Question: FlowQ
0
gravatar for Bennett, Brian
8.0 years ago by
Bennett, Brian10 wrote:
I'm having some trouble getting FlowQ to load on my mac. Below is the attempt to load the package and some session info. I'mprobably missing something specific as all other packages are fine. library (flowQ) Loading required package: outliers Loading required package: mvoutlier Loading required package: compositions Loading required package: rgl Loading required package: tensorA Attaching package: 'tensorA' The following object(s) are masked from 'package:base': norm Loading required package: energy Loading required package: boot Attaching package: 'boot' The following object(s) are masked from 'package:lattice': melanoma The following object(s) are masked from 'package:robustbase': salinity Loading required package: MASS Welcome to compositions, a package for compositional data analysis. Get help with "? compositions" Version info: to ensure compatibility with R > 2.7.0. ".inv" in function names has globaly been replaced by "Inv" similarly ".row" and ".col" respectively by "Row" and "Col". WARNING Please, take into account that this piece of software does complex geometric operations in high-dimensional spaces, possibly using different incompatible geometries. In particular, be advised that arithmetic operations (+ and *) might have non-conventional meanings. Double-check that you are doing reasonable things. The mere fact that the package computes something does not imply that this is reasonable Attaching package: 'compositions' The following object(s) are masked from 'package:flowCore': normalize The following object(s) are masked from 'package:stats': cor, cov, dist, var The following object(s) are masked from 'package:base': %*%, scale, scale.default Loading required package: robCompositions Loading required package: car Loading required package: nnet Loading required package: survival Loading required package: splines Attaching package: 'survival' The following object(s) are masked from 'package:boot': aml The following object(s) are masked from 'package:robustbase': heart Attaching package: 'car' The following object(s) are masked from 'package:boot': logit -------- for references have a look at citation('robCompositions') -------- Attaching package: 'robCompositions' The following object(s) are masked from 'package:compositions': alr, clr, ilr 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 Error : .onAttach failed in attachNamespace() for 'flowQ', details: call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) error: error in running command Error: package/namespace load failed for 'flowQ' ################## then I tired from packages and data and get: Error : .onAttach failed in attachNamespace() for 'flowQ', details: call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) error: error in running command Error: package/namespace load failed for 'flowQ' ################################################# > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools splines stats graphics grDevices utils datasets methods base other attached packages: [1] flowWorkspaceData_0.99.4 flowMeans_1.4.0 flowMerge_2.0.2 multicore_0.1-5 foreach_1.3.2 codetools_0.2-8 [7] iterators_1.0.5 snow_0.3-6 flowClust_2.10.0 ellipse_0.3-5 mnormt_1.4-3 flowStats_1.10.0 [13] cluster_1.14.0 fda_2.2.6 zoo_1.7-2 latticeExtra_0.6-18 RColorBrewer_1.0-5 parody_1.10.0 [19] bioDist_1.24.1 KernSmooth_2.23-6 mvoutlier_1.9.1 robCompositions_1.5.0 car_2.0-10 survival_2.36-9 [25] nnet_7.3-1 compositions_1.10-1 energy_1.3-0 MASS_7.3-14 boot_1.3-2 tensorA_0.36 [31] rgl_0.92.798 outliers_0.14 flowViz_1.16.0 lattice_0.19-31 flowCore_1.18.0 rrcov_1.3-01 [37] pcaPP_1.9-42 mvtnorm_0.9-9991 robustbase_0.7-6 Biobase_2.12.2 loaded via a namespace (and not attached): [1] annotate_1.30.0 AnnotationDbi_1.14.1 DBI_0.2-5 feature_1.2.7 flowQ_1.12.0 geneplotter_1.30.0 graph_1.30.0 [8] grid_2.13.1 ks_1.8.2 RSQLite_0.9-4 stats4_2.13.1 xtable_1.5-6 Brian J. Bennett, PhD bbennett at mednet.ucla.edu<mailto:bbennett at="" mednet.ucla.edu=""> Lusis Laboratory UCLA 3220 MacDonald Research Laboratories 675 Charles Young Drive S. Los Angeles, CA 90095 tel. (310) 206-0133 fax (310) 794-7345 ________________________________ IMPORTANT WARNING: This email (and any attachments) is o...{{dropped:9}}
flowq • 849 views
ADD COMMENTlink modified 8.0 years ago by Greg Finak240 • written 8.0 years ago by Bennett, Brian10
Answer: FlowQ
0
gravatar for Vincent J. Carey, Jr.
8.0 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
Do you have ImageMagick installed? if not, something like fink install imagemagick imagemagick2-dev could get you going, if you have fink... On Wed, Aug 17, 2011 at 8:12 PM, Bennett, Brian <bbennett@mednet.ucla.edu>wrote: > I'm having some trouble getting FlowQ to load on my mac. Below is the > attempt to load the package and some session info. I'mprobably missing > something specific as all other packages are fine. > > > library (flowQ) > Loading required package: outliers > Loading required package: mvoutlier > Loading required package: compositions > Loading required package: rgl > Loading required package: tensorA > > Attaching package: 'tensorA' > > The following object(s) are masked from 'package:base': > > norm > > Loading required package: energy > Loading required package: boot > > Attaching package: 'boot' > > The following object(s) are masked from 'package:lattice': > > melanoma > > The following object(s) are masked from 'package:robustbase': > > salinity > > Loading required package: MASS > Welcome to compositions, a package for compositional data analysis. > > Get help with "? compositions" > Version info: to ensure compatibility with R > 2.7.0. > ".inv" in function names has globaly been replaced by "Inv" > similarly ".row" and ".col" respectively by "Row" and "Col". > > WARNING > Please, take into account that this piece of software does complex > geometric operations in high-dimensional spaces, possibly using > different incompatible geometries. In particular, be advised that > arithmetic operations (+ and *) might have non-conventional meanings. > Double-check that you are doing reasonable things. The mere fact that > the package computes something does not imply that this is reasonable > > Attaching package: 'compositions' > > The following object(s) are masked from 'package:flowCore': > > normalize > > The following object(s) are masked from 'package:stats': > > cor, cov, dist, var > > The following object(s) are masked from 'package:base': > > %*%, scale, scale.default > > Loading required package: robCompositions > Loading required package: car > Loading required package: nnet > Loading required package: survival > Loading required package: splines > > Attaching package: 'survival' > > The following object(s) are masked from 'package:boot': > > aml > > The following object(s) are masked from 'package:robustbase': > > heart > > > Attaching package: 'car' > > The following object(s) are masked from 'package:boot': > > logit > > > -------- > > for references have a look at > citation('robCompositions') > -------- > > > Attaching package: 'robCompositions' > > The following object(s) are masked from 'package:compositions': > > alr, clr, ilr > > 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 > > Error : .onAttach failed in attachNamespace() for 'flowQ', details: > call: mysys("convert -list configure", intern = TRUE, ignore.stderr = > TRUE) > error: error in running command > Error: package/namespace load failed for 'flowQ' > > ################## > then I tired from packages and data and get: > Error : .onAttach failed in attachNamespace() for 'flowQ', details: > call: mysys("convert -list configure", intern = TRUE, ignore.stderr = > TRUE) > error: error in running command > Error: package/namespace load failed for 'flowQ' > ################################################# > > > sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] tools splines stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] flowWorkspaceData_0.99.4 flowMeans_1.4.0 flowMerge_2.0.2 > multicore_0.1-5 foreach_1.3.2 codetools_0.2-8 > [7] iterators_1.0.5 snow_0.3-6 flowClust_2.10.0 > ellipse_0.3-5 mnormt_1.4-3 flowStats_1.10.0 > [13] cluster_1.14.0 fda_2.2.6 zoo_1.7-2 > latticeExtra_0.6-18 RColorBrewer_1.0-5 parody_1.10.0 > [19] bioDist_1.24.1 KernSmooth_2.23-6 mvoutlier_1.9.1 > robCompositions_1.5.0 car_2.0-10 survival_2.36-9 > [25] nnet_7.3-1 compositions_1.10-1 energy_1.3-0 > MASS_7.3-14 boot_1.3-2 tensorA_0.36 > [31] rgl_0.92.798 outliers_0.14 flowViz_1.16.0 > lattice_0.19-31 flowCore_1.18.0 rrcov_1.3-01 > [37] pcaPP_1.9-42 mvtnorm_0.9-9991 robustbase_0.7-6 > Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] annotate_1.30.0 AnnotationDbi_1.14.1 DBI_0.2-5 > feature_1.2.7 flowQ_1.12.0 geneplotter_1.30.0 graph_1.30.0 > [8] grid_2.13.1 ks_1.8.2 RSQLite_0.9-4 > stats4_2.13.1 xtable_1.5-6 > > > > Brian J. Bennett, PhD > bbennett@mednet.ucla.edu<mailto:bbennett@mednet.ucla.edu> > Lusis Laboratory > UCLA > 3220 MacDonald Research Laboratories > 675 Charles Young Drive S. > Los Angeles, CA 90095 > tel. (310) 206-0133 > fax (310) 794-7345 > > > ________________________________ > IMPORTANT WARNING: This email (and any attachments) is o...{{dropped:9}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 8.0 years ago by Vincent J. Carey, Jr.6.3k
Answer: FlowQ
0
gravatar for Greg Finak
8.0 years ago by
Greg Finak240
United States
Greg Finak240 wrote:
Hi, Brian You need to install ImageMagick. It provides the 'convert' command. Greg Finak
ADD COMMENTlink written 8.0 years ago by Greg Finak240
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