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Package 75/208OSArchBUILDCHECKBUILD BIN

GEOquery

1.9.0

Sean Davis
Linux (SUSE 9.2) x86_64 OK  OK 
Linux (SUSE 10.1) x86_64 OK  OK 
Linux (SUSE 9.2) i686 OK  OK 
Solaris 2.9 sparc OK  OK 
Windows Server 2003 x86_64 OK  OK  OK 
Windows Server 2003 NA[ ERROR ]skippedskipped
Mac OS X (10.4.6) i686 OK  OK 
Package: GEOquery
Version: 1.9.0
Command: E:\biocbld\2.0d\R\bin\R.exe CMD build GEOquery
RetCode: 1
Time: 42.5 seconds
Status: ERROR
PackageFile: None

Command output

* checking for file 'GEOquery/DESCRIPTION' ... OK
* preparing 'GEOquery':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
installing R.css in E:/biocbld/2.0d/tmpdir/Rinst390886138


---------- Making package GEOquery ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'GEOquery'
     Formats: text html latex example chm 
  GDS-class                         text    html    latex           chm
  GDS2MA                            text    html    latex   example chm
  GEOData-class                     text    html    latex           chm
  GEODataTable-class                text    html    latex           chm
  GPL-class                         text    html    latex           chm
  GSE-class                         text    html    latex           chm
  GSM-class                         text    html    latex           chm
  dataTable                         text    html    latex           chm
  getGEO                            text    html    latex   example chm
  getGEOfile                        text    html    latex   example chm
  parseGEO                          text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702



Compiling e:\biocbld\2.0d\Rpacks\GEOquery\chm\GEOquery.chm





Compile time: 0 minutes, 0 seconds

12	Topics

61	Local links

1	Internet link

1	Graphic





Created e:\biocbld\2.0d\Rpacks\GEOquery\chm\GEOquery.chm, 28,919 bytes

Compression decreased file by 11,240 bytes.

  adding MD5 sums

* DONE (GEOquery)
* creating vignettes ... ERROR
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1.soft.gz'
ftp data connection made, file length 162380 bytes
opened URL
downloaded 158Kb

trying URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GSM3&form=text&view=full'
Content type 'geo/text' length unknown
opened URL
downloaded 213Kb

trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE462/GSE462_family.soft.gz'
ftp data connection made, file length 550629 bytes
opened URL
downloaded 537Kb

Loading required package: Biobase

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

trying URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL5&form=text&view=full'
Content type 'geo/text' length unknown
opened URL
downloaded 418Kb

Loading required package: limma
entering extended mode
pdflatex.EXE: Windows API error 5: Access is denied.

texify: pdflatex failed for some reason (see log file).
Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet = quiet) : 
	running texi2dvi on 'GEOquery.tex' failed
In addition: There were 23 warnings (use warnings() to see them)
Execution halted