Hi,
I am working on "Microarray Data analysis" using R programming. I need to do
some Gene Ontology and Pathway analysis of the extracted genelist.
For the same i am trying to download some Packages like -
> goTools, topGO for Gene Ontology.
> sigPathway for Pathway analysis.

But unfortunately i am not able to download them successfully, All the time
i am trying, I am getting a "lazy loading failed error!". And this is the
error same for
all the packages which i am trying to download.

Every time am down loading, some portion of the package is getting
downloaded but after some time the downloaded packages gets stored in to a
temp. file
and the downloading is terminated with a lazy loading error!

> source("http://bioconductor.org/biocLite.R")
> biocLite("sigPathway", dependencies=TRUE)

Running biocinstall version 2.3.14 with R version 2.8.1
Your version of R requires version 2.3 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  argument 'lib' is missing: using
'/home/veerendra/R/i486-pc-linux-gnu-library/2.8'
also installing the dependencies ‘hgu95av2.db’, ‘GO.db’, ‘hgu133a.db’,
‘XML’, ‘AnnotationDbi’

trying URL '
http://bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu95av2.db_2.2.5.tar.gz
'
Content type 'application/x-gzip' length 14191802 bytes (13.5 Mb)
opened URL
==================================================
downloaded 13.5 Mb

trying URL '
http://bioconductor.org/packages/2.3/data/annotation/src/contrib/GO.db_2.2.5.tar.gz
'
Content type 'application/x-gzip' length 12812568 bytes (12.2 Mb)
opened URL
==================================================
downloaded 12.2 Mb

trying URL '
http://bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu133a.db_2.2.5.tar.gz
'
Content type 'application/x-gzip' length 17991647 bytes (17.2 Mb)
opened URL
======================================
 downloaded 761 Kb

trying URL '
http://bioconductor.org/packages/2.3/bioc/src/contrib/AnnotationDbi_1.4.3.tar.gz
'
Content type 'application/x-gzip' length 625680 bytes (611 Kb)
opened URL
==================================================
downloaded 611 Kb

trying URL '
http://bioconductor.org/packages/2.3/bioc/src/contrib/sigPathway_1.10.0.tar.gz
'
Content type 'application/x-gzip' length 968137 bytes (945 Kb)
opened URL
==================================================
downloaded 945 Kb

* Installing *source* package 'XML' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package 'XML'
** Removing '/home/veerendra/R/i486-pc-linux-gnu-library/2.8/XML'
* Installing *source* package 'AnnotationDbi' ...
** R
** inst
** preparing package 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)'.

Error in loadNamespace(i, c(lib.loc, .libPaths())) :
  there is no package called 'RSQLite'
Calls: <Anonymous> ... code2LazyLoadDB -> loadNamespace -> namespaceImport
-> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'AnnotationDbi'
** Removing '/home/veerendra/R/i486-pc-linux-gnu-library/2.8/AnnotationDbi'
* Installing *source* package 'sigPathway' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c
calc_gene_set_internal.c -o calc_gene_set_internal.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c
calc_gene_set_stat.c -o calc_gene_set_stat.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c
calc_probe_stat.c -o calc_probe_stat.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c calc_weights.c
-o calc_weights.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c matrix_fn.c -o
matrix_fn.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c permute.c -o
permute.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c shuffle.c -o
shuffle.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c sigPathway.c -o
sigPathway.o
gcc -std=gnu99 -shared  -o sigPathway.so calc_gene_set_internal.o
calc_gene_set_stat.o calc_probe_stat.o calc_weights.o matrix_fn.o permute.o
shuffle.o sigPathway.o -llapack -lblas -lgfortran -lm  -L/usr/lib/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'sigPathway'
     Formats: text html latex example
  MuscleExample                     text    html    latex
  calcTNullFast                     text    html    latex
  calcTStatFast                     text    html    latex   example
  calculate.GSEA                    text    html    latex
  calculate.NGSk                    text    html    latex   example
  calculatePathwayStatistics        text    html    latex   example
  estimateNumPerm                   text    html    latex   example
  getPathwayStatistics.NGSk         text    html    latex
  getPathwayStatistics              text    html    latex
  importGeneSets                    text    html    latex
  rankPathways.NGSk                 text    html    latex
  rankPathways                      text    html    latex
  runSigPathway                     text    html    latex   example
  selectGeneSets                    text    html    latex
  writeSigPathway                   text    html    latex
** building package indices ...
* DONE (sigPathway)
* Installing *source* package 'hgu95av2.db' ...
** R
** inst
** preparing package for lazy loading
Error: package 'AnnotationDbi' required by 'hgu95av2.db' could not be found
Execution halted
ERROR: lazy loading failed for package 'hgu95av2.db'
** Removing '/home/veerendra/R/i486-pc-linux-gnu-library/2.8/hgu95av2.db'
* Installing *source* package 'GO.db' ...
** R
** inst
** preparing package for lazy loading
Error: package 'AnnotationDbi' required by 'GO.db' could not be found
Execution halted
ERROR: lazy loading failed for package 'GO.db'
** Removing '/home/veerendra/R/i486-pc-linux-gnu-library/2.8/GO.db'
* Installing *source* package 'hgu133a.db' ...
** R
** inst
** preparing package for lazy loading
Error: package 'AnnotationDbi' required by 'hgu133a.db' could not be found
Execution halted
ERROR: lazy loading failed for package 'hgu133a.db'
** Removing '/home/veerendra/R/i486-pc-linux-gnu-library/2.8/hgu133a.db'

The downloaded packages are in
    /tmp/Rtmpnf0fC4/downloaded_packages
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  dependency ‘RSQLite’ is not available
2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'XML' had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'AnnotationDbi' had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'hgu95av2.db' had non-zero exit status
5: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'GO.db' had non-zero exit status
6: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'hgu133a.db' had non-zero exit status

Is there any solution for this problem. if its there then please help me
out, As i am facing this problem from last two weeks!.

thank you!

-- 
Veerendra.

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