Hello,
I have some trouble loading the library MSnbase. I already tried to restart R and download the package again several times. It was still working yesterday and I think I have nothing changed.
Cheers,
Marie
> library(MSnbase)
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, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, 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, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unlist, unsplit
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: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
Error in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘limma’
In addition: Warning messages:
1: package ‘Rcpp’ was built under R version 3.2.3
2: In fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.1)
than is installed on your system (0.12.3). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
3: package ‘BiocParallel’ was built under R version 3.2.3
4: replacing previous import by ‘ggplot2::Position’ when loading ‘MSnbase’
5: replacing previous import by ‘ggplot2::unit’ when loading ‘MSnbase’
6: replacing previous import by ‘ggplot2::arrow’ when loading ‘MSnbase’
Error: package or namespace load failed for ‘MSnbase’
> 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
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] ProtGenerics_1.2.1 BiocParallel_1.4.3 mzR_2.4.0 Rcpp_0.12.3 Biobase_2.30.0
[6] BiocGenerics_0.16.1 BiocInstaller_1.20.1
loaded via a namespace (and not attached):
[1] magrittr_1.5 zlibbioc_1.16.0 munsell_0.4.3 colorspace_1.2-6 impute_1.44.0
[6] lattice_0.20-33 stringr_1.0.0 plyr_1.8.3 tools_3.2.2 grid_3.2.2
[11] gtable_0.1.2 affy_1.48.0 lambda.r_1.1.7 futile.logger_1.4.1 preprocessCore_1.32.0
[16] affyio_1.40.0 reshape2_1.4.1 ggplot2_2.0.0 S4Vectors_0.8.11 futile.options_1.0.0
[21] codetools_0.2-14 MALDIquant_1.14 stringi_1.0-1 pcaMethods_1.60.0 scales_0.3.0
[26] stats4_3.2.2
I can reproduce your error when removing
limma:> remove.packages("limma")Removing package from ‘/home/lg390/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
> suppressPackageStartupMessages(library("MSnbase"))
Error in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘limma’
In addition: Warning messages:
1: replacing previous import by ‘ggplot2::Position’ when loading ‘MSnbase’
2: replacing previous import by ‘ggplot2::unit’ when loading ‘MSnbase’
3: replacing previous import by ‘ggplot2::arrow’ when loading ‘MSnbase’
Error: package or namespace load failed for ‘MSnbase’
> BiocInstaller::biocLite("limma")
*** output flushed ***
> suppressPackageStartupMessages(library("MSnbase"))
Warning messages:
1: replacing previous import by ‘ggplot2::Position’ when loading ‘MSnbase’
2: replacing previous import by ‘ggplot2::unit’ when loading ‘MSnbase’
3: replacing previous import by ‘ggplot2::arrow’ when loading ‘MSnbase’
I need to selectively import from ggplot2 to remove this warnings. This is fixed in devel, but not in release - I think you can safely ignore these at the moment - will do it asap.