageDir=idir, empty=TRUE) QA process image information > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] flowQ_1.8.0 latticeExtra_0.6-11 RColorBrewer_1.0-2 parody_1.6.0 bioDist_1.20.0 [6] KernSmooth_2.23-3 mvoutlier_1.4 flowViz_1.12.0 flowCore_1.14.1 rrcov_1.0-01 [11] pcaPP_1.8-1 mvtnorm_0.9-9 robustbase_0.5-0-1 Biobase_2.8.0 lattice_0.18-8 [16] outliers_0.13-2 loaded via a namespace (and not attached): [1] annotate_1.26.0 AnnotationDbi_1.10.1 DBI_0.2-5 feature_1.2.4 geneplotter_1.26.0 [6] graph_1.26.0 grid_2.11.1 ks_1.6.13 MASS_7.3-6 RSQLite_0.9-1 [11] stats4_2.11.1 xtable_1.5-6 >
process flowq • 669 views
ADD COMMENTlink modified 9.1 years ago by Nishant Gopalakrishnan340 • written 9.1 years ago by Karin Breuer20
Answer: flowQ on WinXP: Error in matrix for dimnames
0
gravatar for Nishant Gopalakrishnan
9.1 years ago by
Nishant Gopalakrishnan340 wrote:
Hi Karin, I tried your example with R 2.11.1 , flowQ 1.8.0 and Image magic 6.6.3 on Windows XP, but was unable to reproduce the error you got. Do you have Image magic available on your system path ? . Nishant #--------------------------------------------------------------------- ----- Using ImageMagic library at . (version 6.6.3) > tmp <- tempdir() > fn <- file.path(tmp, "test.jpg") > jpeg(file=fn) > plot(1:3) > dev.off() null device 1 > idir <- file.path(tmp, "images") > g <- qaGraph(fn, imageDir=idir) > g QA process image information > g <- qaGraph(imageDir=idir, empty=TRUE) > g QA process image information > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] flowQ_1.8.0 latticeExtra_0.6-11 RColorBrewer_1.0-2 [4] parody_1.6.0 bioDist_1.20.0 KernSmooth_2.23-3 [7] mvoutlier_1.4 flowViz_1.12.0 flowCore_1.14.1 [10] rrcov_1.0-01 pcaPP_1.8-1 mvtnorm_0.9-92 [13] robustbase_0.5-0-1 Biobase_2.8.0 lattice_0.18-8 [16] outliers_0.13-2 loaded via a namespace (and not attached): [1] annotate_1.26.1 AnnotationDbi_1.10.2 DBI_0.2-5 [4] feature_1.2.4 geneplotter_1.26.0 graph_1.26.0 [7] grid_2.11.1 ks_1.6.13 MASS_7.3-6 [10] RSQLite_0.9-1 stats4_2.11.1 xtable_1.5-6 On 07/19/2010 01:18 PM, Karin Breuer wrote: > Hello everybody, > > I am trying to get flowQ running on Windows XP 2002 Professional SP3 > (ImageMagic 6.6.3). It's running fine on Linux, but for some reason I > get the following error when trying to reproduce the code for basic > functions from the vignette (both for R2.10.1 and R2.11.1) - it does > create the correct output files, though: > > > Error in matrix(c(dims, newDims), ncol = 2, byrow = TRUE, dimnames = > list(ft, : > length of 'dimnames' [1] not equal to array extent > > > See below for full output and sessionInfo. > > I am quite stuck right now and would appreciate any thoughts on this. > Many thanks! > Karin > > > PS: Also, is there a way to prevent flowQ to use the default "convert" > command on a Windows system which hasn't ImageMagic installed? It > totally tries to reformat the file system. > > > ------------------------------------------------------------ > > library(flowQ) > > options(width=70) > > binaryAggregator() > Binary quality score passing the requirements > > discreteAggregator(2) > Discrete quality score not passing the requirements with state warn > > factorAggregator(factor("a", levels=letters[1:3])) > Factorized quality score passing the requirements of value=a > > stringAggregator("test", passed=FALSE) > Textual quality score not passing the requirements of value=test > > numericAggregator(20) > Numeric quality score passing the requirements of value=20 > > rangeAggregator(10, 0, 100) > Range quality score passing the requirements of value=10 > > aggregatorList(bin=binaryAggregator(FALSE), disc=discreteAggregator(1)) > List of 2 aggregators > > tmp <- tempdir() > > fn <- file.path(tmp, "test.jpg") > > jpeg(file=fn) > > plot(1:3) > > dev.off() > null device > 1 > > idir <- file.path(tmp, "images") > > g <- qaGraph(fn, imageDir=idir) > '\\sharename\home\homename' > CMD.EXE was started with the above path as the current directory. > UNC paths are not supported. Defaulting to Windows directory. > Error in matrix(c(dims, newDims), ncol = 2, byrow = TRUE, dimnames = > list(ft, : > length of 'dimnames' [1] not equal to array extent > > g > Error: object 'g' not found > > qaGraph(imageDir=idir, empty=TRUE) > QA process image information > > > > > > sessionInfo() > R version 2.11.1 (2010-05-31) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] flowQ_1.8.0 latticeExtra_0.6-11 RColorBrewer_1.0-2 > parody_1.6.0 bioDist_1.20.0 > [6] KernSmooth_2.23-3 mvoutlier_1.4 flowViz_1.12.0 > flowCore_1.14.1 rrcov_1.0-01 > [11] pcaPP_1.8-1 mvtnorm_0.9-9 robustbase_0.5-0-1 > Biobase_2.8.0 lattice_0.18-8 > [16] outliers_0.13-2 > > loaded via a namespace (and not attached): > [1] annotate_1.26.0 AnnotationDbi_1.10.1 DBI_0.2-5 > feature_1.2.4 geneplotter_1.26.0 > [6] graph_1.26.0 grid_2.11.1 ks_1.6.13 > MASS_7.3-6 RSQLite_0.9-1 > [11] stats4_2.11.1 xtable_1.5-6 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 9.1 years ago by Nishant Gopalakrishnan340
Thanks for your reply, Nishant! Yes, ImageMagic is available - below is the full output when I load flowQ. Unfortunately I can't try any other Windows machines because I don't have administrator rights. Which XServer have you set up with ImageMagick? Thanks, Karin # ---------------------------------------------------------------------- ------------------------------------------------------- > library(flowQ) Loading required package: outliers Loading required package: lattice Loading required package: flowViz Loading required package: flowCore Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: rrcov Loading required package: robustbase Loading required package: pcaPP Loading required package: mvtnorm Scalable Robust Estimators with High Breakdown Point (version 1.0-01) Attaching package: 'flowCore' The following object(s) are masked from 'package:stats': alias, filter KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Loading required package: mvoutlier Loading required package: bioDist Loading required package: KernSmooth Loading required package: parody Loading required package: tools Loading required package: RColorBrewer Loading required package: latticeExtra Attaching package: 'latticeExtra' The following object(s) are masked from 'package:flowViz': ecdfplot Using ImageMagic library at . (version 6.6.3) On 10-07-23 02:29 PM, Nishant Gopalakrishnan wrote: > Hi Karin, > > I tried your example with R 2.11.1 , flowQ 1.8.0 and Image magic 6.6.3 > on Windows XP, but was unable to reproduce the error you got. > Do you have Image magic available on your system path ? . > > Nishant > > #------------------------------------------------------------------- ------- > Using ImageMagic library at . > (version 6.6.3) > >> tmp<- tempdir() >> fn<- file.path(tmp, "test.jpg") >> jpeg(file=fn) >> plot(1:3) >> dev.off() >> > null device > 1 > >> idir<- file.path(tmp, "images") >> g<- qaGraph(fn, imageDir=idir) >> g >> > QA process image information > >> g<- qaGraph(imageDir=idir, empty=TRUE) >> g >> > QA process image information > >> sessionInfo() >> > R version 2.11.1 (2010-05-31) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] flowQ_1.8.0 latticeExtra_0.6-11 RColorBrewer_1.0-2 > [4] parody_1.6.0 bioDist_1.20.0 KernSmooth_2.23-3 > [7] mvoutlier_1.4 flowViz_1.12.0 flowCore_1.14.1 > [10] rrcov_1.0-01 pcaPP_1.8-1 mvtnorm_0.9-92 > [13] robustbase_0.5-0-1 Biobase_2.8.0 lattice_0.18-8 > [16] outliers_0.13-2 > > loaded via a namespace (and not attached): > [1] annotate_1.26.1 AnnotationDbi_1.10.2 DBI_0.2-5 > [4] feature_1.2.4 geneplotter_1.26.0 graph_1.26.0 > [7] grid_2.11.1 ks_1.6.13 MASS_7.3-6 > [10] RSQLite_0.9-1 stats4_2.11.1 xtable_1.5-6 > > On 07/19/2010 01:18 PM, Karin Breuer wrote: > >> Hello everybody, >> >> I am trying to get flowQ running on Windows XP 2002 Professional SP3 >> (ImageMagic 6.6.3). It's running fine on Linux, but for some reason I >> get the following error when trying to reproduce the code for basic >> functions from the vignette (both for R2.10.1 and R2.11.1) - it does >> create the correct output files, though: >> >> >> Error in matrix(c(dims, newDims), ncol = 2, byrow = TRUE, dimnames = >> list(ft, : >> length of 'dimnames' [1] not equal to array extent >> >> >> See below for full output and sessionInfo. >> >> I am quite stuck right now and would appreciate any thoughts on this. >> Many thanks! >> Karin >> >> >> PS: Also, is there a way to prevent flowQ to use the default "convert" >> command on a Windows system which hasn't ImageMagic installed? It >> totally tries to reformat the file system. >> >> >> ------------------------------------------------------------ >> >>> library(flowQ) >>> options(width=70) >>> binaryAggregator() >>> >> Binary quality score passing the requirements >> >>> discreteAggregator(2) >>> >> Discrete quality score not passing the requirements with state warn >> >>> factorAggregator(factor("a", levels=letters[1:3])) >>> >> Factorized quality score passing the requirements of value=a >> >>> stringAggregator("test", passed=FALSE) >>> >> Textual quality score not passing the requirements of value=test >> >>> numericAggregator(20) >>> >> Numeric quality score passing the requirements of value=20 >> >>> rangeAggregator(10, 0, 100) >>> >> Range quality score passing the requirements of value=10 >> >>> aggregatorList(bin=binaryAggregator(FALSE), disc=discreteAggregator(1)) >>> >> List of 2 aggregators >> >>> tmp<- tempdir() >>> fn<- file.path(tmp, "test.jpg") >>> jpeg(file=fn) >>> plot(1:3) >>> dev.off() >>> >> null device >> 1 >> >>> idir<- file.path(tmp, "images") >>> g<- qaGraph(fn, imageDir=idir) >>> >> '\\sharename\home\homename' >> CMD.EXE was started with the above path as the current directory. >> UNC paths are not supported. Defaulting to Windows directory. >> Error in matrix(c(dims, newDims), ncol = 2, byrow = TRUE, dimnames = >> list(ft, : >> length of 'dimnames' [1] not equal to array extent >> >>> g >>> >> Error: object 'g' not found >> >>> qaGraph(imageDir=idir, empty=TRUE) >>> >> QA process image information >> >> >> >> >> >>> sessionInfo() >>> >> R version 2.11.1 (2010-05-31) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 >> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] flowQ_1.8.0 latticeExtra_0.6-11 RColorBrewer_1.0-2 >> parody_1.6.0 bioDist_1.20.0 >> [6] KernSmooth_2.23-3 mvoutlier_1.4 flowViz_1.12.0 >> flowCore_1.14.1 rrcov_1.0-01 >> [11] pcaPP_1.8-1 mvtnorm_0.9-9 robustbase_0.5-0-1 >> Biobase_2.8.0 lattice_0.18-8 >> [16] outliers_0.13-2 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.26.0 AnnotationDbi_1.10.1 DBI_0.2-5 >> feature_1.2.4 geneplotter_1.26.0 >> [6] graph_1.26.0 grid_2.11.1 ks_1.6.13 >> MASS_7.3-6 RSQLite_0.9-1 >> [11] stats4_2.11.1 xtable_1.5-6 >> >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > -- Karin Breuer Terry Fox Laboratory, BC Cancer Agency 675 West 10th Avenue, V5Z 1L3 Vancouver, BC, Canada Phone: +1 (604) 675-8000 x 7755
ADD REPLYlink written 9.1 years ago by Karin Breuer20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 211 users visited in the last hour