I am working through the DESeq2 workflow/tutorial on my own data and everything so far has loaded and run fine. However when I try to install package "org.Hs.eg.db". I get the error below

Appreciate any help as I cannot proceed until this is sorted. :-\

Sue

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
> biocLite("org.Hs.eg.db")
Error: 'no packages in repository (no internet connection?)' while trying http://bioconductor.org/packages/3.1/bioc

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252    LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C                   
[5] LC_TIME=Swedish_Sweden.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocInstaller_1.18.4      AnnotationDbi_1.30.1      Biobase_2.28.0            pheatmap_1.0.7            genefilter_1.50.0        
 [6] PoiClaClu_1.0.2           ggplot2_1.0.1             DESeq2_1.8.1              RcppArmadillo_0.5.500.2.0 Rcpp_0.12.1              
[11] GenomicRanges_1.20.6      GenomeInfoDb_1.4.2        IRanges_2.2.7             S4Vectors_0.6.5           BiocGenerics_0.14.0      

loaded via a namespace (and not attached):
 [1] DBI_0.3.1            Formula_1.2-1        geneplotter_1.46.0   futile.options_1.0.0 RSQLite_1.0.0        lattice_0.20-33     
 [7] foreign_0.8-66       stringr_1.0.0        xtable_1.7-4         labeling_0.3         gridExtra_2.0.0      plyr_1.8.3          
[13] tools_3.2.2          MASS_7.3-44          BiocParallel_1.2.21  annotate_1.46.1      lambda.r_1.1.7       XVector_0.8.0       
[19] futile.logger_1.4.1  scales_0.3.0         nnet_7.3-11          digest_0.6.8         gtable_0.1.2         latticeExtra_0.6-26 
[25] stringi_0.5-5        cluster_2.0.3        reshape2_1.4.1       XML_3.98-1.3         rpart_4.1-10         munsell_0.4.2       
[31] grid_3.2.2           colorspace_1.2-6     magrittr_1.5         Hmisc_3.16-0         splines_3.2.2        survival_2.38-3     
[37] proto_0.3-10         RColorBrewer_1.1-2   acepack_1.3-3.3      locfit_1.5-9.1      

Tried that and returns:

> install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.1/bioc")
Warning in install.packages :
  package ‘org.Hs.eg.db’ is not available (for R version 3.2.2)

Am I correct in thinking then that I need to use an older version of R?

Sue

Still not able to load using both R 3.2.0 and R 3.1.2.

After talking to a colleague now suspect we have some sort of firewall here to prevent database access (Pharma Organisation)- would that explain this error?

Dan are you saying that the below should work instead?

> install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.2/data/annotation")

When I use it it throws up all sorts of errors and AnnotationDbi disappears.

It also freezes RStudio!!

Time to give up I think

Thanks anyway everyone.

Thanks for sticking with it Dan. Not sure which step worked but it appears to have loaded now. It may have been the above command you suggested although it had appeared to download with other but in the wrong location (complicated by using projects in RStudio with different working directory). 

Anyway I will not know for sure until I run the data but fingers crossed

Sue

Hello!

 I have the same problem. i tried this > install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.2/data/annotation")

It seemed worked.

Then I tried:

library(org.Hs.eg.db)
Loading required package: DBI
Error in unloadNamespace(package) : 
  namespace ‘DBI’ is imported by ‘RSQLite’, ‘AnnotationDbi’ so cannot be unloaded
In addition: Warning message:
package ‘DBI’ was built under R version 3.2.5 
Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, 
  error: Package ‘DBI’ version 0.3.1 cannot be unloaded
Error: package or namespace load failed for ‘org.Hs.eg.db

So, it seems that it cannot load the package .

Does anybody use this package under R 3.2.2?

Thank you,

 Irina.