Package: GGtools

Version: 1.5.0

Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD build GGtools

RetCode: 1

Time: 42.4 seconds

Status: ERROR

PackageFile: None

* checking for file 'GGtools/DESCRIPTION' ... OK
* preparing 'GGtools':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
installing R.css in D:/biocbld/bbs-2.1-bioc/tmpdir/Rinst657646411


---------- Making package GGtools ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making minfra.d from minfra.cc
g++   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O2   -c minfra.cc -o minfra.o
minfra.cc: In function `matrix operator/(matrix&, matrix&)':
minfra.cc:459: warning: unused variable 'a2c'
minfra.cc: In function `matrix delete_col(matrix, int)':
minfra.cc:545: warning: unused variable 'ncop'
minfra.cc:545: warning: unused variable 'nresel'
minfra.cc:545: warning: unused variable 'skip'
minfra.cc:546: warning: unused variable 'resbase'
minfra.cc:546: warning: unused variable 'Xbase'
minfra.cc: In function `int split(matrix&, matrix&, matrix*)':
minfra.cc:1210: warning: unused variable 'j'
minfra.cc: In function `matrix* split(matrix&, matrix&)':
minfra.cc:1245: warning: unused variable 'j'
windres -I d:/biocbld/bbs-2.1-bioc/R/include  -i GGtools_res.rc -o GGtools_res.o
g++  -shared -s  -o GGtools.dll GGtools.def minfra.o GGtools_res.o  -Ld:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
Loading required package: methods
Warning: 'chr20meta' looks like a pre-2.4.0 S4 object: please recreate it
  not zipping data
  installing help
Note: unmatched right brace in 'snpMeta-class' on or after line 44
Note: unmatched right brace in 'snpMeta-class.Rd' on or after line 44
 >>> Building/Updating help pages for package 'GGtools'
     Formats: text html latex example chm 
  HM2rac                            text    html    latex   example chm
  HMworkflow                        text    html    latex   example chm
  Strains2rac                       text    html    latex   example chm
  geneLocs                          text    html    latex   example chm
  genoStrings                       text    html    latex   example chm
  make_racExSet                     text    html    latex   example chm
  oGtypeExSet-class                 text    html    latex   example chm
     missing link(s):  ExpressionSet-class eSet-class VersionedBiobase-class Versioned-class
  plot_EvG                          text    html    latex   example chm
  racExSet-class                    text    html    latex   example chm
  snpMeta-class                     text    html    latex   example chm
  snpScreen                         text    html    latex   example chm
  snps                              text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702



Compiling d:\biocbld\bbs-2.1-bioc\meat\GGtools\chm\GGtools.chm





Compile time: 0 minutes, 0 seconds

13	Topics

110	Local links

0	Internet links

1	Graphic





Created d:\biocbld\bbs-2.1-bioc\meat\GGtools\chm\GGtools.chm, 37,856 bytes

Compression decreased file by 39,087 bytes.

  preparing package GGtools for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: hgfocus
Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: mgu74av2
  adding MD5 sums

* DONE (GGtools)
* creating vignettes ... ERROR
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: hgfocus
Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: mgu74av2

Error: processing vignette 'GGoverview.Rnw' failed with diagnostics:
 chunk 3 (label=lksmeta) 
Error in chr20meta[1:4, ] : incorrect number of dimensions
In addition: Warning message:
'chr20meta' looks like a pre-2.4.0 S4 object: please recreate it 
Execution halted