- using R Under development (unstable) (2012-05-22 r59396)
- using platform: x86_64-unknown-linux-gnu (64-bit)
- using session charset: UTF-8
- checking for file ‘GOSim/DESCRIPTION’ ... OK
- this is package ‘GOSim’ version ‘1.2.7.1’
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking whether package ‘GOSim’ can be installed ... [70s/100s] OK
- checking installed package size ... OK
- checking package directory ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... WARNING
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following object(s) are masked from ‘package:stats’:
xtabs
The following object(s) are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
rownames, sapply, setdiff, table, tapply, union, unique
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: DBI
Loading required package: annotate
Loading required package: topGO
Loading required package: graph
Loading required package: SparseM
Package SparseM (0.96) loaded.
To cite, see citation("SparseM")
Attaching package: ‘SparseM’
The following object(s) are masked from ‘package:base’:
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Loading required package: cluster
Loading required package: flexmix
Loading required package: lattice
Loading required package: modeltools
Loading required package: stats4
Loading required package: multcomp
Loading required package: mvtnorm
Loading required package: survival
Loading required package: splines
Loading required package: RBGL
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object(s) are masked from ‘package:SparseM’:
det
Loading required package: corpcor
Loading required package: org.Hs.eg.db
[1] "initializing GOSim package ..."
[1] "-> retrieving GO information for all available genes for organism ‘human’ in GO database"
[1] "-> filtering GO terms according to evidence levels ‘all’"
[1] "-> loading files with information content for corresponding GO category (human)"
Error : .onLoad failed in loadNamespace() for ‘GOSim’, details:
call: find.package(package, lib.loc, verbose = verbose)
error: there is no package called ‘GOSim’
Error: package/namespace load failed for ‘GOSim’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
- checking for unstated dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... NOTE
GOenrichment: warning in get("gomap", env = GOSimEnv): partial argument
match of 'env' to 'envir'
calc.diffusion.kernel: warning in get("gomap", env = GOSimEnv): partial
argument match of 'env' to 'envir'
calcICs: warning in get("gomap", env = GOSimEnv): partial argument
match of 'env' to 'envir'
filterGO: warning in get("gomap", env = GOSimEnv): partial argument
match of 'env' to 'envir'
getDensityFactor: warning in get("nchildren", env = GOSimEnv): partial
argument match of 'env' to 'envir'
getDensityFactor: warning in get("nparents", env = GOSimEnv): partial
argument match of 'env' to 'envir'
getDensityFactor: warning in get("Eavg", env = GOSimEnv): partial
argument match of 'env' to 'envir'
getGOGraph: warning in get("ontology", env = GOSimEnv): partial
argument match of 'env' to 'envir'
getGOInfo: warning in get("ontology", env = GOSimEnv): partial argument
match of 'env' to 'envir'
getGOInfo: warning in get("gomap", env = GOSimEnv): partial argument
match of 'env' to 'envir'
selectPrototypes: warning in get("ontology", env = GOSimEnv): partial
argument match of 'env' to 'envir'
selectPrototypes: warning in get("gomap", env = GOSimEnv): partial
argument match of 'env' to 'envir'
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking compiled code ... OK
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking examples ... [103s/140s] OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking running R code from vignettes ... [55s/75s] OK
- checking re-building of vignette PDFs ... [57s/85s] OK
- checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There was 1 note.
See
‘/data/gannet/tmp/ripley/R/packages/tests-devel/GOSim.Rcheck/00check.log’
for details.