[Bioc-devel] xcms error with R CMD check "checking loading without being on the library search path"
Mike Smith
gr|mbough @end|ng |rom gm@||@com
Thu Mar 14 11:31:31 CET 2024
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.Rainer using 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.rainer using eurac.edu
> github: jorainer
> mastodon: jorainer using fosstodon.org
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
[[alternative HTML version deleted]]
More information about the Bioc-devel
mailing list