Dear BioC list, I have a strange error when I try to load flowQ on R 2.13.0. The installation went fine, with no errors but I am not able to load the library. My apologies if the error is been solved already, please be patient (! :-)), I could not find any solution on this list or on Google. This is the error when I load the library: > library(flowQ) Loading required package: outliers Loading required package: flowViz KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Attaching package: 'flowViz' The following object(s) are masked from 'package:hexbin': hexbin 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:robustbase': salinity The following object(s) are masked from 'package:lattice': melanoma 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 ".inv" in function names has globaly been replaced by "Inv" similarly ".row" and ".col" respectively by "Row" and "Col".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' > And this is my sessioninfo: > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] tools splines grid stats graphics grDevices utils [8] datasets methods base other attached packages: [1] latticeExtra_0.6-18 RColorBrewer_1.0-2 parody_1.10.0 [4] bioDist_1.24.0 KernSmooth_2.23-4 mvoutlier_1.9.1 [7] robCompositions_1.5.0 car_2.0-10 survival_2.36-5 [10] nnet_7.3-1 compositions_1.10-1 energy_1.3-0 [13] MASS_7.3-12 boot_1.2-43 tensorA_0.36 [16] rgl_0.92.798 flowViz_1.16.0 outliers_0.14 [19] flowCore_1.18.0 rrcov_1.3-00 pcaPP_1.9-1 [22] mvtnorm_0.9-999 robustbase_0.7-6 Biobase_2.12.1 [25] hexbin_1.26.0 lattice_0.19-23 loaded via a namespace (and not attached): [1] AnnotationDbi_1.14.1 DBI_0.2-5 RSQLite_0.9-4 [4] annotate_1.30.0 feature_1.2.7 flowQ_1.12.0 [7] geneplotter_1.30.0 graph_1.30.0 ks_1.8.2 [10] stats4_2.13.0 tcltk_2.13.0 xtable_1.5-6 -- > [[alternative HTML version deleted]]

Hi, On Fri, Jun 17, 2011 at 4:41 AM, Ren? Dreos <talponer at="" gmail.com=""> wrote: > Dear BioC list, > > I have a strange error when I try to load flowQ on R 2.13.0. The > installation went fine, with no errors but I am not able to load the > library. My apologies if the error is been solved already, please be patient > (! :-)), I could not find any solution on this list or on Google. This is > the error when I load the library: This is a surprisingly verbose "loading banner" -- which I'm going to cut :-) > >> library(flowQ) [snip] > 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' It looks as if flowQ depends on having imagemagick (http://www.imagemagick.org/script/index.php) installed on your system. The `convert` command is part of imagemagick, and flowQ is trying to invoke that command on your system. If you open up your Terminal and type: $ which convert I guess it doesn't find anything? If that's the case, you'll have to install imagemagick. They recommend doing so through macports, but if you don't want to do that googling for "install imagemagick os x" that will turn up other ways. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact