lgatto / MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics
http://lgatto.github.io/MSnbase/
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issue with loading MSnbase package #541

Closed yaare closed 3 years ago

yaare commented 3 years ago

Hi, I keep getting an error when loading the package. I tried installing "scales" but it's not working. Any help is much appreciated!

Loading required package: 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, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
    colnames, colSums, dirname, 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

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: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: ProtGenerics
Error: package or namespace load failed for ‘MSnbase’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘scales’
Error in .requirePackage(package) : 
  unable to find required package ‘MSnbase’
In addition: Warning messages:
1: In normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="NA": The system cannot find the file specified
2: In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.0)
than is installed on your system (1.0.6). 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.
Loading required package: MSnbase
Error: package or namespace load failed for ‘MSnbase’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘scales’
Error in .requirePackage(package) : 
  unable to find required package ‘MSnbase’
installed.packages("scales")
     Package LibPath Version Priority Depends Imports LinkingTo Suggests Enhances License
     License_is_FOSS License_restricts_use OS_type Archs MD5sum NeedsCompilation Built
> install.packages("scales")
Installing package into ‘C:/Users/___/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)

  There is a binary version available but the source version is later:
       binary source needs_compilation
scales  1.1.0  1.1.1             FALSE

installing the source package ‘scales’

trying URL 'https://cran.rstudio.com/src/contrib/scales_1.1.1.tar.gz'
Content type 'application/x-gzip' length 515201 bytes (503 KB)
downloaded 503 KB

* installing *source* package 'scales' ...
** package 'scales' successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called 'colorspace'
ERROR: lazy loading failed for package 'scales'
* removing 'C:/Users/__/Documents/R/win-library/3.5/scales'
In R CMD INSTALL
Warning in install.packages :
  installation of package ‘scales’ had non-zero exit status

The downloaded source packages are in
    ‘C:\Users\___
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ProtGenerics_1.14.0 S4Vectors_0.20.1    mzR_2.16.2          Rcpp_1.0.6         
[5] Biobase_2.42.0      BiocGenerics_0.28.0

loaded via a namespace (and not attached):
[1] codetools_0.2-18    grid_3.5.3          ncdf4_1.17          impute_1.56.0      
[5] BiocParallel_1.16.6 tools_3.5.3         tinytex_0.30        xfun_0.21          
[9] compiler_3.5.3   
lgatto commented 3 years ago

It seems that colorspace is missing.