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Question: Error: package or namespace load failed for ‘MSnbase’
0
gravatar for Marie
2.7 years ago by
Marie0
Marie0 wrote:

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 

 

ADD COMMENTlink modified 2.7 years ago by Laurent Gatto1.0k • written 2.7 years ago by Marie0
0
gravatar for Laurent Gatto
2.7 years ago by
Laurent Gatto1.0k
United Kingdom
Laurent Gatto1.0k wrote:

I am not sure what happens, and will need to investigate. But in the meantime, this error

Error in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘limma’

indicates that limma is missing.

Could you try to install it and try again.

Laurent

ADD COMMENTlink written 2.7 years ago by Laurent Gatto1.0k

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.

ADD REPLYlink written 2.7 years ago by Laurent Gatto1.0k
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