Question: GOstats install Error : .onLoad failed in loadNamespace() for 'GO.db'
0
gravatar for crafy
22 months ago by
crafy0
crafy0 wrote:

Hi,  I installed GOstats in my R, but got the
following error when trying to load it:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite("GOstats")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
Installing package(s) ‘GOstats’
试开URL’https://bioconductor.org/packages/3.6/bioc/src/contrib/GOstats_2.44.0.tar.gz'
Content type 'application/x-gzip' length 3059148 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

* installing *source* package ‘GOstats’ ...
** R
** data
** inst
** preparing package for lazy loading
Error : .onLoad failed in loadNamespace() for 'GO.db', details:
  call: NULL
  error: C stack usage  7969392 is too close to the limit
ERROR: lazy loading failed for package ‘GOstats’
* removing ‘/home/xuye/R/x86_64-pc-linux-gnu-library/3.4/GOstats’

The downloaded source packages are in
    ‘/tmp/Rtmpn3Obzu/downloaded_packages’
installation path not writeable, unable to update packages: boot, class,
  cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme,
  nnet, rpart, spatial, survival
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GOstats’ had non-zero exit status


> packageVersion("GO.db")
[1] ‘3.5.0’

> library("GO.db")
载入需要的程辑包:AnnotationDbi
载入需要的程辑包:stats4
载入需要的程辑包:BiocGenerics
载入需要的程辑包:parallel

载入程辑包:‘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, cbind, colMeans, colnames,
    colSums, 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

载入需要的程辑包:Biobase
Welcome to Bioconductor

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

载入需要的程辑包:IRanges
载入需要的程辑包:S4Vectors

载入程辑包:‘S4Vectors’

The following object is masked from ‘package:base’:

      expand.grid


> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
[1] GO.db_3.5.0          AnnotationDbi_1.40.0 IRanges_2.12.0      
[4] S4Vectors_0.16.0     Biobase_2.38.0       BiocGenerics_0.24.0 
[7] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15    digest_0.6.15   DBI_0.8         RSQLite_2.0    
 [5] pillar_1.2.1    rlang_0.2.0     blob_1.1.0      tools_3.4.2    
 [9] bit64_0.9-7     bit_1.1-12      compiler_3.4.2  pkgconfig_2.0.1
[13] memoise_1.1.0   tibble_1.4.2   

sessionInfo()

How can I solve this problam?

Thank you very much!

gostats go.db • 342 views
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