rformassspectrometry / RforMassSpectrometry.org

The R for Mass Spectrometry Initiative home page
http://www.rformassspectrometry.org/
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Packages not installing ERROR: dependencies #7

Closed CptChiler closed 5 years ago

CptChiler commented 5 years ago

I tryed to install it with

>BiocManager::install("RforMassSpectrometry/RforMassSpectrometry")

and got this message

Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing github package(s) 'RforMassSpectrometry/RforMassSpectrometry'
Downloading GitHub repo RforMassSpectrometry/RforMassSpectrometry@master
Skipping 3 packages not available: Features, MsExperiment, Spectra
√  checking for file 'C:\Users\ZBS6-Proteomik\AppData\Local\Temp\Rtmp0YkQ8E\remotes968f23386d\rformassspectrometry-RforMassSpectrometry-811b048/DESCRIPTION' ...
-  preparing 'RforMassSpectrometry':
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'RforMassSpectrometry_0.0.1.tar.gz'

ERROR: dependencies 'MsExperiment', 'Spectra', 'Features' are not available for package 'RforMassSpectrometry'
* removing 'C:/Program Files/R/R-3.6.0/library/RforMassSpectrometry'
Error in i.p(...) : 
  (converted from warning) installation of package ‘C:/Users/ZBS6-P~1/AppData/Local/Temp/Rtmp0YkQ8E/file96841376d6e/RforMassSpectrometry_0.0.1.tar.gz’ had non-zero exit status

after this i tryed to install the dependencies 'MsExperiment', 'Spectra', 'Features' with

BiocManager::install("rformassspectrometry/Features")
√  checking for file 'C:\Users\ZBS6-Proteomik\AppData\Local\Temp\Rtmp0YkQ8E\remotes9688ae10c1\rformassspectrometry-Features-e068591/DESCRIPTION' ...
-  preparing 'Features':
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  looking to see if a 'data/datalist' file should be added
-  building 'Features_0.1.0.tar.gz' (3.5s)

* installing *source* package 'Features' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Fehler in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace 'ProtGenerics' 1.16.0 is being loaded, but >= 1.17.2 is required
Ruft auf: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Ausführung angehalten
ERROR: lazy loading failed for package 'Features'
* removing 'C:/Program Files/R/R-3.6.0/library/Features'
Error in i.p(...) : 
  (converted from warning) installation of package ‘C:/Users/ZBS6-P~1/AppData/Local/Temp/Rtmp0YkQ8E/file96848817daa/Features_0.1.0.tar.gz’ had non-zero exit status
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.4

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        rstudioapi_0.10   magrittr_1.5      usethis_1.5.0     devtools_2.0.2    pkgload_1.0.2     R6_2.4.0          rlang_0.3.4      
 [9] tools_3.6.0       pkgbuild_1.0.3    sessioninfo_1.1.1 cli_1.1.0         withr_2.1.2       remotes_2.0.4     yaml_2.2.0        assertthat_0.2.1 
[17] rprojroot_1.3-2   digest_0.6.19     crayon_1.3.4      processx_3.3.1    callr_3.2.0       fs_1.3.1          ps_1.3.0          curl_3.3         
[25] glue_1.3.1        memoise_1.1.0     compiler_3.6.0    desc_1.2.0        backports_1.1.4   prettyunits_1.0.2

hope you can help me thx

lgatto commented 5 years ago

Thank you for your interest.

You need to use the development version of Bioconductor to get access to the development versions of some dependencies to install the packages. That's for example the reason Features fails - it needs at least version 1.17.2 of ProtGenerics.

Note that all the packages you are trying to install are work in progress and at a very early stage (some more than others). RforMassSpectrometry is currently more of a developer-oriented project and not yet mature for production.