ArchR
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Published
20 hours ago •
GreenleafLab
GreenleafLab
Can't install the ArchR on MacOS 15.0.1
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Describe the bug
I followed suggestions from previous posts to revert to an older R version (e.g. 4.1.3) because ArchR would not install with the updated R 4.4. However, I still can't install ArchR. I still receive the same following error even after running install.packages("usethis")
> devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘usethis’
Any suggestions I can check my system or any settings?
Session Info
> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 15.0.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Matrix_1.4-0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.13 compiler_4.1.3 later_1.3.2
[4] BiocManager_1.30.25 urlchecker_1.0.1 profvis_0.4.0
[7] remotes_2.5.0 tools_4.1.3 digest_0.6.37
[10] pkgbuild_1.4.4 pkgload_1.4.0 evaluate_1.0.1
[13] memoise_2.0.1 lifecycle_1.0.4 lattice_0.22-6
[16] rlang_1.1.4 shiny_1.9.1 cli_3.6.3
[19] rstudioapi_0.17.0 yaml_2.3.10 xfun_0.48
[22] fastmap_1.2.0 knitr_1.48 fs_1.6.4
[25] htmlwidgets_1.6.4 grid_4.1.3 R6_2.5.1
[28] rmarkdown_2.28 sessioninfo_1.2.2 magrittr_2.0.3
[31] promises_1.3.0 ellipsis_0.3.2 htmltools_0.5.8.1
[34] mime_0.12 xtable_1.8-4 httpuv_1.6.15
[37] miniUI_0.1.1.1 cachem_1.1.0
Hi @penghy27! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.
Hi Penghyu27,
Thanks for trying to use ArchR! I am not confident that the package is with ArchR, as usethis is a dependency of devtools. Could you do installed.packages() for me?
Thank you for your response! Last night, I used R 4.2, and things seem to be working. However, I'm still encountering problems when installing extra packages using ArchR::installExtraPackages().
Below is a list of my currently installed packages. Could you please advise on how to resolve the installation issues?
Thank you!
> installed.packages()
Package
abind "abind"
annotate "annotate"
AnnotationDbi "AnnotationDbi"
ArchR "ArchR"
askpass "askpass"
base "base"
base64enc "base64enc"
BH "BH"
Biobase "Biobase"
BiocFileCache "BiocFileCache"
BiocGenerics "BiocGenerics"
BiocIO "BiocIO"
BiocManager "BiocManager"
BiocParallel "BiocParallel"
BiocVersion "BiocVersion"
biomaRt "biomaRt"
Biostrings "Biostrings"
bit "bit"
bit64 "bit64"
bitops "bitops"
blob "blob"
boot "boot"
brew "brew"
brio "brio"
BSgenome "BSgenome"
BSgenome.Dmelanogaster.UCSC.dm6 "BSgenome.Dmelanogaster.UCSC.dm6"
BSgenome.Hsapiens.UCSC.hg19 "BSgenome.Hsapiens.UCSC.hg19"
bslib "bslib"
cachem "cachem"
Cairo "Cairo"
callr "callr"
caTools "caTools"
chromVAR "chromVAR"
circlize "circlize"
class "class"
cli "cli"
clipr "clipr"
clue "clue"
cluster "cluster"
CNEr "CNEr"
codetools "codetools"
colorspace "colorspace"
commonmark "commonmark"
compiler "compiler"
ComplexHeatmap "ComplexHeatmap"
cowplot "cowplot"
cpp11 "cpp11"
crayon "crayon"
credentials "credentials"
crosstalk "crosstalk"
curl "curl"
data.table "data.table"
datasets "datasets"
DBI "DBI"
dbplyr "dbplyr"
DelayedArray "DelayedArray"
desc "desc"
devtools "devtools"
diffobj "diffobj"
digest "digest"
DirichletMultinomial "DirichletMultinomial"
doParallel "doParallel"
LibPath
abind "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
annotate "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
AnnotationDbi "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
ArchR "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
askpass "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
base "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
base64enc "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BH "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
Biobase "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocFileCache "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocGenerics "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocIO "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocManager "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocParallel "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocVersion "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
biomaRt "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
Biostrings "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
bit "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
bit64 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
bitops "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
blob "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
boot "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
brew "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
brio "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BSgenome "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BSgenome.Dmelanogaster.UCSC.dm6 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BSgenome.Hsapiens.UCSC.hg19 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
bslib "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
cachem "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
Cairo "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
callr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
caTools "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
chromVAR "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
circlize "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
class "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
cli "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
clipr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
clue "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
cluster "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
CNEr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
codetools "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
colorspace "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
commonmark "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
compiler "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
ComplexHeatmap "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
cowplot "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
cpp11 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
crayon "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
credentials "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
crosstalk "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
curl "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
data.table "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
datasets "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
DBI "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
dbplyr "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
DelayedArray "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
desc "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
devtools "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
diffobj "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
digest "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
DirichletMultinomial "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
doParallel "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
Version Priority
abind "1.4-8" NA
annotate "1.74.0" NA
AnnotationDbi "1.58.0" NA
ArchR "1.0.2" NA
askpass "1.2.1" NA
base "4.2.3" "base"
base64enc "0.1-3" NA
BH "1.84.0-0" NA
Biobase "2.56.0" NA
BiocFileCache "2.4.0" NA
BiocGenerics "0.42.0" NA
BiocIO "1.6.0" NA
BiocManager "1.30.25" NA
BiocParallel "1.30.4" NA
BiocVersion "3.15.2" NA
biomaRt "2.52.0" NA
Biostrings "2.64.1" NA
bit "4.5.0" NA
bit64 "4.5.2" NA
bitops "1.0-9" NA
blob "1.2.4" NA
boot "1.3-31" "recommended"
brew "1.0-10" NA
brio "1.1.5" NA
BSgenome "1.64.0" NA
BSgenome.Dmelanogaster.UCSC.dm6 "1.4.1" NA
BSgenome.Hsapiens.UCSC.hg19 "1.4.3" NA
bslib "0.8.0" NA
cachem "1.1.0" NA
Cairo "1.6-2" NA
callr "3.7.6" NA
caTools "1.18.3" NA
chromVAR "1.18.0" NA
circlize "0.4.16" NA
class "7.3-22" "recommended"
cli "3.6.3" NA
clipr "0.8.0" NA
clue "0.3-65" NA
cluster "2.1.6" "recommended"
CNEr "1.32.0" NA
codetools "0.2-20" "recommended"
colorspace "2.1-1" NA
commonmark "1.9.2" NA
compiler "4.2.3" "base"
ComplexHeatmap "2.12.1" NA
cowplot "1.1.3" NA
cpp11 "0.5.0" NA
crayon "1.5.3" NA
credentials "2.0.2" NA
crosstalk "1.2.1" NA
curl "5.2.3" NA
data.table "1.16.2" NA
datasets "4.2.3" "base"
DBI "1.2.3" NA
dbplyr "2.5.0" NA
DelayedArray "0.22.0" NA
desc "1.4.3" NA
devtools "2.4.5" NA
diffobj "0.3.5" NA
digest "0.6.37" NA
DirichletMultinomial "1.38.0" NA
doParallel "1.0.17" NA
Depends
abind "R (>= 1.5.0)"
annotate "R (>= 2.10), AnnotationDbi (>= 1.27.5), XML"
AnnotationDbi "R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=\n0.29.2), Biobase (>= 1.17.0), IRanges"
ArchR ""
askpass NA
base NA
base64enc "R (>= 2.9.0)"
BH NA
Biobase "R (>= 2.10), BiocGenerics (>= 0.27.1), utils"
BiocFileCache "R (>= 3.4.0), dbplyr (>= 1.0.0)"
BiocGenerics "R (>= 4.0.0), methods, utils, graphics, stats"
BiocIO "R (>= 4.0)"
BiocManager NA
BiocParallel "methods, R (>= 3.5.0)"
BiocVersion "R (>= 4.2.0)"
biomaRt "methods"
Biostrings "R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=\n0.27.12), IRanges (>= 2.30.1), XVector (>= 0.29.2),\nGenomeInfoDb"
bit "R (>= 3.4.0)"
bit64 "R (>= 3.0.1), bit (>= 4.0.0), utils, methods, stats"
bitops NA
blob NA
boot "R (>= 3.0.0), graphics, stats"
brew NA
brio "R (>= 3.6)"
BSgenome "R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>=\n0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.25.6),\nGenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer\n(>= 1.39.7)"
BSgenome.Dmelanogaster.UCSC.dm6 "BSgenome (>= 1.35.10)"
BSgenome.Hsapiens.UCSC.hg19 "BSgenome (>= 1.54.0)"
bslib "R (>= 2.10)"
cachem NA
Cairo "R (>= 2.4.0)"
callr "R (>= 3.4)"
caTools "R (>= 3.6.0)"
chromVAR "R (>= 3.5.0)"
circlize "R (>= 4.0.0), graphics"
class "R (>= 3.0.0), stats, utils"
cli "R (>= 3.4)"
clipr NA
clue "R (>= 3.2.0)"
cluster "R (>= 3.5.0)"
CNEr "R (>= 3.5.0)"
codetools "R (>= 2.1)"
colorspace "R (>= 3.0.0), methods"
commonmark NA
compiler NA
ComplexHeatmap "R (>= 3.5.0), methods, grid, graphics, stats, grDevices"
cowplot "R (>= 3.5.0)"
cpp11 "R (>= 3.6.0)"
crayon NA
credentials NA
crosstalk NA
curl "R (>= 3.0.0)"
data.table "R (>= 3.3.0)"
datasets NA
DBI "methods, R (>= 3.0.0)"
dbplyr "R (>= 3.6)"
DelayedArray "R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>=\n0.37.0), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2),\nIRanges (>= 2.17.3)"
desc "R (>= 3.4)"
devtools "R (>= 3.0.2), usethis (>= 2.1.6)"
diffobj "R (>= 3.1.0)"
digest "R (>= 3.3.0)"
DirichletMultinomial "S4Vectors, IRanges"
doParallel "R (>= 2.14.0), foreach (>= 1.2.0), iterators (>= 1.0.0),\nparallel, utils"
Imports
abind "methods, utils"
annotate "Biobase, DBI, xtable, graphics, utils, stats, methods,\nBiocGenerics (>= 0.13.8), httr"
AnnotationDbi "DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST"
ArchR "ggplot2, SummarizedExperiment, data.table, Matrix, rhdf5,\nmagrittr, S4Vectors (>= 0.9.25), BiocGenerics, Rcpp (>=\n0.12.16), matrixStats, plyr, nabor, motifmatchr, chromVAR,\nuwot, ggrepel, Rsamtools, gtable, gtools, stringr, grid,\ngridExtra, Biostrings, ComplexHeatmap, GenomicRanges"
askpass "sys (>= 2.1)"
base NA
base64enc NA
BH NA
Biobase "methods"
BiocFileCache "methods, stats, utils, dplyr, RSQLite, DBI, rappdirs,\nfilelock, curl, httr"
BiocGenerics "methods, utils, graphics, stats"
BiocIO "BiocGenerics, S4Vectors, methods, tools"
BiocManager "utils"
BiocParallel "stats, utils, futile.logger, parallel, snow, codetools"
BiocVersion NA
biomaRt "utils, XML (>= 3.99-0.7), AnnotationDbi, progress, stringr,\nhttr, digest, BiocFileCache, rappdirs, xml2"
Biostrings "methods, utils, grDevices, graphics, stats, crayon"
bit NA
bit64 NA
bitops NA
blob "methods, rlang, vctrs (>= 0.2.1)"
boot NA
brew NA
brio NA
BSgenome "methods, utils, stats, matrixStats, BiocGenerics, S4Vectors,\nIRanges, XVector (>= 0.29.3), GenomeInfoDb, GenomicRanges,\nBiostrings, Rsamtools, rtracklayer"
BSgenome.Dmelanogaster.UCSC.dm6 "BSgenome"
BSgenome.Hsapiens.UCSC.hg19 "BSgenome"
bslib "base64enc, cachem, fastmap (>= 1.1.1), grDevices, htmltools\n(>= 0.5.8), jquerylib (>= 0.1.3), jsonlite, lifecycle, memoise\n(>= 2.0.1), mime, rlang, sass (>= 0.4.9)"
cachem "rlang, fastmap (>= 1.2.0)"
Cairo "grDevices, graphics"
callr "processx (>= 3.6.1), R6, utils"
caTools "bitops"
chromVAR "IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor,\nBiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools,\nS4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats,\nutils, graphics, DT, Rtsne, Matrix, SummarizedExperiment,\nRColorBrewer, BSgenome"
circlize "GlobalOptions (>= 0.1.2), shape, grDevices, utils, stats,\ncolorspace, methods, grid"
class "MASS"
cli "utils"
clipr "utils"
clue "stats, cluster, graphics, methods"
cluster "graphics, grDevices, stats, utils"
CNEr "Biostrings (>= 2.33.4), DBI (>= 0.7), RSQLite (>= 0.11.4),\nGenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.23.16),\nrtracklayer (>= 1.25.5), XVector (>= 0.5.4), GenomicAlignments\n(>= 1.1.9), methods, S4Vectors (>= 0.13.13), IRanges (>=\n2.5.27), readr (>= 0.2.2), BiocGenerics, tools, parallel,\nreshape2 (>= 1.4.1), ggplot2 (>= 2.1.0), poweRlaw (>= 0.60.3),\nannotate (>= 1.50.0), GO.db (>= 3.3.0), R.utils (>= 2.3.0),\nKEGGREST (>= 1.14.0)"
codetools NA
colorspace "graphics, grDevices, stats"
commonmark NA
compiler NA
ComplexHeatmap "circlize (>= 0.4.14), GetoptLong, colorspace, clue,\nRColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges,\nmatrixStats, foreach, doParallel, codetools"
cowplot "ggplot2 (>= 3.4.0), grid, gtable, grDevices, methods, rlang,\nscales"
cpp11 NA
crayon "grDevices, methods, utils"
credentials "openssl (>= 1.3), sys (>= 2.1), curl, jsonlite, askpass"
crosstalk "htmltools (>= 0.3.6), jsonlite, lazyeval, R6"
curl NA
data.table "methods"
datasets NA
DBI NA
dbplyr "blob (>= 1.2.0), cli (>= 3.6.1), DBI (>= 1.1.3), dplyr (>=\n1.1.2), glue (>= 1.6.2), lifecycle (>= 1.0.3), magrittr,\nmethods, pillar (>= 1.9.0), purrr (>= 1.0.1), R6 (>= 2.2.2),\nrlang (>= 1.1.1), tibble (>= 3.2.1), tidyr (>= 1.3.0),\ntidyselect (>= 1.2.1), utils, vctrs (>= 0.6.3), withr (>=\n2.5.0)"
DelayedArray "stats"
desc "cli, R6, utils"
devtools "cli (>= 3.3.0), desc (>= 1.4.1), ellipsis (>= 0.3.2), fs (>=\n1.5.2), lifecycle (>= 1.0.1), memoise (>= 2.0.1), miniUI (>=\n0.1.1.1), pkgbuild (>= 1.3.1), pkgdown (>= 2.0.6), pkgload (>=\n1.3.0), profvis (>= 0.3.7), rcmdcheck (>= 1.4.0), remotes (>=\n2.4.2), rlang (>= 1.0.4), roxygen2 (>= 7.2.1), rversions (>=\n2.1.1), sessioninfo (>= 1.2.2), stats, testthat (>= 3.1.5),\ntools, urlchecker (>= 1.0.1), utils, withr (>= 2.5.0)"
diffobj "crayon (>= 1.3.2), tools, methods, utils, stats"
digest "utils"
DirichletMultinomial "stats4, methods, BiocGenerics"
doParallel NA
LinkingTo
abind NA
annotate NA
AnnotationDbi NA
ArchR "Rcpp"
askpass NA
base NA
base64enc NA
BH NA
Biobase NA
BiocFileCache NA
BiocGenerics NA
BiocIO NA
BiocManager NA
BiocParallel "BH"
BiocVersion NA
biomaRt NA
Biostrings "S4Vectors, IRanges, XVector"
bit NA
bit64 NA
bitops NA
blob NA
boot NA
brew NA
brio NA
BSgenome NA
BSgenome.Dmelanogaster.UCSC.dm6 NA
BSgenome.Hsapiens.UCSC.hg19 NA
bslib NA
cachem NA
Cairo NA
callr NA
caTools NA
chromVAR "Rcpp, RcppArmadillo"
circlize NA
class NA
cli NA
clipr NA
clue NA
cluster NA
CNEr "S4Vectors, IRanges, XVector"
codetools NA
colorspace NA
commonmark NA
compiler NA
ComplexHeatmap NA
cowplot NA
cpp11 NA
crayon NA
credentials NA
crosstalk NA
curl NA
data.table NA
datasets NA
DBI NA
dbplyr NA
DelayedArray "S4Vectors"
desc NA
devtools NA
diffobj NA
digest NA
DirichletMultinomial NA
doParallel NA
Suggests
abind NA
annotate "hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,\nrae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,\norg.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit,"
AnnotationDbi "hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit,\nTxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db,\nAnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr"
ArchR NA
askpass "testthat"
base "methods"
base64enc NA
BH NA
Biobase "tools, tkWidgets, ALL, RUnit, golubEsets"
BiocFileCache "testthat, knitr, BiocStyle, rmarkdown, rtracklayer"
BiocGenerics "Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray,\nBiostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2,\nflowClust, MSnbase, annotate, RUnit"
BiocIO "testthat, knitr, rmarkdown, BiocStyle"
BiocManager "BiocVersion, BiocStyle, remotes, rmarkdown, testthat, withr,\ncurl, knitr"
BiocParallel "BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,\nRmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,\nTxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,\nRsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle,\nknitr, batchtools, data.table"
BiocVersion NA
biomaRt "BiocStyle, knitr, rmarkdown, testthat, mockery"
Biostrings "BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=\n1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),\nBSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,\nhgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy\n(>= 1.41.3), affydata (>= 1.11.5), RUnit"
bit "testthat (>= 0.11.0), roxygen2, knitr, markdown, rmarkdown,\nmicrobenchmark, bit64 (>= 4.0.0), ff (>= 4.0.0)"
bit64 NA
bitops NA
blob "covr, crayon, pillar (>= 1.2.1), testthat"
boot "MASS, survival"
brew "testthat (>= 3.0.0)"
brio "covr, testthat (>= 3.0.0)"
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BSgenome.Hsapiens.UCSC.hg19 ""
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class NA
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clipr "covr, knitr, rmarkdown, rstudioapi (>= 0.5), testthat (>=\n2.0.0)"
clue "e1071, lpSolve (>= 5.5.7), quadprog (>= 1.4-8), relations"
cluster "MASS, Matrix"
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codetools NA
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commonmark "curl, testthat, xml2"
compiler NA
ComplexHeatmap "testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff,\nfastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport,\ngrImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12),\ngridGraphics, gplots, rmarkdown, Cairo"
cowplot "Cairo, covr, dplyr, forcats, gridGraphics (>= 0.4-0), knitr,\nlattice, magick, maps, PASWR, patchwork, rmarkdown, ragg,\ntestthat (>= 1.0.0), tidyr, vdiffr (>= 0.3.0), VennDiagram"
cpp11 "bench, brio, callr, cli, covr, decor, desc, ggplot2, glue,\nknitr, lobstr, mockery, progress, rmarkdown, scales, Rcpp,\ntestthat (>= 3.2.0), tibble, utils, vctrs, withr"
crayon "mockery, rstudioapi, testthat, withr"
credentials "testthat, knitr, rmarkdown"
crosstalk "shiny, ggplot2, testthat (>= 2.1.0), sass, bslib"
curl "spelling, testthat (>= 1.0.0), knitr, jsonlite, later,\nrmarkdown, httpuv (>= 1.4.4), webutils"
data.table "bit64 (>= 4.0.0), bit (>= 4.0.4), R.utils, xts, zoo (>=\n1.8-1), yaml, knitr, markdown"
datasets NA
DBI "arrow, blob, covr, DBItest, dbplyr, downlit, dplyr, glue,\nhms, knitr, magrittr, nanoarrow (>= 0.3.0.1), RMariaDB,\nrmarkdown, rprojroot, RSQLite (>= 1.1-2), testthat (>= 3.0.0),\nvctrs, xml2"
dbplyr "bit64, covr, knitr, Lahman, nycflights13, odbc (>= 1.4.2),\nRMariaDB (>= 1.2.2), rmarkdown, RPostgres (>= 1.4.5),\nRPostgreSQL, RSQLite (>= 2.3.1), testthat (>= 3.1.10)"
DelayedArray "BiocParallel, HDF5Array (>= 1.17.12), genefilter,\nSummarizedExperiment, airway, lobstr, DelayedMatrixStats,\nknitr, rmarkdown, BiocStyle, RUnit"
desc "callr, covr, gh, spelling, testthat, whoami, withr"
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diffobj "knitr, rmarkdown"
digest "tinytest, simplermarkdown"
DirichletMultinomial "lattice, parallel, MASS, RColorBrewer, xtable"
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[ reached getOption("max.print") -- omitted 224 rows ]
Hi Penghy27, Are you getting the same issue with installExtraPackages() with usethis? Overall the function just tries to install Seurat, Cairo, harmony, preswto, shiny, rhandsontable and shinythemes. I see you have Cairo, but are you getting an error with installation of the other packages?
Best,
Immanuel
Hi Immanuel, Thanks for your prompt response. Yes, I have Cairo installed, but I encountered errors on Seurat, igraph, dotCall64, spam, spatstat.geom, and spatstat.random. I used install.packages() to install these packages, but the errors persist. The error messages indicate issues with multiple dependencies during the installation of the Seurat package.
For example, when I try to install Seurat, I encounter errors like the one above. I also attempted to install other packages, such as igraph and spam, but the issues persist.
Thank you for your assistance.
Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-igraph/00new/igraph/libs/igraph.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-igraph/00new/igraph/libs/igraph.so, 0x0006): symbol not found in flat namespace '_igraphdnaupd_'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/igraph’
Warning in install.packages :
installation of package ‘igraph’ had non-zero exit status
ERROR: dependency ‘dotCall64’ is not available for package ‘spam’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/spam’
Warning in install.packages :
installation of package ‘spam’ had non-zero exit status
ERROR: dependency ‘deldir’ is not available for package ‘spatstat.geom’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/spatstat.geom’
Warning in install.packages :
installation of package ‘spatstat.geom’ had non-zero exit status
ERROR: dependency ‘spatstat.geom’ is not available for package ‘spatstat.random’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/spatstat.random’
Warning in install.packages :
installation of package ‘spatstat.random’ had non-zero exit status
ERROR: dependency ‘spam’ is not available for package ‘SeuratObject’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/SeuratObject’
Warning in install.packages :
installation of package ‘SeuratObject’ had non-zero exit status
ERROR: dependencies ‘spatstat.geom’, ‘spatstat.random’ are not available for package ‘spatstat.explore’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/spatstat.explore’
Warning in install.packages :
installation of package ‘spatstat.explore’ had non-zero exit status
ERROR: dependencies ‘SeuratObject’, ‘igraph’, ‘spatstat.explore’, ‘spatstat.geom’ are not available for package ‘Seurat’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Seurat’
Warning in install.packages :
installation of package ‘Seurat’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/l8/b2285nqj68x2y4sdjnfwd4v80000gn/T/RtmpmwvVr1/downloaded_packages’
Hi penghy27 this is something I'm not 100% familiar with and it seems like a system issue with your R environment and your compiler. When I read through some other literature, I see that you could alleviate this by by going into ~/.R/Makevars and setting your compiler to clang.
CC = clang
CXX = clang++
Could you try doing this, restarting your R environment, and try reinstalling a few of the packages?
Hi Immanuel, thank you for your suggestions. Unfortunately, reinstalling the packages still failed after setting the compiler to clang, even after restarting the R environment and macOS. It's strange that I can't load the ArchR library after the restart. Maybe I need to check the dependencies or any conflicts in the environment. Could you share the information what version of R, Bioconductor, and operation system you use?