sesameDataCache() ExperimentHub Caching fails

Question

sesameDataCache() ExperimentHub Caching fails

dvera opened this issue 8 months ago · comments

library(sesame)
Loading required package: sesameData
Loading required package: ExperimentHub
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’:

anyDuplicated, aperm, 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.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Registered S3 methods overwritten by 'dbplyr':
method from
print.tbl_lazy
print.tbl_sql
Loading sesameData.

SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
Please cache auxiliary data by "sesameDataCache()".
This needs to be done only once per SeSAMe installation.

sesame_checkVersion() # run this to document versions
SeSAMe requires matched versions of R, sesame, sesameData and ExperimentHub.
Here is the current versions installed:
R: 4.3.1
Bioconductor: 3.18
sesame: 1.20.0
sesameData: 1.20.0
ExperimentHub: 2.10.0

sesameDataCache()
/home/username/.cache/R/ExperimentHub
does not exist, create directory? (yes/no): yes
Metadata (N=91):

ExperimentHub Caching fails:
error in evaluating the argument 'x' in selecting a method for function 'query': Failed to collect lazy table.
Caused by error in db_collect():
! Arguments in ... must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?

traceback()
No traceback available

sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so; LAPACK version 3.11.0

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 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

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

other attached packages:
[1] sesame_1.20.0 sesameData_1.20.0 ExperimentHub_2.10.0 AnnotationHub_3.10.0 BiocFileCache_2.10.0 dbplyr_2.4.0 BiocGenerics_0.48.0

loaded via a namespace (and not attached):
[1] tidyselect_1.2.0 dplyr_1.1.3 blob_1.2.4 filelock_1.0.2 Biostrings_2.70.1 bitops_1.0-7
[7] fastmap_1.1.1 RCurl_1.98-1.12 promises_1.2.1 digest_0.6.33 mime_0.12 lifecycle_1.0.3
[13] ellipsis_0.3.2 KEGGREST_1.42.0 interactiveDisplayBase_1.40.0 RSQLite_2.3.1 magrittr_2.0.3 compiler_4.3.1
[19] rlang_1.1.1 tools_4.3.1 utf8_1.2.4 yaml_2.3.7 knitr_1.44 S4Arrays_1.2.0
[25] bit_4.0.5 curl_5.1.0 DelayedArray_0.28.0 plyr_1.8.9 RColorBrewer_1.1-3 abind_1.4-5
[31] BiocParallel_1.36.0 purrr_1.0.2 grid_4.3.1 stats4_4.3.1 preprocessCore_1.64.0 fansi_1.0.5
[37] wheatmap_0.2.0 xtable_1.8-4 colorspace_2.1-0 ggplot2_3.4.4 scales_1.2.1 SummarizedExperiment_1.32.0
[43] cli_3.6.1 rmarkdown_2.25 crayon_1.5.2 generics_0.1.3 reshape2_1.4.4 httr_1.4.7
[49] tzdb_0.4.0 DBI_1.1.3 cachem_1.0.8 stringr_1.5.0 zlibbioc_1.48.0 parallel_4.3.1
[55] AnnotationDbi_1.64.0 BiocManager_1.30.22 XVector_0.42.0 matrixStats_1.0.0 vctrs_0.6.4 Matrix_1.5-4.1
[61] IRanges_2.36.0 hms_1.1.3 S4Vectors_0.40.0 bit64_4.0.5 glue_1.6.2 codetools_0.2-19
[67] stringi_1.7.12 gtable_0.3.4 BiocVersion_3.18.0 later_1.3.1 GenomeInfoDb_1.38.0 GenomicRanges_1.54.0
[73] munsell_0.5.0 tibble_3.2.1 pillar_1.9.0 rappdirs_0.3.3 htmltools_0.5.6.1 GenomeInfoDbData_1.2.11
[79] R6_2.5.1 lattice_0.21-8 evaluate_0.22 shiny_1.7.5.1 Biobase_2.62.0 readr_2.1.4
[85] png_0.1-8 memoise_2.0.1 httpuv_1.6.12 Rcpp_1.0.11 SparseArray_1.2.0 xfun_0.40
[91] MatrixGenerics_1.14.0 pkgconfig_2.0.3

Daniel Vera · Answer 1 · Sat Oct 28 2023 01:15:03 GMT+0800 (China Standard Time)

ExperimentHub()
Error in collect():
! Failed to collect lazy table.
Caused by error in db_collect():
! Arguments in ... must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
Run rlang::last_trace() to see where the error occurred.

rlang::last_trace()
<error/rlang_error>
Error in collect():
! Failed to collect lazy table.
Caused by error in db_collect():
! Arguments in ... must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?

Backtrace:
▆

├─ExperimentHub::ExperimentHub()
│ └─AnnotationHub::.Hub(...)
│ └─AnnotationHub:::.create_cache(...)
│ └─BiocFileCache::BiocFileCache(cache = cache, ask = ask)
│ └─BiocFileCache:::.sql_create_db(bfc)
│ └─BiocFileCache:::.sql_validate_version(bfc)
│ └─BiocFileCache:::.sql_schema_version(bfc)
│ ├─base::tryCatch(...)
│ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
│ └─tbl(src, "metadata") %>% collect(Inf)
├─dplyr::collect(., Inf)
└─dbplyr:::collect.tbl_sql(., Inf)
├─base::tryCatch(...)
│ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
│ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
│ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
└─dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...)

Wanding Zhou - Bioinformatics · Answer 2 · Sat Oct 28 2023 01:19:43 GMT+0800 (China Standard Time)

There was a bug reported relating to BiocFileCache compatibility with the new version dbplyr. This affected BiocFileCache, ExperimentHub, and AnnotationHub. This has already been corrected in BiocFileCache versions 2.10.1 (Release_3_18) and 2.11.1 (devel/3.19) respectively. can you try updating?

SeungJin Park · Answer 3 · Tue Oct 31 2023 14:00:09 GMT+0800 (China Standard Time)

I got same issue although i installed BiocFileCache 2.10.1 and ExperimentHub 2.10.0.
Any other solution?

VivianBailey · Answer 4 · Fri Nov 10 2023 02:08:01 GMT+0800 (China Standard Time)

Same error here. I updated my BiocFileCache to 2.10.1 and ExperimentHub to 2.10.0, then ran sesameDataCache(). I am able to load the example successfully.

ardan33 · Answer 5 · Fri Dec 01 2023 21:59:01 GMT+0800 (China Standard Time)

Did this get resolved? I am having the same issue and have also already updated..

Wanding Zhou - Bioinformatics · Answer 6 · Fri Dec 01 2023 22:02:15 GMT+0800 (China Standard Time)

@ardan33 What's your ExperimentHub, BiocFileCache and AnnotationHub versions? I believe it should've been solved in the latest 2.11.1.

ardan33 · Answer 7 · Fri Dec 01 2023 22:09:28 GMT+0800 (China Standard Time)

@zwdzwd my versions are:
BiocManager_1.30.22 sesame_1.20.0
sesameData_1.20.0
ExperimentHub_2.10.0
AnnotationHub_3.10.0
BiocFileCache_2.10.1

Is it ExperimentHub that needs updated to 2.11.1?

ardan33 · Answer 8 · Fri Dec 01 2023 22:26:14 GMT+0800 (China Standard Time)

it also looks like I did get some errors when installing multiple packages that are like this:

Installation paths not writeable, unable to update packages
path: /opt/R/lib/R/library
packages:
bslib, cluster, foreign, haven, htmlwidgets, KernSmooth, lattice, Matrix, mgcv, nlme, rpart, scales, spatial, stringi, survival, tinytex, TTR

Wanding Zhou - Bioinformatics · Answer 9 · Fri Dec 01 2023 22:36:01 GMT+0800 (China Standard Time)

It's interesting that I have the same version numbers as you listed. and I just deleted my cache and re-cached without issue. Let me poke things around more

ardan33 · Answer 10 · Fri Dec 01 2023 22:40:11 GMT+0800 (China Standard Time)

okay, thank you! I think that maybe the packages didn't fully install correctly even though it lists the correct versions when I run sessioninfo(). I am trying to re-install as we speak in a new library location to see if that fixes it.

ardan33 · Answer 11 · Fri Dec 01 2023 22:43:36 GMT+0800 (China Standard Time)

I believe that what I just did with installing in a new lib location fixed the issue. Thanks for looking into this!