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Question: Can't load package "org.Hs.eg.db"
2
gravatar for sjmonkley
2.2 years ago by
sjmonkley20
Sweden
sjmonkley20 wrote:

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      

ADD COMMENTlink modified 17 months ago by iankoudinova10 • written 2.2 years ago by sjmonkley20

First off I would just try again in case it was a temporary network issue.

Second of all, what's the output of

library(BiocInstaller)
biocinstallRepos()

?

ADD REPLYlink written 2.2 years ago by Dan Tenenbaum ♦♦ 8.2k

It is still not loading.

output of 

> library(BiocInstaller)
> biocinstallRepos()
                                              BioCsoft                                                BioCann 
           "http://bioconductor.org/packages/3.1/bioc" "http://bioconductor.org/packages/3.1/data/annotation
                                               BioCexp                                              BioCextra 
"http://bioconductor.org/packages/3.1/data/experiment"           "http://bioconductor.org/packages/3.1/extra
                                                  CRAN                                              CRANextra 
                             "http://cran.rstudio.com"                   "http://www.stats.ox.ac.uk/pub/RWin

Sue

ADD REPLYlink written 2.1 years ago by sjmonkley20

OK, can you try

install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.1/bioc")

Does that work?

And can you tell us where you are located? 

 

ADD REPLYlink written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for sjmonkley
2.1 years ago by
sjmonkley20
Sweden
sjmonkley20 wrote:

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

ADD COMMENTlink written 2.1 years ago by sjmonkley20
1

For R 3.2 you may have to use a different url:

install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.2/bioc")
ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by dalloliogm40

Same response as previous. I am going to try and earlier version of R

 

ADD REPLYlink written 2.1 years ago by sjmonkley20
0
gravatar for sjmonkley
2.1 years ago by
sjmonkley20
Sweden
sjmonkley20 wrote:

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?

ADD COMMENTlink written 2.1 years ago by sjmonkley20

the firewall is probably the cause, because the same URLs work for me. You can try a ping http://bioconductor.org/packages/3.1/bioc to see it the connection is blocked. Talk to your IT.

ADD REPLYlink written 2.1 years ago by dalloliogm40

I am not sure that is quite it. It is only the 'org.Hs.eg.db' package that is the problem. Others load fine.(eg DESeq2, SeqGSEA).

I am wondering if  'org.Hs.eg.db' involves access to a Hs gene annotation database and that is the issue.

Sue

ADD REPLYlink written 2.1 years ago by sjmonkley20
1

No, there is nothing special about it but it does have a slightly different url path (contains /data/annotation/ instead of /bioc/) so if your system administrators have authorized certain URLs on the firewall and not others that could be an issue.

Yes, the firewall could definitely be an issue.

No, you do not need to install an older version of R. org.Hs.eg.db is still available for the most recent version.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for sjmonkley
2.1 years ago by
sjmonkley20
Sweden
sjmonkley20 wrote:

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.

ADD COMMENTlink written 2.1 years ago by sjmonkley20
1

No, I would say try

install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.1/data/annotation")

 

Since you are using Bioconductor 3.1 not 3.2.

Does that work? It would help to see all the errors you are getting.

 

ADD REPLYlink written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for sjmonkley
2.1 years ago by
sjmonkley20
Sweden
sjmonkley20 wrote:

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

ADD COMMENTlink written 2.1 years ago by sjmonkley20
0
gravatar for iankoudinova
17 months ago by
iankoudinova10
iankoudinova10 wrote:

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.

ADD COMMENTlink written 17 months ago by iankoudinova10

Actually this is not the same problem. The original poster's problem had to to with firewalls and installing the package. You are able to install it but not load it. 

As a side note, you should use biocLite() to install Bioconductor packages, then you won't have to worry about getting the wrong version of packages.

But I don't know exactly what the problem is here. Can you send the output of sessionInfo() after you attempt to load org.Hs.eg.db?

 

ADD REPLYlink written 17 months ago by Dan Tenenbaum ♦♦ 8.2k

here sessionInfo():

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] org.Hs.eg.db_3.2.3   RSQLite_1.0.0        DBI_0.4-1            AnnotationDbi_1.32.3 Biobase_2.30.0       GenomicRanges_1.22.4 GenomeInfoDb_1.6.3   IRanges_2.4.8        S4Vectors_0.8.11    
[10] BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
[1] zlibbioc_1.16.0 XVector_0.10.0  tools_3.2.2    

I run biocLite() and not the loading works.

 Thank you very much

ADD REPLYlink written 17 months ago by iankoudinova10
1

I am sorry.

I meant: "The package is loaded now."

Thank you

ADD REPLYlink written 17 months ago by iankoudinova10

So do you mean the problem is solved? If so I will mark this thread as answered.

ADD REPLYlink written 17 months ago by Dan Tenenbaum ♦♦ 8.2k
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