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R en Bioconductor op f8

 
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Vorige onderwerp :: Volgende onderwerp  
Auteur Bericht
NikkiMassa



Geregistreerd op: 17 Sep 2006
Berichten: 355
Woonplaats: Vries

BerichtGeplaatst: Wo Dec 05, 2007 3:32 pm    Onderwerp: R en Bioconductor op f8 Reageren met citaat

Hallo,

Ik studeer bio-informatica en voor statistiek maken we gebruik van R. Mijn docent is bezig een eigen methode/boek te schrijven. De titel dekt de lading: Introduction to Statistics for Bioinformatics using R. In zijn methode maakt hij veel gebruik van de dataset van Golub et al. (1999). Deze is onder R beschikbaar in de package "multtest", onderdeel van Bioconductor.

Ik heb niet heel lang geleden f8 geinstalleerd van de live cd.
Ik heb R geinstalleerd door in Yumex onder Group View > Applications > Engineering and Scientific (was al aangevinkt) R aan te vinken en te laten installeren. Met succes.

De package "multtest" lukte mij dus niet. In eerste instantie heb ik dit geprobeerd (als su, in R):
Code:
> install.packages(c("multtest"),repo="http://cran.r-project.org",dep=TRUE)
Warning in install.packages(c("multtest"), repo = "http://cran.r-project.org",  :
  argument 'lib' is missing: using '/usr/lib/R/library'
trying URL 'http://cran.r-project.org/src/contrib/multtest_1.16.1.tar.gz'
Content type 'application/x-gzip' length 1406437 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb

/usr/lib/R/library
* Installing *source* package 'multtest' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'multtest'
** Removing '/usr/lib/R/library/multtest'

The downloaded packages are in
        /tmp/RtmpTb1jyD/downloaded_packages
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages(c("multtest"), repo = "http://cran.r-project.org",  :
  dependency ‘Biobase’ is not available
2: In install.packages(c("multtest"), repo = "http://cran.r-project.org",  :
  installation of package 'multtest' had non-zero exit status


In de methode van mijn docent stond het volgende:
docent schreef:
In the sequel we shall often use packages from Bioconductor (...) and can be installed within an R session, as follows.
> source("http://www.bioconductor.org/biocLite.R")
> biocLite()


Ik heb dit gedaan, code volgt onderaan. Het is ook niet gelukt.

Mijn vraag is: wat ging er mis? Hoe kan ik dit oplossen? Iemand een idee?


Code:
>su -
>R -q

Code:
> source("http://www.bioconductor.org/biocLite.R")
> biocLite()
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Will install the following packages:
 [1] "affy"         "affydata"     "affyPLM"      "annaffy"      "annotate"
 [6] "Biobase"      "Biostrings"   "DynDoc"       "gcrma"        "genefilter"
[11] "geneplotter"  "hgu95av2"     "limma"        "marray"       "matchprobes"
[16] "multtest"     "ROC"          "vsn"          "xtable"       "affyQCReport"
Please wait...

Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
  argument 'lib' is missing: using '/usr/lib/R/library'
also installing the dependencies ‘RSQLite’, ‘affyio’, ‘preprocessCore’, ‘AnnotationDbi’, ‘simpleaffy’

trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.6-4.tar.gz'
Content type 'application/x-gzip' length 735519 bytes (718 Kb)
opened URL
==================================================
downloaded 718 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/affyio_1.6.1.tar.gz'
Content type 'application/x-gzip' length 69112 bytes (67 Kb)
opened URL
==================================================
downloaded 67 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/preprocessCore_1.0.0.tar.gz'
Content type 'application/x-gzip' length 48446 bytes (47 Kb)
opened URL
==================================================
downloaded 47 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/AnnotationDbi_1.0.6.tar.gz'
Content type 'application/x-gzip' length 228996 bytes (223 Kb)
opened URL
==================================================
downloaded 223 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/simpleaffy_2.14.05.tar.gz'
Content type 'application/x-gzip' length 567142 bytes (553 Kb)
opened URL
==================================================
downloaded 553 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/affy_1.16.0.tar.gz'
Content type 'application/x-gzip' length 1380054 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb

trying URL 'http://bioconductor.org/packages/2.1/data/experiment/src/contrib/affydata_1.11.3.tar.gz'
Content type 'application/x-gzip' length 9863394 bytes (9.4 Mb)
opened URL
==================================================
downloaded 9.4 Mb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/affyPLM_1.14.0.tar.gz'
Content type 'application/x-gzip' length 6437706 bytes (6.1 Mb)
opened URL
==================================================
downloaded 6.1 Mb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/annaffy_1.10.1.tar.gz'
Content type 'application/x-gzip' length 174088 bytes (170 Kb)
opened URL
==================================================
downloaded 170 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/annotate_1.16.1.tar.gz'
Content type 'application/x-gzip' length 1526767 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/Biobase_1.16.1.tar.gz'
Content type 'application/x-gzip' length 1879216 bytes (1.8 Mb)
opened URL
==================================================
downloaded 1.8 Mb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/Biostrings_2.6.6.tar.gz'
Content type 'application/x-gzip' length 504738 bytes (492 Kb)
opened URL
==================================================
downloaded 492 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/DynDoc_1.16.0.tar.gz'
Content type 'application/x-gzip' length 11306 bytes (11 Kb)
opened URL
==================================================
downloaded 11 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/gcrma_2.10.0.tar.gz'
Content type 'application/x-gzip' length 108450 bytes (105 Kb)
opened URL
==================================================
downloaded 105 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/genefilter_1.16.0.tar.gz'
Content type 'application/x-gzip' length 242543 bytes (236 Kb)
opened URL
==================================================
downloaded 236 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/geneplotter_1.16.0.tar.gz'
Content type 'application/x-gzip' length 1465687 bytes (1.4 Mb)
opened URL
==================================================
downloaded 1.4 Mb

trying URL 'http://bioconductor.org/packages/2.1/data/annotation/src/contrib/hgu95av2_2.0.1.tar.gz'
Content type 'application/x-gzip' length 8198233 bytes (7.8 Mb)
opened URL
==================================================
downloaded 7.8 Mb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/limma_2.12.0.tar.gz'
Content type 'application/x-gzip' length 737774 bytes (720 Kb)
opened URL
==================================================
downloaded 720 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/marray_1.16.0.tar.gz'
Content type 'application/x-gzip' length 3981777 bytes (3.8 Mb)
opened URL
==================================================
downloaded 3.8 Mb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/matchprobes_1.10.0.tar.gz'
Content type 'application/x-gzip' length 7655447 bytes (7.3 Mb)
opened URL
==================================================
downloaded 7.3 Mb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/multtest_1.18.0.tar.gz'
Content type 'application/x-gzip' length 1402877 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/ROC_1.12.0.tar.gz'
Content type 'application/x-gzip' length 94802 bytes (92 Kb)
opened URL
==================================================
downloaded 92 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/vsn_3.2.1.tar.gz'
Content type 'application/x-gzip' length 1804554 bytes (1.7 Mb)
opened URL
==================================================
downloaded 1.7 Mb

trying URL 'http://cran.fhcrc.org/src/contrib/xtable_1.5-2.tar.gz'
Content type 'application/x-gzip' length 161231 bytes (157 Kb)
opened URL
==================================================
downloaded 157 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/affyQCReport_1.16.0.tar.gz'
Content type 'application/x-gzip' length 131242 bytes (128 Kb)
opened URL
==================================================
downloaded 128 Kb

/usr/lib/R/library
* Installing *source* package 'RSQLite' ...
/usr/lib/R/bin/config: line 126: make: command not found
/usr/lib/R/bin/config: line 188: make: command not found
/usr/lib/R/bin/config: line 126: make: command not found
/usr/lib/R/bin/config: line 188: make: command not found
checking for gcc... no
checking for cc... no
checking for cc... no
checking for cl... no
configure: error: no acceptable C compiler found in $PATH
See `config.log' for more details.
ERROR: configuration failed for package 'RSQLite'
** Removing '/usr/lib/R/library/RSQLite'
/usr/lib/R/library
* Installing *source* package 'affyio' ...
creating cache ./config.cache
checking how to run the C preprocessor... /lib/cpp
checking for main in -lz... no
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
chmod: cannot access `/usr/lib/R/library/affyio/libs/*': No such file or directory
ERROR: compilation failed for package 'affyio'
** Removing '/usr/lib/R/library/affyio'
/usr/lib/R/library
* Installing *source* package 'preprocessCore' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'preprocessCore'
** Removing '/usr/lib/R/library/preprocessCore'
/usr/lib/R/library
* Installing *source* package 'Biobase' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'Biobase'
** Removing '/usr/lib/R/library/Biobase'
/usr/lib/R/library
* Installing *source* package 'Biostrings' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'Biostrings'
** Removing '/usr/lib/R/library/Biostrings'
/usr/lib/R/library
* Installing *source* package 'DynDoc' ...
** R
** preparing package for lazy loading
Creating a new generic function for "summary" in "DynDoc"
** help
 >>> Building/Updating help pages for package 'DynDoc'
     Formats: text html latex example
  DynDoc-class                      text    html    latex
  SweaveOptions-class               text    html    latex
  Vignette-class                    text    html    latex
  chunkList-class                   text    html    latex   example
  codeChunk-class                   text    html    latex   example
  getPkgVigList                     text    html    latex   example
  getVignette                       text    html    latex
  getVignetteCode                   text    html    latex
  getVignetteHeader                 text    html    latex
  tangleToR                         text    html    latex   example
  vignetteCode-class                text    html    latex
** building package indices ...
* DONE (DynDoc)
/usr/lib/R/library
* Installing *source* package 'hgu95av2' ...
** R
** data
**  moving datasets to lazyload DB
** help
 >>> Building/Updating help pages for package 'hgu95av2'
     Formats: text html latex example
  hgu95av2                          text    html    latex
  hgu95av2ACCNUM                    text    html    latex   example
  hgu95av2CHR                       text    html    latex   example
  hgu95av2CHRLENGTHS                text    html    latex   example
  hgu95av2CHRLOC                    text    html    latex   example
  hgu95av2ENTREZID                  text    html    latex   example
  hgu95av2ENZYME                    text    html    latex   example
  hgu95av2ENZYME2PROBE              text    html    latex   example
  hgu95av2GENENAME                  text    html    latex   example
  hgu95av2GO                        text    html    latex   example
  hgu95av2GO2ALLPROBES              text    html    latex   example
  hgu95av2GO2PROBE                  text    html    latex   example
  hgu95av2MAP                       text    html    latex   example
  hgu95av2OMIM                      text    html    latex   example
  hgu95av2ORGANISM                  text    html    latex   example
  hgu95av2PATH                      text    html    latex   example
  hgu95av2PATH2PROBE                text    html    latex   example
  hgu95av2PFAM                      text    html    latex   example
  hgu95av2PMID                      text    html    latex   example
  hgu95av2PMID2PROBE                text    html    latex   example
  hgu95av2PROSITE                   text    html    latex   example
  hgu95av2QC                        text    html    latex
  hgu95av2QCDATA                    text    html    latex
  hgu95av2REFSEQ                    text    html    latex   example
  hgu95av2SYMBOL                    text    html    latex   example
  hgu95av2UNIGENE                   text    html    latex   example
** building package indices ...
* DONE (hgu95av2)
/usr/lib/R/library
* Installing *source* package 'limma' ...
** R
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'limma'
     Formats: text html latex example
  01Introduction                    text    html    latex
  02classes                         text    html    latex
  03reading                         text    html    latex
  04Background                      text    html    latex
  05Normalization                   text    html    latex
  06linearmodels                    text    html    latex
  07SingleChannel                   text    html    latex
  08Tests                           text    html    latex
  09Diagnostics                     text    html    latex
  10Other                           text    html    latex
  LargeDataObject                   text    html    latex   example
  PrintLayout                       text    html    latex   example
  TestResults                       text    html    latex   example
  anova-method                      text    html    latex
  arrayWeights                      text    html    latex   example
  arrayWeightsQuick                 text    html    latex   example
  asMatrixWeights                   text    html    latex   example
  asdataframe                       text    html    latex
  asmalist                          text    html    latex
  asmatrix                          text    html    latex
  auROC                             text    html    latex   example
  avedups                           text    html    latex
  backgroundcorrect                 text    html    latex   example
  blockDiag                         text    html    latex   example
  bwss                              text    html    latex
  bwss.matrix                       text    html    latex
  cbind                             text    html    latex   example
  changelog                         text    html    latex
  channel2M                         text    html    latex   example
  classifytests                     text    html    latex   example
  contrasts.fit                     text    html    latex   example
  controlStatus                     text    html    latex   example
  convest                           text    html    latex   example
  decideTests                       text    html    latex
  dim                               text    html    latex   example
  dimnames                          text    html    latex
  dnormexp                          text    html    latex
  dupcor                            text    html    latex   example
  ebayes                            text    html    latex   example
  exprsMA                           text    html    latex
  exprset2                          text    html    latex
  fitfdist                          text    html    latex
  fitted.MArrayLM                   text    html    latex
  geneSetTest                       text    html    latex   example
  getSpacing                        text    html    latex   example
  getlayout                         text    html    latex   example
  gls.series                        text    html    latex
  gridspotrc                        text    html    latex
  heatdiagram                       text    html    latex   example
  helpMethods                       text    html    latex   example
  imageplot                         text    html    latex   example
  imageplot3by2                     text    html    latex
  intraspotCorrelation              text    html    latex   example
  isfullrank                        text    html    latex   example
  isnumeric                         text    html    latex   example
  kooperberg                        text    html    latex   example
  limmaUsersGuide                   text    html    latex   example
  lm.series                         text    html    latex
  lmFit                             text    html    latex   example
  lmscFit                           text    html    latex   example
  loessfit                          text    html    latex   example
  m.spot                            text    html    latex
  ma3x3                             text    html    latex   example
  makeContrasts                     text    html    latex   example
  makeunique                        text    html    latex   example
  malist                            text    html    latex
  marraylm                          text    html    latex
  mdplot                            text    html    latex
  merge                             text    html    latex   example
  mergeScansRG                      text    html    latex   example
  modelMatrix                       text    html    latex   example
  modifyWeights                     text    html    latex   example
  mrlm                              text    html    latex
  normalizeMedianAbsValues          text    html    latex   example
  normalizeRobustSpline             text    html    latex   example
  normalizeWithinArrays             text    html    latex   example
  normalizebetweenarrays            text    html    latex   example
  normalizeprintorder               text    html    latex   example
  normalizequantiles                text    html    latex
  normexp                           text    html    latex
  normexpfit                        text    html    latex   example
  normexpsignal                     text    html    latex   example
  plotDensities                     text    html    latex   example
  plotFB                            text    html    latex
  plotlines                         text    html    latex
  plotma                            text    html    latex   example
  plotma3by2                        text    html    latex
  plotprinttiploess                 text    html    latex
  poolvar                           text    html    latex   example
  printHead                         text    html    latex
  printorder                        text    html    latex   example
  printtipWeights                   text    html    latex   example
  protectMetachar                   text    html    latex   example
  qqt                               text    html    latex   example
  qualwt                            text    html    latex   example
  read.columns                      text    html    latex
  read.maimages                     text    html    latex   example
  read.matrix                       text    html    latex
  read.series                       text    html    latex
  readGPRHeader                     text    html    latex
  readImaGeneHeader                 text    html    latex   example
  readSpotTypes                     text    html    latex
  readTargets                       text    html    latex
  readgal                           text    html    latex   example
  removeext                         text    html    latex   example
  residuals.MArrayLM                text    html    latex
  rg.genepix                        text    html    latex
  rg.quantarray                     text    html    latex
  rg.series.spot                    text    html    latex
  rg.spot                           text    html    latex
  rglist                            text    html    latex
  splitName                         text    html    latex
  squeezeVar                        text    html    latex   example
  strsplit2                         text    html    latex   example
  subsetting                        text    html    latex   example
  summary                           text    html    latex
  targetsA2C                        text    html    latex   example
  tmixture                          text    html    latex
  toptable                          text    html    latex   example
  trigammainverse                   text    html    latex   example
  trimWhiteSpace                    text    html    latex   example
  uniquegenelist                    text    html    latex   example
  unwrapdups                        text    html    latex   example
  venn                              text    html    latex   example
  volcanoplot                       text    html    latex   example
  weightedmedian                    text    html    latex   example
  writefit                          text    html    latex
  zscore                            text    html    latex   example
** building package indices ...
* DONE (limma)
/usr/lib/R/library
* Installing *source* package 'ROC' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'ROC'
** Removing '/usr/lib/R/library/ROC'
/usr/lib/R/library
* Installing *source* package 'xtable' ...
** R
** data
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'xtable'
     Formats: text html latex example
  print.xtable                      text    html    latex
  string                            text    html    latex
  table.attributes                  text    html    latex
  tli                               text    html    latex
  xtable                            text    html    latex   example
** building package indices ...
* DONE (xtable)
/usr/lib/R/library
* Installing *source* package 'AnnotationDbi' ...
** R
** inst
** preparing package for lazy loading
Error: package 'Biobase' required by 'AnnotationDbi' could not be found
Execution halted
ERROR: lazy loading failed for package 'AnnotationDbi'
** Removing '/usr/lib/R/library/AnnotationDbi'
/usr/lib/R/library
* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... /lib/cpp
checking for main in -lz... no
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
chmod: cannot access `/usr/lib/R/library/affy/libs/*': No such file or directory
ERROR: compilation failed for package 'affy'
** Removing '/usr/lib/R/library/affy'
/usr/lib/R/library
* Installing *source* package 'marray' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: limma
** help
 >>> Building/Updating help pages for package 'marray'
     Formats: text html latex example
  boxplot                           text    html    latex   example
  bracketMethods                    text    html    latex
  cbind                             text    html    latex   example
  checkTargetInfo                   text    html    latex   example
  coerce-methods                    text    html    latex
  dim                               text    html    latex   example
  findID                            text    html    latex   example
  htmlPage                          text    html    latex   example
  image                             text    html    latex   example
  ma2D                              text    html    latex   example
  maBoxplot                         text    html    latex   example
Note: unmatched right brace in 'maColorBar' on or after line 10
  maColorBar                        text    html    latex   example
  maCompCoord                       text    html    latex   example
  maCompInd                         text    html    latex   example
  maCompLayout                      text    html    latex   example
  maCompNormA                       text    html    latex   example
  maCompPlate                       text    html    latex   example
  maCoord2Ind                       text    html    latex   example
  maDefaultPar                      text    html    latex   example
  maDotsDefaults                    text    html    latex   example
  maDotsMatch                       text    html    latex   example
  maGenControls                     text    html    latex   example
  maGeneTable                       text    html    latex   example
  maImage                           text    html    latex   example
  maImage.func                      text    html    latex   example
  maInd2Coord                       text    html    latex   example
  maLegendLines                     text    html    latex   example
Note: unmatched right brace in 'maLoess' on or after line 33
  maLoess                           text    html    latex   example
  maLoessLines                      text    html    latex   example
  maMAD                             text    html    latex   example
  maMed                             text    html    latex   example
  maNA                              text    html    latex
  maNorm                            text    html    latex   example
  maNorm2D                          text    html    latex   example
  maNormLoess                       text    html    latex   example
  maNormMAD                         text    html    latex   example
  maNormMain                        text    html    latex   example
  maNormMed                         text    html    latex   example
  maNormScale                       text    html    latex   example
  maNum2Logic                       text    html    latex   example
  maPalette                         text    html    latex   example
Note: unmatched right brace in 'maPlot' on or after line 27
  maPlot                            text    html    latex   example
  maPlot.func                       text    html    latex   example
  maSelectGnames                    text    html    latex   example
  maText                            text    html    latex   example
Note: unmatched right brace in 'maTop' on or after line 18
  maTop                             text    html    latex   example
  maTwoSamples                      text    html    latex
  mapGeneInfo                       text    html    latex   example
  marray-internal                   text    html    latex
  marrayInfo-class                  text    html    latex   example
  marrayLayout-class                text    html    latex   example
  marrayNorm-class                  text    html    latex   example
  marrayRaw-class                   text    html    latex   example
  opVersionID                       text    html    latex   example
Note: unmatched right brace in 'plotMA' on or after line 59
  plotMA                            text    html    latex   example
  print-methods                     text    html    latex
  read.Galfile                      text    html    latex   example
  read.marrayInfo                   text    html    latex   example
  read.marrayLayout                 text    html    latex   example
  read.marrayRaw                    text    html    latex   example
  rm.na                             text    html    latex   example
  showLargeObject                   text    html    latex   example
  stat.confband.text                text    html    latex   example
  stat.gnames                       text    html    latex   example
  swirl                             text    html    latex
  write.list                        text    html    latex   example
  write.marray                      text    html    latex   example
  write.xls                         text    html    latex   example
** building package indices ...
* DONE (marray)
/usr/lib/R/library
* Installing *source* package 'multtest' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'multtest'
** Removing '/usr/lib/R/library/multtest'
/usr/lib/R/library
* Installing *source* package 'affydata' ...
** R
** data
** inst
** help
 >>> Building/Updating help pages for package 'affydata'
     Formats: text html latex example
  Dilution                          text    html    latex
** building package indices ...
* DONE (affydata)
/usr/lib/R/library
* Installing *source* package 'annaffy' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
  there is no package called 'Biobase'
Error: package 'Biobase' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'annaffy'
** Removing '/usr/lib/R/library/annaffy'
/usr/lib/R/library
* Installing *source* package 'annotate' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
  there is no package called 'Biobase'
Error: package 'Biobase' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'annotate'
** Removing '/usr/lib/R/library/annotate'
/usr/lib/R/library
* Installing *source* package 'matchprobes' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'matchprobes'
** Removing '/usr/lib/R/library/matchprobes'
/usr/lib/R/library
* Installing *source* package 'vsn' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'vsn'
** Removing '/usr/lib/R/library/vsn'
/usr/lib/R/library
* Installing *source* package 'gcrma' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'gcrma'
** Removing '/usr/lib/R/library/gcrma'
/usr/lib/R/library
* Installing *source* package 'genefilter' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'genefilter'
** Removing '/usr/lib/R/library/genefilter'
/usr/lib/R/library
* Installing *source* package 'geneplotter' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: annotate
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
  there is no package called 'annotate'
Error: package 'annotate' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'geneplotter'
** Removing '/usr/lib/R/library/geneplotter'
/usr/lib/R/library
* Installing *source* package 'simpleaffy' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'simpleaffy'
** Removing '/usr/lib/R/library/simpleaffy'
/usr/lib/R/library
* Installing *source* package 'affyPLM' ...
** libs
/usr/lib/R/bin/SHLIB: line 161: make: command not found
ERROR: compilation failed for package 'affyPLM'
** Removing '/usr/lib/R/library/affyPLM'
/usr/lib/R/library
* Installing *source* package 'affyQCReport' ...
** R
** inst
** help
 >>> Building/Updating help pages for package 'affyQCReport'
     Formats: text html latex example
  QCReport                          text    html    latex   example
  affyQAReport                      text    html    latex   example
  borderQC1                         text    html    latex   example
  borderQC2                         text    html    latex   example
  correlationPlot                   text    html    latex   example
  signalDist                        text    html    latex   example
  titlePage                         text    html    latex   example
** building package indices ...
* DONE (affyQCReport)

The downloaded packages are in
        /tmp/RtmpTb1jyD/downloaded_packages
Updating HTML index of packages in '.Library'
There were 18 warnings (use warnings() to see them)

Code:
> warnings()
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'RSQLite' had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'affyio' had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'preprocessCore' had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'Biobase' had non-zero exit status
5: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'Biostrings' had non-zero exit status
6: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'ROC' had non-zero exit status
7: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'AnnotationDbi' had non-zero exit status
8: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'affy' had non-zero exit status
9: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'multtest' had non-zero exit status
10: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'annaffy' had non-zero exit status
11: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'annotate' had non-zero exit status
12: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'matchprobes' had non-zero exit status
13: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'vsn' had non-zero exit status
14: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'gcrma' had non-zero exit status
15: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'genefilter' had non-zero exit status
16: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'geneplotter' had non-zero exit status
17: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'simpleaffy' had non-zero exit status
18: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  ... :
  installation of package 'affyPLM' had non-zero exit status
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sciurius



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BerichtGeplaatst: Wo Dec 05, 2007 5:31 pm    Onderwerp: Reageren met citaat

Het lijkt erop dat je geen C-compiler en build-tools hebt geïnstalleerd.
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NikkiMassa



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BerichtGeplaatst: Vr Dec 07, 2007 11:55 am    Onderwerp: Reageren met citaat

Ik zie t staan:
Code:
checking for gcc... no
checking for cc... no
checking for cc... no
checking for cl... no
configure: error: no acceptable C compiler found in $PATH

Ik heb eerst C compiler gegoogled en kwam op deze website uit: http://www.mjmwired.net/resources/mjm-fedora-f8.html#compat.
Ik heb met yum gechecked wat er bij mij geinstalleerd is aan GCC:
Code:
[root@localhost nikki]# yum list *gcc*
Loading "priorities" plugin
0 packages excluded due to repository priority protections
Installed Packages
libgcc.i386                              4.1.2-33               installed
Available Packages
arm-gp2x-linux-gcc.i386                  4.1.2-7.fc8            fedora
arm-gp2x-linux-gcc-c++.i386              4.1.2-7.fc8            fedora
avr-gcc.i386                             4.1.2-5.fc8            fedora
avr-gcc-c++.i386                         4.1.2-5.fc8            fedora
compat-gcc-34.i386                       3.4.6-8                fedora
compat-gcc-34-c++.i386                   3.4.6-8                fedora
compat-gcc-34-g77.i386                   3.4.6-8                fedora
compat-libgcc-296.i386                   2.96-139               fedora
gcc.i386                                 4.1.2-33               fedora
gcc-c++.i386                             4.1.2-33               fedora
gcc-gfortran.i386                        4.1.2-33               fedora
gcc-gnat.i386                            4.1.2-33               fedora
gcc-java.i386                            4.1.2-33               fedora
gcc-objc.i386                            4.1.2-33               fedora
gcc-objc++.i386                          4.1.2-33               fedora


Heb ik nu wel een geinstalleerde compiler maar kan R er niet bij? Of heb ik het verkeerde voor ogen?

Dan build tools:
wat het zijn daar kan ik me wel iets bij voorstellen. Ook wel dat ze nodig zijn. Ook wel dat het commando 'make' er deel van uit maakt. Maar welke packages moeten er geinstalleerd zijn om de juiste build tools te heben?

Ik heb gezocht op make, ik print hier wat list er van zei maar heb ook gekeken met info. Ik print hier niet alles, ik bedoel, een package als WindowMaker, makehuman of perl-Class-MakeMethods is het zeker niet.
Code:
[root@localhost nikki]# yum list *make*
Loading "priorities" plugin
0 packages excluded due to repository priority protections
Installed Packages
MAKEDEV.i386                             3.23-1.2               installed
Available Packages
automake.noarch                          1.10-6                 fedora
automake14.noarch                        1.4p6-15.fc7           fedora
automake15.noarch                        1.5-22                 fedora
automake16.noarch                        1.6.3-14               fedora
automake17.noarch                        1.7.9-11               fedora
cmake.i386                               2.4.7-3.fc8            fedora
gnustep-make.i386                        1.12.0-5.fc6           fedora
imake.i386                               1.0.2-5.fc8            fedora
kadu-wmaker_docking.i386                 0.5.0-4.fc8            fedora
make.i386                                1:3.81-10.fc8          fedora
texmaker.i386                            1:1.6-3.fc8            fedora

Moet ik misschien gnustep-make.i368 of make.i368 hebben?
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Gul Dukat



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BerichtGeplaatst: Vr Dec 07, 2007 12:59 pm    Onderwerp: Reageren met citaat

Installeer het volgende eens en probeer het dan nogmaals:
Code:

yum groupinstall "Development Tools"

en
Code:

yum install kernel-devel
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NikkiMassa



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BerichtGeplaatst: Vr Dec 07, 2007 3:35 pm    Onderwerp: Reageren met citaat

Nou,
Code:
su-
yum groupinstall "Development Tools"
yum install kernel-devel

uitgevoerd, vervolgens:
Code:
R
source("http://www.bioconductor.org/biocLite.R")
biocLite()

waarna er een hoop lettertjes op mijn beeldscherm verschenen,
Code:
install.packages(c("multtest"),repo="http://cran.r-project.org",dep=TRUE)

is uiteindelijk afgelopen met een vrolijk "Done!".
Ik heb het gecheckt, ik kan de package "multtest" nu gewoon gebruiken. Probleem opgelost.

Dus, grote dank sciurius en Gul Dukat!
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Gul Dukat



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BerichtGeplaatst: Vr Dec 07, 2007 3:47 pm    Onderwerp: Reageren met citaat

Graag gedaan. Smile
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