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!
