Package: beadarray

Version: 1.0.0

Command: /loc/biocbuild/1.8d/R/bin/R CMD check beadarray_1.0.0.tar.gz

RetCode: 0

Time: 232.2 seconds

Status: OK

CheckDir: beadarray.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.8d/Rpacks/beadarray.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '1.0.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'beadarray' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* creating beadarray-Ex.R ... OK
* checking examples ... OK
* creating beadarray-manual.tex ... OK
* checking beadarray-manual.tex ... OK

* Installing *source* package 'beadarray' ...
** libs
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc -shared -L/usr/local/lib64 -o beadarray.so findProbeIndices.o   
** R
** data
** inst
** preparing package for lazy loading
Loading required package: limma
Loading required package: pixmap
** help
There were 29 warnings (use warnings() to see them)
 >>> Building/Updating help pages for package 'beadarray'
     Formats: text html latex example 
  BLData                            text    html    latex
  BSData                            text    html    latex
  BeadLevelList                     text    html    latex
  BeadSummaryList                   text    html    latex
  LargeDataObject                   text    html    latex   example
  backgroundCorrectBeads            text    html    latex   example
  biotin_controls                   text    html    latex
  cbind                             text    html    latex
  checkRandomness                   text    html    latex   example
  createBeadSummaryData             text    html    latex   example
  cy3_controls                      text    html    latex
  dim                               text    html    latex
  dimnames                          text    html    latex
  displayTIFFImage                  text    html    latex   example
  findAllOutliers                   text    html    latex   example
  findBeadStatus                    text    html    latex   example
  findHighestChis                   text    html    latex   example
  findHighestSD                     text    html    latex   example
  findLowestCounts                  text    html    latex   example
  findMostOutliers                  text    html    latex   example
  getDimensions                     text    html    latex   example
  getMeanIntensities                text    html    latex   example
  getProbeCoords                    text    html    latex   example
  getProbeIDs                       text    html    latex   example
  getProbeInfo                      text    html    latex
  getProbeIntensities               text    html    latex   example
  getUnregisteredBeads              text    html    latex   example
  histBeadCounts                    text    html    latex   example
  housekeeping_controls             text    html    latex
  hs_controls                       text    html    latex
  labelling_controls                text    html    latex
  ls_controls                       text    html    latex
  matrix.mean                       text    html    latex
  medianNormalise                   text    html    latex   example
  neg_controls                      text    html    latex
  other_controls                    text    html    latex
  pairwiseMA                        text    html    latex   example
  plotArray                         text    html    latex
  plotBeadIntensities               text    html    latex   example
  plotBeadLocations                 text    html    latex   example
  plotCluster                       text    html    latex
  plotDistances                     text    html    latex   example
  plotMA.beads                      text    html    latex
  plotMAXY                          text    html    latex   example
  plotOnSAM                         text    html    latex
  plotProbeDistances                text    html    latex   example
  plotProbeVariation                text    html    latex
  plotXY.beads                      text    html    latex
  probeDiagnostics                  text    html    latex   example
  qsplineNormalise                  text    html    latex   example
  quantileNormalise                 text    html    latex   example
  readBeadImages                    text    html    latex   example
  readBeadSummaryData               text    html    latex   example
  readBeadSummaryTargets            text    html    latex   example
  readBeadTargets                   text    html    latex   example
  readNonXYData                     text    html    latex   example
  readProbeInfo                     text    html    latex
  removeArrays                      text    html    latex   example
  subsetting                        text    html    latex
** building package indices ...
* DONE (beadarray)