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

[Bruno pereira]

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://support.bioconductor.org/ . For details see also

https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.




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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