Hi Johannes, I think RCurl is imported via the package dependency chain of xcms -> SummarizedExperiment -> GenomeInfoDb -> RCurl.
It looks like Hervé removed this dependency from GenomeInfoDb recently ( https://code.bioconductor.org/browse/GenomeInfoDb/commit/9562907f6800cf6052fff9fb2f85329ff44790b6), and the change is present in both RELEASE_3_18 and devel. There was a post a few weeks ago about how a few heavily used CRAN packages are essentially abandoned (XML and RCurl) and there's been a bit of a concerted effort to move away from them in the core BioC packages if possible - hence why Hervé has made that change. As for why R CMD check is complaining, my guess would be that you have some saved data in xcms that expects RCurl to be available when it is loaded - presumably this object was created when the dependency chain above was valid. Now GenomeInfoDb has been changed, RCurl doesn't get installed with xcms in a fresh R/Bioconductor install like your Docker container. Then when you load the object via data() R complains about missing the expected RCurl package. That's just an educated guess, but seems plausible to me. Best, Mike On Wed, 13 Mar 2024 at 10:10, Rainer Johannes <johannes.rai...@eurac.edu> wrote: > Dear all, > > we're having some rather strange errors with R CMD check on the xcms > package recently: it will fail with this warning (which then becomes an > error): > > ✔ checking whether the namespace can be loaded with stated dependencies > (5.9s) > ✔ checking whether the namespace can be unloaded cleanly (6.1s) > W checking loading without being on the library search path (5.3s) > Loading required package: BiocParallel > Loading required package: MSnbase > Loading required package: BiocGenerics > > Attaching package: ‘BiocGenerics’ > > The following objects are masked from ‘package:stats’: > > IQR, mad, sd, var, xtabs > > The following objects are masked from ‘package:base’: > > Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, > as.data.frame, basename, cbind, colnames, dirname, do.call, > duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, > lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, > pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, > tapply, union, unique, unsplit, which.max, which.min > > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > > Loading required package: mzR > Loading required package: Rcpp > Loading required package: S4Vectors > Loading required package: stats4 > > Attaching package: ‘S4Vectors’ > > The following object is masked from ‘package:utils’: > > findMatches > > The following objects are masked from ‘package:base’: > > I, expand.grid, unname > > Loading required package: ProtGenerics > > Attaching package: ‘ProtGenerics’ > > The following object is masked from ‘package:stats’: > > smooth > > > This is MSnbase version 2.28.1 > Visit https://lgatto.github.io/MSnbase/ to get started. > > > Attaching package: ‘MSnbase’ > > The following object is masked from ‘package:base’: > > trimws > > Loading required package: RCurl > Error: package or namespace load failed for ‘xcms’ in > .requirePackage(package): > unable to find required package ‘RCurl’ > In addition: Warning message: > In library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, : > there is no package called ‘RCurl’ > Execution halted > > It looks like this package has a loading problem when not on .libPaths: > see the messages for details. > > > This is rather puzzling, since we're not using, requiring or importing > RCurl at all. Also, so far I've never seen this check "checking loading > without being on the library search path" before. > > I will try to figure out what is going on and where/which package is > causing this problem, but would be great if someone has a solution or at > least a hint. > > thanks! > jo > > I was running this for xcms from the RELEASE_3_18 branch using the > bioconductor/bioconductor_docker:RELEASE_3_18. The sessionInfo (after > loading xcms): > > > sessionInfo() > R version 4.3.2 (2023-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 22.04.3 LTS > > Matrix products: default > BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 > LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; > LAPACK version 3.10.0 > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] 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 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > time zone: Etc/UTC > tzcode source: system (glibc) > > attached base packages: > [1] stats4 stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] xcms_4.0.2 MSnbase_2.28.1 ProtGenerics_1.34.0 > [4] S4Vectors_0.40.2 mzR_2.36.0 Rcpp_1.0.11 > [7] Biobase_2.62.0 BiocGenerics_0.48.1 BiocParallel_1.36.0 > > loaded via a namespace (and not attached): > [1] bitops_1.0-7 rlang_1.1.1 > [3] magrittr_2.0.3 clue_0.3-65 > [5] MassSpecWavelet_1.68.0 matrixStats_1.2.0 > [7] compiler_4.3.2 callr_3.7.3 > [9] vctrs_0.6.4 pkgconfig_2.0.3 > [11] MetaboCoreUtils_1.11.1 crayon_1.5.2 > [13] XVector_0.42.0 utf8_1.2.4 > [15] ps_1.7.5 preprocessCore_1.64.0 > [17] MultiAssayExperiment_1.28.0 zlibbioc_1.48.0 > [19] GenomeInfoDb_1.38.7 progress_1.2.3 > [21] DelayedArray_0.28.0 parallel_4.3.2 > [23] prettyunits_1.2.0 cluster_2.1.4 > [25] R6_2.5.1 RColorBrewer_1.1-3 > [27] limma_3.58.1 GenomicRanges_1.54.1 > [29] SummarizedExperiment_1.32.0 iterators_1.0.14 > [31] IRanges_2.36.0 igraph_2.0.2 > [33] Matrix_1.6-5 splines_4.3.2 > [35] tidyselect_1.2.1 abind_1.4-5 > [37] doParallel_1.0.17 codetools_0.2-19 > [39] affy_1.80.0 curl_5.1.0 > [41] processx_3.8.2 pkgbuild_1.4.2 > [43] lattice_0.22-5 tibble_3.2.1 > [45] plyr_1.8.9 withr_2.5.1 > [47] desc_1.4.2 survival_3.5-7 > [49] Spectra_1.12.0 pillar_1.9.0 > [51] affyio_1.72.0 BiocManager_1.30.22 > [53] MatrixGenerics_1.14.0 foreach_1.5.2 > [55] MALDIquant_1.22.2 ncdf4_1.22 > [57] generics_0.1.3 rprojroot_2.0.3 > [59] xopen_1.0.0 RCurl_1.98-1.14 > [61] hms_1.1.3 ggplot2_3.5.0 > [63] munsell_0.5.0 scales_1.3.0 > [65] MsExperiment_1.4.0 glue_1.6.2 > [67] MsFeatures_1.10.0 lazyeval_0.2.2 > [69] tools_4.3.2 mzID_1.40.0 > [71] robustbase_0.99-2 QFeatures_1.12.0 > [73] vsn_3.70.0 RANN_2.6.1 > [75] fs_1.6.3 XML_3.99-0.16.1 > [77] grid_4.3.2 impute_1.76.0 > [79] MsCoreUtils_1.15.1 colorspace_2.1-0 > [81] GenomeInfoDbData_1.2.11 cli_3.6.1 > [83] rcmdcheck_1.4.0 fansi_1.0.5 > [85] S4Arrays_1.2.1 dplyr_1.1.4 > [87] AnnotationFilter_1.26.0 pcaMethods_1.94.0 > [89] gtable_0.3.4 DEoptimR_1.1-3 > [91] digest_0.6.33 SparseArray_1.2.4 > [93] multtest_2.58.0 lifecycle_1.0.3 > [95] statmod_1.5.0 MASS_7.3-60 > > > Johannes Rainer, PhD > > Eurac Research > Institute for Biomedicine > Via A.-Volta 21, I-39100 Bolzano, Italy > > email: johannes.rai...@eurac.edu > github: jorainer > mastodon: jorai...@fosstodon.org > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
