Question: GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
0
gravatar for james.dalgleish
6 weeks ago by
james.dalgleish30 wrote:

So, this may be pretty big problem that may affect many packages, including mine. I hope others are not having the same issue, but I cannot get GenomicRanges to load because it wants a newer version of S4Vectors than exists on Bioconductor(see https://bioconductor.org/packages/release/bioc/html/S4Vectors.html, at the bottom, it's version 0.22.1). It's probably a quick fix, but I thought I would bring it to your attention.

> library(GenomicRanges)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Error: package ‘S4Vectors’ 0.22.1 was found, but >= 0.23.19 is required by ‘GenomicRanges’

To show that the old version is still being installed by default:

> BiocManager::install("S4Vectors")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'S4Vectors'
trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/S4Vectors_0.22.1.tar.gz'
Content type 'application/x-gzip' length 637005 bytes (622 KB)
downloaded 622 KB

This is a problem for me because I have Bioconductor dependencies on my package and now my installation instructions will fail (as will basically any package installation attempt).

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/local/intel/compilers_and_libraries_2019.1.144/linux/mkl/lib/intel64_lin/libmkl_rt.so

Random number generation:
 RNG:     Mersenne-Twister
 Normal:  Inversion
 Sample:  Rounding

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

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] BiocGenerics_0.30.0 ggplot2_3.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2             XVector_0.24.0         GenomeInfoDb_1.20.0
 [4] pillar_1.4.2           compiler_3.6.0         prettyunits_1.0.2
 [7] progress_1.2.2         zlibbioc_1.30.0        bitops_1.0-6
[10] tools_3.6.0            biomaRt_2.40.5         zeallot_0.1.0
[13] digest_0.6.21          bit_1.1-14             RSQLite_2.1.2
[16] memoise_1.1.0          tibble_2.1.3           gtable_0.3.0
[19] pkgconfig_2.0.3        rlang_0.4.0            DBI_1.0.0
[22] GenomeInfoDbData_1.2.1 httr_1.4.1             stringr_1.4.0
[25] withr_2.1.2            dplyr_0.8.3            hms_0.5.1
[28] Biostrings_2.52.0      IRanges_2.18.3         S4Vectors_0.22.1
[31] vctrs_0.2.0            bit64_0.9-7            grid_3.6.0
[34] tidyselect_0.2.5       glue_1.3.1             Biobase_2.44.0
[37] R6_2.4.0               AnnotationDbi_1.46.1   XML_3.98-1.20
[40] purrr_0.3.2            blob_1.2.0             magrittr_1.5
[43] GenomicRanges_1.37.16  scales_1.0.0           backports_1.1.5
[46] assertthat_0.2.1       colorspace_1.4-1       stringi_1.4.3
[49] RCurl_1.95-4.12        lazyeval_0.2.2         munsell_0.5.0
[52] crayon_1.3.4
>
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by james.dalgleish30
Answer: GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
0
gravatar for Martin Morgan
6 weeks ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

Likely you have mixed release (even numbered version 'y' in x.y.z) and devel (odd numbered y) versions of packages. What does

BiocManager::valid()

report? The BiocManager vignette has information about maintaining different releases.

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Martin Morgan ♦♦ 24k

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by james.dalgleish30

Here's the requested output in the comment.

> BiocManager::valid()

* sessionInfo()

R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/local/intel/compilers_and_libraries_2019.1.144/linux/mkl/lib/intel64_lin/libmkl_rt.so

Random number generation:
 RNG:     Mersenne-Twister
 Normal:  Inversion
 Sample:  Rounding

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

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] CNVScope_2.7.2.5            ggplot2_3.2.1
 [3] GenomicInteractions_1.19.0  InteractionSet_1.13.0
 [5] SummarizedExperiment_1.15.9 DelayedArray_0.10.0
 [7] BiocParallel_1.18.1         matrixStats_0.55.0
 [9] Biobase_2.44.0              GenomicRanges_1.37.16
[11] GenomeInfoDb_1.20.0         IRanges_2.19.16
[13] S4Vectors_0.23.25           BiocGenerics_0.31.6

loaded via a namespace (and not attached):
  [1] spam_2.3-0               backports_1.1.5          circlize_0.4.8
  [4] Hmisc_4.2-0              BiocFileCache_1.8.0      plyr_1.8.4
  [7] igraph_1.2.4.1           lazyeval_0.2.2           splines_3.6.0
 [10] digest_0.6.21            foreach_1.4.7            ensembldb_2.9.6
 [13] htmltools_0.3.6          viridis_0.5.1            tiff_0.1-5
 [16] gdata_2.18.0             magrittr_1.5             checkmate_1.9.4
 [19] memoise_1.1.0            BSgenome_1.53.2          cluster_2.1.0
 [22] doParallel_1.0.15        gclus_1.3.2              Biostrings_2.52.0
 [25] acnr_1.0.0               spatialfil_0.15          prettyunits_1.0.2
 [28] jpeg_0.1-8               colorspace_1.4-1         blob_1.2.0
 [31] rappdirs_0.3.1           xfun_0.10                dplyr_0.8.3
 [34] crayon_1.3.4             RCurl_1.95-4.12          jsonlite_1.6
 [37] zeallot_0.1.0            survival_2.44-1.1        VariantAnnotation_1.31.4
 [40] iterators_1.0.12         glue_1.3.1               registry_0.5-1
 [43] gtable_0.3.0             zlibbioc_1.30.0          XVector_0.24.0
 [46] webshot_0.5.1            shape_1.4.4              maps_3.3.0
 [49] abind_1.4-5              scales_1.0.0             DBI_1.0.0
 [52] Rcpp_1.0.2               HiCseg_1.1               viridisLite_0.3.0
 [55] xtable_1.8-4             progress_1.2.2           htmlTable_1.13.2
 [58] foreign_0.8-72           bit_1.1-14               dotCall64_1.0-0
 [61] Formula_1.2-3            htmlwidgets_1.3          httr_1.4.1
 [64] gplots_3.0.1.1           RColorBrewer_1.1-2       acepack_1.4.1
 [67] pkgconfig_2.0.3          XML_3.98-1.20            Gviz_1.29.3
 [70] nnet_7.3-12              dbplyr_1.4.2             tidyselect_0.2.5
 [73] rlang_0.4.0              reshape2_1.4.3           later_1.0.0
 [76] AnnotationDbi_1.46.1     visNetwork_2.0.8         munsell_0.5.0
 [79] OpenImageR_1.1.5         tools_3.6.0              rslurm_0.4.0
 [82] RSQLite_2.1.2            stringr_1.4.0            heatmaply_0.16.0
 [85] knitr_1.25               bit64_0.9-7              shinycssloaders_0.2.0
 [88] caTools_1.17.1.2         purrr_0.3.2              dendextend_1.12.0
 [91] AnnotationFilter_1.9.0   mime_0.7                 biomaRt_2.40.5
 [94] compiler_3.6.0           shinythemes_1.1.2        rstudioapi_0.10
 [97] plotly_4.9.0             curl_4.2                 png_0.1-7
[100] tibble_2.1.3             stringi_1.4.3            GenomicFeatures_1.37.4
[103] fields_9.8-6             lattice_0.20-38          ProtGenerics_1.16.0
[106] Matrix_1.2-17            shinyjs_1.0              vctrs_0.2.0
[109] pillar_1.4.2             lifecycle_0.1.0          BiocManager_1.30.4
[112] GlobalOptions_0.1.1      data.table_1.12.4        bitops_1.0-6
[115] seriation_1.2-8          httpuv_1.5.2             rtracklayer_1.45.6
[118] R6_2.4.0                 latticeExtra_0.6-28      TSP_1.1-7
[121] promises_1.0.1           KernSmooth_2.23-15       gridExtra_2.3
[124] codetools_0.2-16         dichromat_2.0-0          gtools_3.8.1
[127] MASS_7.3-51.4            assertthat_0.2.1         withr_2.1.2
[130] GenomicAlignments_1.21.7 Rsamtools_2.1.6          GenomeInfoDbData_1.2.1
[133] jointseg_1.0.2           hms_0.5.1                grid_3.6.0
[136] rpart_4.1-15             tidyr_1.0.0              logging_0.10-108
[139] biovizBase_1.33.1        shiny_1.3.2              base64enc_0.1-3
ADD REPLYlink written 6 weeks ago by james.dalgleish30

The remainder of the BiocManager::valid() output is below (it was over 5000 characters).

Bioconductor version '3.9'

  * 5 packages out-of-date
  * 140 packages too new

create a valid installation with

  BiocManager::install(c(
    "affycoretools", "airway", "AllelicImbalance", "AnnotationFilter",
    "annotatr", "apeglm", "arrayQualityMetrics", "ballgown", "BANOVA",
    "baySeq", "beadarray", "BiocGenerics", "biovizBase", "BitSeq", "BSgenome",
    "bsseq", "BubbleTree", "bumphunter", "ChIPpeakAnno", "ChIPQC",
    "ChIPseeker", "chipseq", "ChIPseqR", "ChIPsim", "ChromHeatMap", "chromVAR",
    "cicero", "cn.farms", "cn.mops", "CNEr", "CODEX", "coMET", "copynumber",
    "crlmm", "csaw", "cummeRbund", "DaMiRseq", "DESeq2", "DEXSeq", "DiffBind",
    "diffHic", "diffloop", "DMRcate", "DMRcatedata", "dmrseq", "DRIMSeq",
    "DropletUtils", "DSS", "easyRNASeq", "EDASeq", "ELMER", "ELMER.data",
    "ensembldb", "ensemblVEP", "esATAC", "exomeCopy", "fastseg", "ffpe",
    "fission", "FlowSorted.Blood.450k", "FlowSorted.Blood.EPIC",
    "FlowSorted.CordBlood.450k", "FlowSorted.CordBloodCombined.450k",
    "FourCSeq", "frma", "genbankr", "geneLenDataBase", "genomeIntervals",
    "GenomicAlignments", "GenomicDataCommons", "GenomicFeatures",
    "GenomicInteractions", "GenomicRanges", "genoset", "GenVisR", "ggbio",
    "girafe", "goseq", "groHMM", "Gviz", "htmltools", "htmlwidgets", "iCNV",
    "Imetagene", "intansv", "InteractionSet", "IRanges",
    "IsoformSwitchAnalyzeR", "JunctionSeq", "lumi", "MAST", "metagene",
    "methylKit", "methylumi", "minfi", "missMethyl", "MotifDb", "motifmatchr",
    "motifRG", "MultiAssayExperiment", "MutationalPatterns", "mygene",
    "nucleR", "oligo", "oligoClasses", "OmicCircos", "OrganismDbi",
    "parathyroidSE", "polspline", "promises", "PureCN", "regioneR",
    "Repitools", "ReportingTools", "rGADEM", "RiboProfiling", "riboSeqR",
    "RIPSeeker", "RnBeads", "Rsamtools", "rtracklayer", "RUVSeq", "S4Vectors",
    "SC3", "scater", "scDD", "scran", "scRNAseq", "seqbias", "sesame",
    "ShortRead", "signeR", "SingleCellExperiment", "singscore", "SNPchip",
    "SomaticSignatures", "SummarizedExperiment", "systemPipeR", "TCGAbiolinks",
    "TCGAbiolinksGUI", "TFBSTools", "TitanCNA", "VanillaICE",
    "VariantAnnotation", "wateRmelon"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

ADD REPLYlink written 6 weeks ago by james.dalgleish30

If you're wanting to use the devel version of Bioconductor, then indicate that with BiocManager

BiocManager::install(version="devel")

and then re-run BiocManager::valid() -- it will indicate that there are a few packages that are out-of-date, and you should then update them.

If you're wanting to use the release version of Bioconductor, then copy and paste the command above into your R session (and take a break for coffee!).

If you want to have two different installations of Bioconductor, then follow the instructions in the vignette.

ADD REPLYlink written 6 weeks ago by Martin Morgan ♦♦ 24k
Answer: GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
0
gravatar for james.dalgleish
6 weeks ago by
james.dalgleish30 wrote:

Here's what I did to solve it:

remotes::install_github("Bioconductor/BiocGenerics")
remotes::install_github("Bioconductor/S4Vectors")
remotes::install_github("Bioconductor/IRanges")
remotes::install_github("Bioconductor/GenomicRanges")

GenomicRanges now loads.

> library(BiocGenerics)
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

> packageVersion("BiocGenerics")
[1] ‘0.31.6’
> packageVersion("S4Vectors")
[1] ‘0.23.25’
> library(GenomicRanges)
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
ADD COMMENTlink written 6 weeks ago by james.dalgleish30

I guess BiocManager::valid() is almost as displeased as before; use BiocManager rather than github to manage your installations.

The solution used here, to install Bioconductor packages from github, is not recommended at all.

ADD REPLYlink written 6 weeks ago by Martin Morgan ♦♦ 24k
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