[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
Wed Mar 13 10:06:11 CET 2024
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
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