[Bioc-devel] mzR and Rccp issue when building package

[Laurent Gatto]

I can trigger a new installation to get a new binary built against Rcpp 1.0.5, which should sort out that warning (which is harmless by the way).

A note about xcmsSet objects though: you are using an outdated xcmsSet class; it is strongly suggested to change from the old xcms user interface functions (xcmsSet and alike) to the new functions that make use of the MSnbase package to represent the mass spec data [1].

Best wishes,

Laurent

[1] https://support.bioconductor.org/p/133388/#133400

________________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Bruno pereira <pereirinha_bp using hotmail.com>
Sent: 18 November 2020 11:29
To: bioc-devel using r-project.org
Subject: [Bioc-devel] mzR and Rccp issue when building package

Hello,

My name is Bruno Pereira and i�m from Portugal. I am developing na R package that serves as a repository of datasets for another package. One of the datasets has an S4 object of class xcmsSet which means i need to add to my description file xcms. However when i try to check or even submit this package to Cran, i get a couple of warnings due to mzR and Rcpp versions, not allowing the package to be accepted.

The output of the warnings is:

Warning 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsupport.bioconductor.org%2F&data=04%7C01%7Claurent.gatto%40uclouvain.be%7C8b6d7a0d078b4d1b722408d88bbbaaf2%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637412986152262230%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=k3HVn0SW1sjJSytAFf%2B5UtybIKtJJVwyCEdMQx%2FSpBw%3D&reserved=0 . For details see also

https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsneumann%2FmzR%2Fwiki%2FmzR-Rcpp-compiler-linker-issue&data=04%7C01%7Claurent.gatto%40uclouvain.be%7C8b6d7a0d078b4d1b722408d88bbbaaf2%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637412986152262230%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=aKS5q1ldBdBlgmSADxihX732Q8zJ1tVFDh2GwPIdR2s%3D&reserved=0.




My sessionInfo() is:
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

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

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

other attached packages:
[1] specmine.datasets_0.0.1 devtools_2.3.2          usethis_1.6.3

loaded via a namespace (and not attached):
[1] ProtGenerics_1.20.0         bitops_1.0-6                matrixStats_0.57.0
 [4] fs_1.5.0                    doParallel_1.0.16           RColorBrewer_1.1-2
 [7] rprojroot_2.0.2             GenomeInfoDb_1.24.2         MSnbase_2.14.2
[10] tools_4.0.2                 affyio_1.58.0               R6_2.5.0
[13] BiocGenerics_0.34.0         colorspace_2.0-0            withr_2.3.0
[16] tidyselect_1.1.0            prettyunits_1.1.1           processx_3.4.4
[19] compiler_4.0.2              MassSpecWavelet_1.54.0      preprocessCore_1.50.0
[22] cli_2.1.0                   Biobase_2.48.0              xml2_1.3.2
[25] desc_1.2.0                  DelayedArray_0.14.1         scales_1.1.1
[28] DEoptimR_1.0-8              robustbase_0.93-6           affy_1.66.0
[31] callr_3.5.1                 stringr_1.4.0               digest_0.6.27
[34] XVector_0.28.0              pkgconfig_2.0.3             sessioninfo_1.1.1
[37] limma_3.44.3                rlang_0.4.8                 rstudioapi_0.13
[40] impute_1.62.0               generics_0.1.0              mzID_1.26.0
[43] BiocParallel_1.22.0         dplyr_1.0.2                 RCurl_1.98-1.2
[46] magrittr_1.5                GenomeInfoDbData_1.2.3      MALDIquant_1.19.3
[49] Matrix_1.2-18               Rcpp_1.0.5                  munsell_0.5.0
[52] S4Vectors_0.26.1            fansi_0.4.1                 lifecycle_0.2.0
[55] vsn_3.56.0                  stringi_1.5.3               MASS_7.3-53
[58] SummarizedExperiment_1.18.2 zlibbioc_1.34.0             pkgbuild_1.1.0
[61] plyr_1.8.6                  grid_4.0.2                  parallel_4.0.2
[64] crayon_1.3.4                lattice_0.20-41             mzR_2.22.0
[67] xcms_3.10.2                 knitr_1.30                  ps_1.4.0
[70] pillar_1.4.6                GenomicRanges_1.40.0        codetools_0.2-18
[73] stats4_4.0.2                pkgload_1.1.0               XML_3.99-0.5
[76] glue_1.4.2                  pcaMethods_1.80.0           remotes_2.2.0
[79] BiocManager_1.30.10         foreach_1.5.1               vctrs_0.3.5
[82] testthat_3.0.0              gtable_0.3.0                RANN_2.6.1
[85] purrr_0.3.4                 assertthat_0.2.1            ggplot2_3.3.2
[88] xfun_0.19                   roxygen2_7.1.1              ncdf4_1.17
[91] tibble_3.0.4                iterators_1.0.13            memoise_1.1.0
[94] IRanges_2.22.2              ellipsis_0.3.1

Best regards,
Bruno Pereira.


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