isobar 1.5.0
Florian P Breitwieser
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/isobar | | Last Changed Rev: 70825 / Revision: 72575 | | Last Changed Date: 2012-10-29 07:23:47 -0700 (Mon, 29 Oct 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | ERROR | skipped | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | [ ERROR ] | skipped | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ERROR | skipped | skipped |
| petty | Mac OS X Leopard (10.5.8) / i386 | ERROR | skipped | skipped |
* checking for file ‘isobar/DESCRIPTION’ ... OK
* preparing ‘isobar’:
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist
Welcome to Bioconductor
Vignettes contain introductory material; view with
‘browseVignettes()’. To cite Bioconductor, see
‘citation("Biobase")’, and for packages ‘citation("pkgname")’.
Loading required package: plyr
Welcome to isobar (v 1.5.0)
‘openVignette("isobar")’ and ‘?isobar’ provide help on usage.
Attaching package: ‘isobar’
The following object is masked from ‘package:base’:
paste0
Loading required package: startupmsg
:startupmsg> Utilities for start-up messages (version 0.7.2)
:startupmsg>
:startupmsg> For more information see ?"startupmsg",
:startupmsg> NEWS("startupmsg")
Loading required package: sfsmisc
Loading required package: SweaveListingUtils
:SweaveListingUtils> Utilities for Sweave together with
:SweaveListingUtils> TeX listings package (version
:SweaveListingUtils> 0.5.5)
:SweaveListingUtils>
:SweaveListingUtils> Some functions from package ‘base’
:SweaveListingUtils> are intentionally masked ---see
:SweaveListingUtils> SweaveListingMASK().
:SweaveListingUtils>
:SweaveListingUtils> Note that global options are
:SweaveListingUtils> controlled by
:SweaveListingUtils> SweaveListingoptions() ---c.f.
:SweaveListingUtils> ?"SweaveListingoptions".
:SweaveListingUtils>
:SweaveListingUtils> For more information see
:SweaveListingUtils> ?"SweaveListingUtils",
:SweaveListingUtils> NEWS("SweaveListingUtils")
:SweaveListingUtils> There is a vignette to this
:SweaveListingUtils> package; try
:SweaveListingUtils> vignette("ExampleSweaveListingUtils").
Attaching package: ‘SweaveListingUtils’
The following object is masked from ‘package:base’:
library, require
:distr> Object oriented implementation of distributions (version
:distr> 2.3.3)
:distr>
:distr> Attention: Arithmetics on distribution objects are
:distr> understood as operations on corresponding random variables
:distr> (r.v.s); see distrARITH().
:distr>
:distr> Some functions from package ‘stats’ are intentionally masked
:distr> ---see distrMASK().
:distr>
:distr> Note that global options are controlled by distroptions()
:distr> ---c.f. ?"distroptions".
:distr>
:distr> For more information see ?"distr", NEWS("distr"), as well as
:distr> http://distr.r-forge.r-project.org/
:distr> Package "distrDoc" provides a vignette to this package as
:distr> well as to several extension packages; try
:distr> vignette("distr").
Attaching package: ‘distr’
The following object is masked from ‘package:stats’:
df, qqplot, sd
Loading required package: ggplot2
‘opts’ is deprecated. Use ‘theme’ instead. (Deprecated; last used in version 0.9.1)
theme_text is deprecated. Use ‘element_text’ instead. (Deprecated; last used in version 0.9.1)
LOG: isotopeImpurities.corrected: TRUE
LOG: is.normalized: TRUE
normalizing ibspiked_set1.ibspectra.csv [14991 spectra]
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 114: 1.2721
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 115: 1.0747
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 116: 1.0355
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 117: 1
Warning in .local(x, channel1, channel2, ...) : removing 481 NA points
Warning in .local(x, channel1, channel2, ...) : removing 481 NA points
Error: processing vignette ‘isobar.Rnw’ failed with diagnostics:
chunk 12 (label = calc-noisemodel)
Error in as.data.frame.default(proteinGroup(x)) :
cannot coerce class "structure("ProteinGroup", package = "isobar")" to a data.frame
Execution halted