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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Failed to install signac. Error: object ‘recvData’ is not exported by 'namespace:parallel' #1809

Closed elegantmedstu closed 1 month ago

elegantmedstu commented 1 month ago

Hi, I had an error when installing signac and would like to ask for your help.
Error: object ‘recvData’ is not exported by 'namespace:parallel'

devtools::install_git("https://ghp.ci/https://github.com/stuart-lab/signac.git") Downloading git repo https://ghp.ci/https://github.com/stuart-lab/signac.git '/usr/bin/git' clone --depth 1 --no-hardlinks https://ghp.ci/https://github.com/stuart-lab/signac.git /tmp/RtmpCe9iX1/file37fc0c2cf06a87 Cloning into '/tmp/RtmpCe9iX1/file37fc0c2cf06a87'... remote: Enumerating objects: 262, done. remote: Counting objects: 100% (262/262), done. remote: Compressing objects: 100% (253/253), done. remote: Total 262 (delta 13), reused 154 (delta 4), pack-reused 0 (from 0) Receiving objects: 100% (262/262), 2.81 MiB | 6.00 KiB/s, done. Resolving deltas: 100% (13/13), done. These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: gtable (0.3.5 -> 0.3.6 ) [CRAN] 5: dotCall64 (1.1-1 -> 1.2 ) [CRAN] 6: spam (2.10-0 -> 2.11-0) [CRAN] 7: patchwork (1.2.0 -> 1.3.0 ) [CRAN] 8: data.table (1.16.0 -> 1.16.2) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3 ── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/tmp/RtmpCe9iX1/file37fc0c2cf06a87/DESCRIPTION’ ... ─ preparing ‘Signac’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories Removed empty directory ‘Signac/.github’ Removed empty directory ‘Signac/pkgdown’ Removed empty directory ‘Signac/vignettes’ ─ building ‘Signac_1.14.0.tar.gz’

sessionInfo()

R version 4.3.3 (2024-02-29) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 8

Matrix products: default BLAS/LAPACK: /home/QYH/mambaforge/envs/R4.4/lib/libopenblasp-r0.3.27.so; LAPACK version 3.12.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/New_York tzcode source: system (glibc)

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

other attached packages: [1] ggplot2_3.5.1

loaded via a namespace (and not attached): [1] gtable_0.3.5 remotes_2.5.0 htmlwidgets_1.6.4 devtools_2.4.5 processx_3.8.4 RcppRoll_0.3.1
[7] lattice_0.22-6 callr_3.7.6 ps_1.8.0 vctrs_0.6.5 tools_4.3.3 bitops_1.0-8
[13] generics_0.1.3 stats4_4.3.3 tibble_3.2.1 fansi_1.0.6 pkgconfig_2.0.3 Matrix_1.6-5
[19] data.table_1.16.0 S4Vectors_0.42.1 lifecycle_1.0.4 GenomeInfoDbData_1.2.12 stringr_1.5.1 compiler_4.3.3
[25] Rsamtools_2.20.0 Biostrings_2.72.1 munsell_0.5.1 codetools_0.2-20 httpuv_1.6.15 GenomeInfoDb_1.40.1
[31] usethis_3.0.0 htmltools_0.5.8.1 urlchecker_1.0.1 pillar_1.9.0 later_1.3.2 crayon_1.5.3
[37] ellipsis_0.3.2 BiocParallel_1.38.0 cachem_1.1.0 sessioninfo_1.2.2 mime_0.12 tidyselect_1.2.1
[43] digest_0.6.37 stringi_1.8.4 purrr_1.0.2 dplyr_1.1.4 listenv_0.9.1 fastmap_1.2.0
[49] grid_4.3.3 colorspace_2.1-1 cli_3.6.3 magrittr_2.0.3 patchwork_1.2.0 pkgbuild_1.4.4
[55] utf8_1.2.4 withr_3.0.1 scales_1.3.0 UCSC.utils_1.0.0 promises_1.3.0 XVector_0.44.0
[61] httr_1.4.7 globals_0.16.3 memoise_2.0.1 shiny_1.9.1 GenomicRanges_1.56.1 IRanges_2.38.1
[67] miniUI_0.1.1.1 profvis_0.3.8 rlang_1.1.4 Rcpp_1.0.13 xtable_1.8-4 glue_1.8.0
[73] BiocGenerics_0.50.0 pkgload_1.4.0 rstudioapi_0.16.0 jsonlite_1.8.8 R6_2.5.1 fs_1.6.4
[79] zlibbioc_1.50.0

elegantmedstu commented 1 month ago

I think I may have solved the problem. In my environment, it seems to be a problem caused by the package parallelly. After I uninstalled the package, I successfully installed signac. I hope it can give people with similar problems a reference. Thanks.

library(parallelly) Error: package or namespace load failed for ‘parallelly’: object ‘recvData’ is not exported by 'namespace:parallel' In addition: Warning message: package ‘parallelly’ was built under R version 4.4.1 remove.packages("parallelly", lib="~/mambaforge/envs/R4.4/lib/R/library")