[Bioc-devel] xcms error with R CMD check "checking loading without being on the library search path"
Rainer Johannes
Joh@nne@@R@|ner @end|ng |rom eur@c@edu
Thu Mar 14 14:04:30 CET 2024
Dear Mike,
thanks for the excellent explanation - and yes, I think you're right (after some feedback also from Vince and Herve). I did re-save the objects bundled within xcms with a fresh installation and am now re-running a bunch of tests with different containers.
thanks!
jo
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
Mike Smith wrote:
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<mailto: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<http://pmax.int/>, pmin,
pmin.int<http://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<http://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<mailto:johannes.rainer using eurac.edu>
github: jorainer
mastodon: jorainer using fosstodon.org<mailto:jorainer using fosstodon.org>
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