[BioC] FlowQ

[Bennett, Brian]

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 ".inv" in function names has globaly been replaced by "Inv"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


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