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Question: Gage package; go.gset() function error: argument "go_id" is missing
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gravatar for Miskey, Csaba
4 months ago by
Germany
Miskey, Csaba20 wrote:

Dear All,

The go.gsets function of gage send the following error:

 go.hs <- go.gsets(species="human")

Gene ID type for 'human' is: 'EG'
Error in initialize(value, ...) :
  argument "go_id" is missing, with no default

Where should the 'go_id' argument be specified?

kg.hsa <- kegg.gsets(species = "hsa", id.type = "kegg")

runs without an error.

Many thanks!
Csaba

>sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] gageData_2.14.0      GO.db_3.4.1          org.Hs.eg.db_3.4.1   AnnotationDbi_1.38.2 IRanges_2.10.5      
 [6] S4Vectors_0.14.7     Biobase_2.36.2       BiocGenerics_0.22.1  BiocInstaller_1.26.1 gage_2.26.3         

loaded via a namespace (and not attached):
 [1] graph_1.54.0      Rcpp_0.12.16      XVector_0.16.0    zlibbioc_1.22.0   bit_1.1-12        R6_2.2.2         
 [7] blob_1.1.1        httr_1.3.1        tools_3.4.4       png_0.1-7         DBI_1.0.0         bit64_0.9-7      
[13] digest_0.6.15     curl_2.8.1        KEGGREST_1.16.1   memoise_1.1.0     RSQLite_2.1.1     compiler_3.4.4   
[19] Biostrings_2.44.2 pkgconfig_2.0.1 

ADD COMMENTlink modified 4 months ago by James W. MacDonald47k • written 4 months ago by Miskey, Csaba20
3
gravatar for James W. MacDonald
4 months ago by
United States
James W. MacDonald47k wrote:

The version of R/Bioconductor you are using is old and no longer supported. This function works for me in a current install. If you still have a problem after upgrading, please let us know.

> z <- go.gsets()
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
    colnames, colSums, dirname, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Gene ID type for 'human' is: 'EG'

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

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

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

other attached packages:
[1] GO.db_3.6.0          org.Hs.eg.db_3.6.0   AnnotationDbi_1.42.0
[4] IRanges_2.14.1       S4Vectors_0.18.1     Biobase_2.40.0      
[7] BiocGenerics_0.26.0  gage_2.30.0          BiocInstaller_1.30.0

loaded via a namespace (and not attached):
 [1] graph_1.58.0      Rcpp_0.12.16      XVector_0.20.0    zlibbioc_1.26.0  
 [5] bit_1.1-12        R6_2.2.2          blob_1.1.1        httr_1.3.1       
 [9] tools_3.5.0       png_0.1-7         DBI_1.0.0         bit64_0.9-7      
[13] digest_0.6.15     KEGGREST_1.20.0   memoise_1.1.0     RSQLite_2.1.0    
[17] compiler_3.5.0    Biostrings_2.48.0 pkgconfig_2.0.1 
ADD COMMENTlink written 4 months ago by James W. MacDonald47k

I should have checked. Many thanks!
 

ADD REPLYlink written 4 months ago by Miskey, Csaba20

Hi James,

I wanted upgrade, but BiocInstaller 1.3 needs R >= 3.5.0

source("https://bioconductor.org/biocLite.R")

"Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install"

However, R 3.5 is not yet available for Ubuntu 14.04 LTS.

Can you suggest a workaround? Or, all I can do is wait?

Thanks!

ADD REPLYlink modified 3 months ago • written 3 months ago by Miskey, Csaba20
1

There are two main ways of installing R on a Ubuntu box. You can use a package installer like apt, or you can install from source. There are compelling arguments for using package installers for most software on Linux, due to the fact that you automatically get all necessary dependencies automatically.

I have never found this to be true for R however. I use a Debian Jessie box at work, and although I do know there are deb packages for this OS, not having sudo privileges, I find the deb packages to be less useful. I just get the sources from CRAN and compile myself. During compilation I specify a prefix dir where I have write access, and just install there. It's like three lines of code:

./configure --prefix=/data/oldR/R-3.5.0 -with-tcl-config=/usr/lib/x86_64-linux-gnu/tcl8.5/tclConfig.sh --with-tk-config=/usr/lib/x86_64-linux-gnu/tk8.5/tkConfig.sh --enable-R-shlib

make

make install

I have to include the tcl and tk config scripts for some reason that is lost to me now, as well as building a shared libR. You may or may not need to do that, and prior to this Jessie box I never did. But now I have complete control over my R installation, instead of having to rely on Dirk Eddelbuettel and friends to build the deb packages for me or my sysadmin to install the new version.

And I have many versions of R, which is nice for me, because I may need to re-run some old code for a client and they might not want anything to change (which is inevitable if you use a different version of R/BioC):

$ ls /data/oldR | sed 's/\t/\n/g'
R-2.15.1
R-3.0.0
R-3.0.1
R-3.0.2
R-3.1.0
R-3.1.1
R-3.2.0
R-3.2.1
R-3.2.2
R-3.2.3
R-3.3.0
R-3.3.1
R-3.4.0
R-3.4.2
R-3.5.0
R-devel

 

ADD REPLYlink written 3 months ago by James W. MacDonald47k
1

And with all those old versions of R I have symlinks, so e.g.,

R-2.15.1

will start that R version.

ADD REPLYlink written 3 months ago by James W. MacDonald47k

Great!

Many thanks, James!

ADD REPLYlink written 3 months ago by Miskey, Csaba20

This is what worked for me to compile R 3.5.0 from source to my home on Ubuntu 14.04.5 LTS:

./configure CFLAGS=-fPIC CXXFLAGS=-fPIC --enable-shared --prefix=/home/miscs/R/Rversions/3.5.0 --enable-R-shlib  --with-blas --with-lapack  --with-tcktk

 

ADD REPLYlink written 3 months ago by Miskey, Csaba20
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