readH5AD() example failing

milanmlft commented 3 years ago

When running the example from readH5AD():

library(zellkonverter)
file <- system.file("extdata", "krumsiek11.h5ad", package = "zellkonverter")
sce <- readH5AD(file)
#> sh: ~/Library/Caches/basilisk/1.2.1/0/etc/profile.d/conda.sh: No such file or directory
#> Warning in system(paste(act.cmd, collapse = " "), intern = TRUE): running
#> command '. '~/Library/Caches/basilisk/1.2.1/0/etc/profile.d/conda.sh' &&
#> conda activate && /Library/Frameworks/R.framework/Resources/bin/Rscript --
#> default-packages=NULL -e "con <- socketConnection(port=11727, open='wb',
#> blocking=TRUE);serialize(Sys.getenv(), con);close(con)"' had status 1
#> Warning in socketAccept(soc, blocking = TRUE, open = "a+b"): problem in
#> accepting connections on this socket
#> Error in socketAccept(soc, blocking = TRUE, open = "a+b"): cannot open the connection

^{Created on 2021-01-27 by the reprex package (v1.0.0)}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.0.3 (2020-10-10) #> os macOS Catalina 10.15.7 #> system x86_64, darwin17.0 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Europe/Brussels #> date 2021-01-27 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date lib source #> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0) #> backports 1.2.1 2020-12-09 [1] CRAN (R 4.0.3) #> basilisk 1.2.1 2020-12-16 [1] Bioconductor #> basilisk.utils 1.2.1 2020-12-16 [1] Bioconductor #> Biobase 2.50.0 2020-10-27 [1] Bioconductor #> BiocGenerics 0.36.0 2020-10-27 [1] Bioconductor #> bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0) #> cli 2.2.0 2020-11-20 [1] CRAN (R 4.0.2) #> crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0) #> DelayedArray 0.16.1 2021-01-22 [1] Bioconductor #> digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2) #> ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0) #> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0) #> fansi 0.4.2 2021-01-15 [1] CRAN (R 4.0.2) #> filelock 1.0.2 2018-10-05 [1] CRAN (R 4.0.2) #> fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) #> GenomeInfoDb 1.26.2 2020-12-08 [1] standard (@1.26.2) #> GenomeInfoDbData 1.2.4 2020-10-29 [1] Bioconductor #> GenomicRanges 1.42.0 2020-10-27 [1] Bioconductor #> glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) #> highr 0.8 2019-03-20 [1] CRAN (R 4.0.0) #> htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.2) #> IRanges 2.24.1 2020-12-12 [1] standard (@2.24.1) #> jsonlite 1.7.2 2020-12-09 [1] standard (@1.7.2) #> knitr 1.31 2021-01-27 [1] CRAN (R 4.0.3) #> lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.3) #> lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0) #> magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.2) #> Matrix 1.3-2 2021-01-06 [2] CRAN (R 4.0.2) #> MatrixGenerics 1.2.0 2020-10-27 [1] Bioconductor #> matrixStats 0.57.0 2020-09-25 [1] CRAN (R 4.0.2) #> pillar 1.4.7 2020-11-20 [1] CRAN (R 4.0.2) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.0) #> R.cache 0.14.0 2019-12-06 [1] CRAN (R 4.0.0) #> R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.0.2) #> R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.0.2) #> R.utils 2.10.1 2020-08-26 [1] CRAN (R 4.0.2) #> rappdirs 0.3.2 2021-01-27 [1] CRAN (R 4.0.3) #> Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.0.2) #> RCurl 1.98-1.2 2020-04-18 [1] CRAN (R 4.0.0) #> reprex 1.0.0 2021-01-27 [1] CRAN (R 4.0.3) #> reticulate 1.18 2020-10-25 [1] CRAN (R 4.0.2) #> rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.2) #> rmarkdown 2.6 2020-12-14 [1] standard (@2.6) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.2) #> S4Vectors 0.28.1 2020-12-09 [1] standard (@0.28.1) #> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0) #> SingleCellExperiment 1.12.0 2020-10-27 [1] Bioconductor #> stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0) #> styler 1.3.2 2020-02-23 [1] CRAN (R 4.0.0) #> SummarizedExperiment 1.20.0 2020-10-27 [1] Bioconductor #> tibble 3.0.5 2021-01-15 [1] CRAN (R 4.0.2) #> vctrs 0.3.6 2020-12-17 [1] CRAN (R 4.0.3) #> withr 2.4.1 2021-01-26 [1] CRAN (R 4.0.3) #> xfun 0.20 2021-01-06 [1] CRAN (R 4.0.2) #> XVector 0.30.0 2020-10-27 [1] Bioconductor #> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0) #> zellkonverter * 1.0.0 2020-10-28 [1] Bioconductor #> zlibbioc 1.36.0 2020-10-27 [1] Bioconductor #> #> [1] /Users/milan/Library/R/4.0/library #> [2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library ```

The message sh: ~/Library/Caches/basilisk/1.2.1/0/etc/profile.d/conda.sh: No such file or directory also confuses me, because I'm quite sure it's present:

$ ls ~/Library/Caches/basilisk/1.2.1/0/etc/profile.d
conda.csh
conda.sh

Seems that there is some problem with the basilisk environment. Tried removing the conda environment and re-installing zellkonverter, but no luck. Any idea how to fix this?

Thanks a lot!

LTLA commented 3 years ago

This is known (caused by rappdirs update today) and fixed in basilisk.utils 1.2.2. You can pull it from GitHub:

BiocManager::install("LTLA/basilisk.utils@RELEASE_3_12")

Or wait for a day and pull it from BioC when the new build propagates tomorrow.

milanmlft commented 3 years ago

Thanks, that worked!

theislab / zellkonverter

readH5AD() example failing #36