R CMD check problems

[jorainer]

We're now having problems with R CMD check for the xcms devel branch: https://github.com/sneumann/xcms/actions/runs/8232884721/job/22511239538#step:21:127

Seems related to the RCurl package that is not found on the path (although it is in fact installed?). No idea where this error comes from and also how we could fix it. Adding RCurl into Depends fixes it, but that's IMHO not a workable solution, because we don't even use RCurl within xcms.

I have the same problem running R CMD check locally (with R devel), @sneumann , can you please verify/check on your setup too?

[jorainer]

I get the same error with the BioC 3.18 version:

> library(xcms)
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

```r
sessionInfo()
> 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_1.2.0            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                

[jorainer]

Running this on a vanilla bioconductor/bioconductor_docker:RELEASE_3_18 complains that data("xdata") fails because it requires RCurl. The suggestion from Vince was to add RCurl to Suggests.

MSnbase had the XML package in the Imports, and RCurl seems to be a dependency of XML. Recently XML was moved in MSnbase to Suggests.

I re-created all internal RData files in data/ to ensure that the saved objects don't have any reference anymore to RCurl/XML

[jorainer]

Latest comment from Herve:

If installing xcms and alll its deps from source on bioconductor_docker:RELEASE_3_18, the problem goes away. This is a strong indication that this is an S4 cache issue with some of the binaries. Will try to narrow down the list of binaries that are actually causing the problem.

So, will try installing all packages from source instead to see if error disappears.

[jorainer]

After installing all required packages from source for xcms and the RELEASE_3_18 docker image there are no more warnings or errors with xcms (4.0.2). Evaluating now also using the devel branch.

[jorainer]

All good with devel branch too (if all required packages are installed from source).