rformassspectrometry / Spectra

Low level infrastructure to handle MS spectra
https://rformassspectrometry.github.io/Spectra/
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Error: 'joinSpectraData' is not an exported object from 'namespace:Spectra' #170

Closed plantton closed 3 years ago

plantton commented 3 years ago

I cannot invoke joinSpectraData function in R.

> devtools::install_github("rformassspectrometry/Spectra")
Skipping install of 'Spectra' from a github remote, the SHA1 (f8ee67f9) has not changed since last install.
  Use `force = TRUE` to force installation
> 
> sciex2 <- joinSpectraData(sciex, spv, by.y = "spectrumId")
Error in joinSpectraData(sciex, spv, by.y = "spectrumId") : 
  could not find function "joinSpectraData"

Session info:

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RSQLite_2.2.1       devtools_2.3.2      usethis_1.6.3       MsBackendSql_0.5.1  Spectra_1.1.12      BiocParallel_1.24.1
 [7] ggplot2_3.3.2       msdata_0.28.0       MSnbase_2.16.0      ProtGenerics_1.23.5 S4Vectors_0.28.1    mzR_2.25.1         
[13] Rcpp_1.0.5          Biobase_2.50.0      BiocGenerics_0.36.0

loaded via a namespace (and not attached):
 [1] vsn_3.58.0            pkgload_1.1.0         bit64_4.0.5           foreach_1.5.1         assertthat_0.2.1     
 [6] BiocManager_1.30.10   affy_1.68.0           blob_1.2.1            remotes_2.2.0         impute_1.64.0        
[11] sessioninfo_1.1.1     pillar_1.4.7          lattice_0.20-41       glue_1.4.2            limma_3.46.0         
[16] digest_0.6.27         colorspace_2.0-0      preprocessCore_1.52.0 plyr_1.8.6            MALDIquant_1.19.3    
[21] XML_3.99-0.5          pkgconfig_2.0.3       zlibbioc_1.36.0       purrr_0.3.4           scales_1.1.1         
[26] processx_3.4.4        affyio_1.60.0         tibble_3.0.4          generics_0.1.0        IRanges_2.24.1       
[31] ellipsis_0.3.1        withr_2.3.0           cli_2.2.0             magrittr_2.0.1        crayon_1.3.4         
[36] memoise_1.1.0         ps_1.4.0              fs_1.5.0              ncdf4_1.17            fansi_0.4.1          
[41] doParallel_1.0.16     MASS_7.3-53           pkgbuild_1.1.0        tools_4.0.3           prettyunits_1.1.1    
[46] lifecycle_0.2.0       munsell_0.5.0         callr_3.5.1           pcaMethods_1.82.0     compiler_4.0.3       
[51] mzID_1.28.0           rlang_0.4.9           grid_4.0.3            iterators_1.0.13      rstudioapi_0.13      
[56] MsCoreUtils_1.3.2     testthat_3.0.0        gtable_0.3.0          codetools_0.2-18      DBI_1.1.0            
[61] curl_4.3              R6_2.5.0              dplyr_1.0.2           bit_4.0.4             rprojroot_2.0.2      
[66] desc_1.2.0            vctrs_0.3.5           tidyselect_1.1.0