mzR and Rcpp issue
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Entering edit mode
Hans • 0
@hans-24157
Last seen 8 months ago

Hello, I have an Issue with mzR in MetaboAnalystR Library.

I followed the instructions on this site

Provided that the 3rd suggestion did not work, I am posting that issue here.


> library(MetaboAnalystR)
MetaboAnalystR 3.0.3 initialized Successfully !
https://github.com/xia-lab/MetaboAnalystR
There were 12 warnings (use warnings() to see them)
> warnings()
Mensagens de aviso:
1: In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.4.6)
than is installed on your system (1.0.5). 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.
2: replacing previous import ‘MSnbase::normalize’ by ‘igraph::normalize’ when loading ‘MetaboAnalystR’
3: replacing previous import ‘data.table::melt’ by ‘reshape::melt’ when loading ‘MetaboAnalystR’
4: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘MetaboAnalystR’
5: replacing previous import ‘pls::loadings’ by ‘stats::loadings’ when loading ‘MetaboAnalystR’
6: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘MetaboAnalystR’
7: replacing previous import ‘MSnbase::smooth’ by ‘stats::smooth’ when loading ‘MetaboAnalystR’
8: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘MetaboAnalystR’
9: replacing previous import ‘igraph::groups’ by ‘dplyr::groups’ when loading ‘MetaboAnalystR’
10: replacing previous import ‘reshape::rename’ by ‘dplyr::rename’ when loading ‘MetaboAnalystR’
11: replacing previous import ‘data.table::transpose’ by ‘purrr::transpose’ when loading ‘MetaboAnalystR’
12: replacing previous import ‘reshape::melt’ by ‘reshape2::melt’ when loading ‘MetaboAnalystR’

sessionInfo( )

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

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

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

other attached packages:
[1] MetaboAnalystR_3.0.3

loaded via a namespace (and not attached):
  [1] TH.data_1.0-10        fgsea_1.14.0          colorspace_2.0-0      ellipsis_0.3.1        class_7.3-17          siggenes_1.62.0       pls_2.7-3            
  [8] rstudioapi_0.13       mzR_2.22.0            affyio_1.58.0         bit64_4.0.5           lubridate_1.7.9.2     prodlim_2019.11.13    mvtnorm_1.1-1        
 [15] mathjaxr_1.0-1        xml2_1.3.2            codetools_0.2-18      splines_4.0.3         ncdf4_1.17            mnormt_2.0.2          doParallel_1.0.16    
 [22] impute_1.62.0         scrime_1.3.5          TFisher_0.2.0         jsonlite_1.7.1        pROC_1.16.2           caret_6.0-86          vsn_3.56.0           
 [29] graph_1.66.0          httr_1.4.2            BiocManager_1.30.10   compiler_4.0.3        Matrix_1.2-18         limma_3.44.3          crmn_0.0.21          
 [36] htmltools_0.5.0       prettyunits_1.1.1     tools_4.0.3           igraph_1.2.6          gtable_0.3.0          glue_1.4.2            affy_1.66.0          
 [43] reshape2_1.4.4        dplyr_1.0.2           fastmatch_1.1-0       Rcpp_1.0.5            MALDIquant_1.19.3     Biobase_2.48.0        vctrs_0.3.4          
 [50] multtest_2.44.0       rsm_2.10.2            preprocessCore_1.50.0 nlme_3.1-150          iterators_1.0.13      gbRd_0.4-11           timeDate_3043.102    
 [57] stringr_1.4.0         gower_0.2.2           rbibutils_1.4         lifecycle_0.2.0       gtools_3.8.2          XML_3.99-0.5          edgeR_3.30.3         
 [64] zlibbioc_1.34.0       MASS_7.3-53           zoo_1.8-8             scales_1.1.1          ipred_0.9-9           MSnbase_2.14.2        pcaMethods_1.80.0    
 [71] hms_0.5.3             ProtGenerics_1.20.0   parallel_4.0.3        RBGL_1.64.0           sandwich_3.0-0        RColorBrewer_1.1-2    memoise_1.1.0        
 [78] gridExtra_2.3         ggplot2_3.3.2         rpart_4.1-15          stringi_1.5.3         reshape_0.8.8         RSQLite_2.2.1         mutoss_0.1-12        
 [85] S4Vectors_0.26.1      foreach_1.5.1         plotrix_3.7-8         caTools_1.18.0        BiocGenerics_0.34.0   BiocParallel_1.22.0   lava_1.6.8.1         
 [92] Rdpack_2.1            rlang_0.4.8           pkgconfig_2.0.3       bitops_1.0-6          mzID_1.26.0           lattice_0.20-41       purrr_0.3.4          
 [99] recipes_0.1.15        bit_4.0.4             tidyselect_1.1.0      plyr_1.8.6            magrittr_1.5          R6_2.5.0              IRanges_2.22.2       
[106] gplots_3.1.0          generics_0.1.0        multcomp_1.4-15       DBI_1.1.0             withr_2.3.0           pillar_1.4.6          sn_1.6-2             
[113] survival_3.2-7        nnet_7.3-14           tibble_3.0.4          crayon_1.3.4          KernSmooth_2.23-18    tmvnsim_1.0-2         progress_1.2.2       
[120] locfit_1.5-9.4        grid_4.0.3            data.table_1.13.2     blob_1.2.1            ModelMetrics_1.2.2.2  metap_1.4             digest_0.6.27        
[127] numDeriv_2016.8-1.1   stats4_4.0.3          munsell_0.5.0

Thank you all in advance for helping.

Issue Rcpp mzR • 185 views
ADD COMMENT
3
Entering edit mode
@laurent-gatto-5645
Last seen 29 days ago
Belgium

There's no issue with mzR. The difference in Rcpp version is harmless (it wasn't a long time ago).

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