Question

Error during installation packages

0

Entering edit mode

Elodie Chapeaublanc ▴ 70

@elodie-chapeaublanc-4525

Last seen 10.2 years ago

Dear list, I try to install BrainArray EntrezGene version 12.1 packages (build genome version hg18) for U95av2 on U133Plus2 affymetrix arrays, but I have got two errors. I have got the lastest version of R and Bioconductor : sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] BiocInstaller_1.12.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0 [7] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] IRanges_1.20.6 stats4_3.0.2 tools_3.0.2 When I try to install R CMD INSTALL hgu95av2hsentrezg.db_12.1.0.tar.gz, I have got error message : * installing to library ?/home/echapeaublanc/R/x86_64-pc-linux-gnu-library/3.0? * installing *source* package ?hgu95av2hsentrezg.db? ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'hgu95av2hsentrezg.db', details: call: checkDBSCHEMA(dbconn, schema) error: invalid DB schema version (found 2.0, expected 2.1) Erreur : le chargement a ?chou? Ex?cution arr?t?e ERROR: loading failed * removing ?/home/echapeaublanc/R/x86_64-pc-linux-gnu- library/3.0/hgu95av2hsentrezg.db? For the cdf pacakges : R CMD INSTALL hgu95av2hsentrezgcdf_12.1.0.tar.gz * installing to library ?/home/echapeaublanc/R/x86_64-pc-linux-gnu-library/3.0? * installing *source* package ?hgu95av2hsentrezgcdf? ... ERROR: a 'NAMESPACE' file is required * removing ?/home/echapeaublanc/R/x86_64-pc-linux-gnu- library/3.0/hgu95av2hsentrezgcdf? How can I use the old BrainArray packages ? Thanks Elodie -- -- Elodie Chapeaublanc IE Bioinformatique ?quipe Oncologie Mol?culaire Institut Curie - UMR 144 - CNRS 26 rue d'Ulm - 75248 Paris Cedex 05 Tel: +33 1 56 24 63 57 Email: elodie.chapeaublanc at curie.fr

cdf cdf • 1.6k views

ADD COMMENT • link updated 10.8 years ago by James W. MacDonald 67k • written 10.8 years ago by Elodie Chapeaublanc ▴ 70

score 0 · Answer 1 · 2014-01-30

Hi Elodie, On 1/30/2014 7:44 AM, Elodie Chapeaublanc wrote: > > Dear list, > > I try to install BrainArray EntrezGene version 12.1 packages (build > genome version hg18) for U95av2 on U133Plus2 affymetrix arrays, but I > have got two errors. > > I have got the lastest version of R and Bioconductor : > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C > [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 > [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 > [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] BiocInstaller_1.12.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 > [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0 > [7] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] IRanges_1.20.6 stats4_3.0.2 tools_3.0.2 > > > When I try to install R CMD INSTALL hgu95av2hsentrezg.db_12.1.0.tar.gz, > I have got error message : > > * installing to library > ?/home/echapeaublanc/R/x86_64-pc-linux-gnu-library/3.0? > * installing *source* package ?hgu95av2hsentrezg.db? ... > ** R > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > Error : .onLoad failed in loadNamespace() for 'hgu95av2hsentrezg.db', > details: > call: checkDBSCHEMA(dbconn, schema) > error: invalid DB schema version (found 2.0, expected 2.1) > Erreur : le chargement a ?chou? > Ex?cution arr?t?e > ERROR: loading failed > * removing > ?/home/echapeaublanc/R/x86_64-pc-linux-gnu- library/3.0/hgu95av2hsentrezg.db? > > > > For the cdf pacakges : R CMD INSTALL hgu95av2hsentrezgcdf_12.1.0.tar.gz > * installing to library > ?/home/echapeaublanc/R/x86_64-pc-linux-gnu-library/3.0? > * installing *source* package ?hgu95av2hsentrezgcdf? ... > ERROR: a 'NAMESPACE' file is required > * removing > ?/home/echapeaublanc/R/x86_64-pc-linux-gnu- library/3.0/hgu95av2hsentrezgcdf? > > > How can I use the old BrainArray packages ? By installing the correct version of R. On the page where you downloaded the cdf it says: *Version 12 (Data Sources <http: brainarray.mbni.med.umich.edu="" brainarray="" database="" customcdf="" 12="" .1.0="" version.html="">)* On Dec 2, 2009, version 12.0.0 is upgraded to 12.1.0 in order to be compatible with R 2.10 and Bioc 2.5 So you need R-2.10, after which you can simply use biocLite() to install. Best, Jim > > Thanks > > Elodie > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099