LowMACA

Package: LowMACA
Type: Package
Title: LowMACA - Low frequency Mutation Analysis via Consensus
Alignment
Version: 1.4.2
Date: 2015-04-29
Author: Stefano de Pretis , Giorgio Melloni
Maintainer: Stefano de Pretis <ste.depo@gmail.com>, Giorgio Melloni <melloni.giorgio@gmail.com>
Description: The LowMACA package is a simple suite of tools to investigate and analyze the mutation profile of several proteins or pfam domains via consensus alignment. You can conduct an hypothesis driven exploratory analysis using our package simply providing a set of genes or pfam domains of your interest.
License: GPL-3
Depends: R (>= 2.10)
Imports: cgdsr, parallel, stringr, reshape2, data.table, RColorBrewer,
methods, LowMACAAnnotation, BiocParallel, motifStack,
Biostrings
Suggests: BiocStyle, knitr, rmarkdown
VignetteBuilder: knitr
biocViews: SomaticMutation, SequenceMatching, WholeGenome, Sequencing,
Alignment, DataImport, MultipleSequenceAlignment
SystemRequirements: clustalo, gs, perl
NeedsCompilation: no
Packaged: 2016-05-16 05:24:01 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'LowMACA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'LowMACA'
    finding HTML links ... done
    BLOSUM62                                html  
    LowMACA-class                           html  
Rd warning: /tmp/RtmpBe85uT/R.INSTALL74a57fb31a15/LowMACA/man/LowMACA-class.Rd:62: missing file link 'AAMultipleAlignment'
Rd warning: /tmp/RtmpBe85uT/R.INSTALL74a57fb31a15/LowMACA/man/LowMACA-class.Rd:71: missing file link 'getMutationData'
    LowMACA-package                         html  
    LowMACA_AML                             html  
    alignSequences                          html  
    allPfamAnalysis                         html  
Rd warning: /tmp/RtmpBe85uT/R.INSTALL74a57fb31a15/LowMACA/man/allPfamAnalysis.Rd:52: missing file link 'BiocParallelParam'
Rd warning: /tmp/RtmpBe85uT/R.INSTALL74a57fb31a15/LowMACA/man/allPfamAnalysis.Rd:54: missing file link 'bpparam'
    bpAll                                   html  
    entropy                                 html  
    getMutations                            html  
Rd warning: /tmp/RtmpBe85uT/R.INSTALL74a57fb31a15/LowMACA/man/getMutations.Rd:20: missing file link 'getMutationData'
Rd warning: /tmp/RtmpBe85uT/R.INSTALL74a57fb31a15/LowMACA/man/getMutations.Rd:32: missing file link 'getMutationData'
    lfm                                     html  
    lfmSingleSequence                       html  
Rd warning: /tmp/RtmpBe85uT/R.INSTALL74a57fb31a15/LowMACA/man/lfmSingleSequence.Rd:26: missing file link 'BiocParallelParam'
Rd warning: /tmp/RtmpBe85uT/R.INSTALL74a57fb31a15/LowMACA/man/lfmSingleSequence.Rd:28: missing file link 'bpparam'
    lmAlignment                             html  
    lmEntropy                               html  
    lmMutations                             html  
    lmObj                                   html  
    lmParams                                html  
    lmPlot                                  html  
    lmPlotSingleSequence                    html  
    mapMutations                            html  
    newLowMACA                              html  
    nullProfile                             html  
    parallelize                             html  
    protter                                 html  
    setup                                   html  
    showTumorType                           html  
Rd warning: /tmp/RtmpBe85uT/R.INSTALL74a57fb31a15/LowMACA/man/showTumorType.Rd:19: missing file link 'getCancerStudies'
Rd warning: /tmp/RtmpBe85uT/R.INSTALL74a57fb31a15/LowMACA/man/showTumorType.Rd:26: missing file link 'getCancerStudies'
** building package indices
** installing vignettes
** testing if installed package can be loaded
Checking if clustalo is in the PATH...
Warning in .ClustalChecks(ClustalCommand = "clustalo") :
  Clustal Omega is not in the PATH:
You can either change clustalo command using lmParams function or use the web service. See ?setup
Checking perl installation...
Checking perl modules XML::Simple and LWP...
Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .).
BEGIN failed--compilation aborted.
Warning: running command '/usr/bin/perl -MXML::Simple -e 1' had status 2
Warning in .PerlModuleChecks(stop = FALSE, perl = "perl") :
  XML::Simple module for perl is not installed. 
            If you don't want to install a local clustal omega and use the web service, XML::Simple is required

* DONE (LowMACA)
Making 'packages.html' ... done