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Bioconductor / UniProt.ws

R Interface to UniProt Web Services
https://bioconductor.org/packages/UniProt.ws
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Error running UniProt.ws(taxId=9606) #26

Open CreLox opened 1 day ago

CreLox commented 1 day ago

up <- UniProt.ws(taxId=9606)

Error in validObject(.Object) : invalid class “UniProt.ws” object: 1: invalid object for slot "taxIdUniprots" in class "UniProt.ws": got class "NULL", should be or extend class "character" invalid class “UniProt.ws” object: 2: invalid object for slot "organism" in class "UniProt.ws": got class "NULL", should be or extend class "character"

LiNk-NY commented 1 day ago

Hi @CreLox

This works for me in Bioc old release version 3.19, release 3.20, and devel 3.21. Please provide your session info if you are still seeing issues.

Best regards, Marcel

mattlee821 commented 1 day ago

i get the same error using Bioc 3.19 and 3.20; info below from 3.19:

up <- UniProt.ws(taxId = 9606) | | 0% Error in validObject(.Object) : invalid class “UniProt.ws” object: 1: invalid object for slot "taxIdUniprots" in class "UniProt.ws": got class "NULL", should be or extend class "character" invalid class “UniProt.ws” object: 2: invalid object for slot "organism" in class "UniProt.ws": got class "NULL", should be or extend class "character"

sessionInfo() R version 4.4.2 (2024-10-31) Platform: aarch64-apple-darwin20 Running under: macOS Sequoia 15.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Paris tzcode source: internal

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

other attached packages: [1] UniProt.ws_2.44.0 RSQLite_2.3.7 BiocGenerics_0.50.0

loaded via a namespace (and not attached): [1] bit_4.5.0 jsonlite_1.8.9 dplyr_1.1.4 compiler_4.4.2 BiocManager_1.30.25
[6] crayon_1.5.3 BiocBaseUtils_1.6.0 filelock_1.0.3 tidyselect_1.2.1 Biobase_2.64.0
[11] blob_1.2.4 Biostrings_2.72.1 progress_1.2.3 IRanges_2.38.1 png_0.1-8
[16] fastmap_1.2.0 R6_2.5.1 XVector_0.44.0 rjsoncons_1.3.1 generics_0.1.3
[21] curl_6.0.0 GenomeInfoDb_1.40.1 tibble_3.2.1 AnnotationDbi_1.66.0 GenomeInfoDbData_1.2.12 [26] DBI_1.2.3 pillar_1.9.0 rlang_1.1.4 utf8_1.2.4 KEGGREST_1.44.1
[31] cachem_1.1.0 bit64_4.5.2 memoise_2.0.1 cli_3.6.3 magrittr_2.0.3
[36] zlibbioc_1.50.0 digest_0.6.37 httpcache_1.2.0 dbplyr_2.5.0 hms_1.1.3
[41] lifecycle_1.0.4 BiocFileCache_2.12.0 prettyunits_1.2.0 S4Vectors_0.42.1 vctrs_0.6.5
[46] glue_1.8.0 stats4_4.4.2 fansi_1.0.6 httr_1.4.7 tools_4.4.2
[51] pkgconfig_2.0.3 UCSC.utils_1.0.0

CreLox commented 1 day ago

Hi @CreLox

This works for me in Bioc old release version 3.19, release 3.20, and devel 3.21. Please provide your session info if you are still seeing issues.

Best regards, Marcel

library(UniProt.ws) 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,
table, tapply, union, unique, unsplit, which.max, which.min

Loading required package: RSQLite

up <- UniProt.ws(taxId=9606) | | 0% Error in validObject(.Object) : invalid class “UniProt.ws” object: 1: invalid object for slot "taxIdUniprots" in class "UniProt.ws": got class "NULL", should be or extend class "character" invalid class “UniProt.ws” object: 2: invalid object for slot "organism" in class "UniProt.ws": got class "NULL", should be or extend class "character" sessionInfo() R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS Ventura 13.6.9

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Berlin tzcode source: internal

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

other attached packages: [1] UniProt.ws_2.44.0 RSQLite_2.3.7 BiocGenerics_0.50.0

loaded via a namespace (and not attached): [1] bit_4.5.0 jsonlite_1.8.9 dplyr_1.1.4 compiler_4.4.1
[5] crayon_1.5.3 BiocBaseUtils_1.6.0 filelock_1.0.3 tidyselect_1.2.1
[9] Biobase_2.64.0 blob_1.2.4 Biostrings_2.72.1 IRanges_2.38.1
[13] progress_1.2.3 png_0.1-8 fastmap_1.2.0 R6_2.5.1
[17] XVector_0.44.0 rjsoncons_1.3.1 generics_0.1.3 curl_5.2.3
[21] GenomeInfoDb_1.40.1 tibble_3.2.1 AnnotationDbi_1.66.0 GenomeInfoDbData_1.2.12 [25] DBI_1.2.3 pillar_1.9.0 rlang_1.1.4 utf8_1.2.4
[29] KEGGREST_1.44.1 cachem_1.1.0 bit64_4.5.2 memoise_2.0.1
[33] cli_3.6.3 magrittr_2.0.3 zlibbioc_1.50.0 digest_0.6.37
[37] httpcache_1.2.0 dbplyr_2.5.0 hms_1.1.3 lifecycle_1.0.4
[41] BiocFileCache_2.12.0 prettyunits_1.2.0 S4Vectors_0.42.1 vctrs_0.6.5
[45] glue_1.8.0 stats4_4.4.1 fansi_1.0.6 httr_1.4.7
[49] tools_4.4.1 pkgconfig_2.0.3 UCSC.utils_1.0.0

LiNk-NY commented 1 day ago

Please make sure that you have the latest packages installed by doing BiocManager::valid(). I have asked Hervé @hpages if he knows more about the error. I suspect that a subset of packages are out of date or need to be re-installed.

hpages commented 1 day ago

Can't reproduce with 9606 but I get this error if I use an invalid tax id:

> up <- UniProt.ws(taxId = 0)
Error in validObject(.Object) : 
  invalid class “UniProt.ws” object: 1: invalid object for slot "taxIdUniprots" in class "UniProt.ws": got class "logical", should be or extend class "character"
invalid class “UniProt.ws” object: 2: invalid object for slot "organism" in class "UniProt.ws": got class "logical", should be or extend class "character"

In this case queryUniProt() (called by UniProt.ws()) returns a 0-row data.frame with columns of type logical instead of character, which is why we get an invalid object later:

> results <- queryUniProt(query = paste0("taxonomy_id:", 0), c("accession", "organism_name"), n = 25, pageSize = 25)
> results
[1] Entry    Organism
<0 rows> (or 0-length row.names)
> sapply(results, class)
    Entry  Organism 
"logical" "logical"

I suspect that in the case of @CreLox and @mattlee821 above, they also get a 0-row data.frame with columns of type logical, but I don't know why they would get it for tax id 9606. Internet connectivity issue? I didn't dig further into queryUniProt()'s implementation.

H.

Camsid commented 1 day ago

Hi. Here is my session info:

sessionInfo() R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS 15.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago tzcode source: internal

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

other attached packages: [1] jsonlite_1.8.9 httr_1.4.7 UniProt.ws_2.44.0 RSQLite_2.3.7 BiocGenerics_0.50.0 [6] readxl_1.4.3 dplyr_1.1.4 biomaRt_2.60.1

loaded via a namespace (and not attached): [1] rappdirs_0.3.3 utf8_1.2.4 generics_0.1.3 xml2_1.3.6
[5] stringi_1.8.4 hms_1.1.3 digest_0.6.37 magrittr_2.0.3
[9] fastmap_1.2.0 blob_1.2.4 cellranger_1.1.0 progress_1.2.3
[13] AnnotationDbi_1.66.0 GenomeInfoDb_1.40.1 DBI_1.2.3 BiocManager_1.30.25
[17] purrr_1.0.2 fansi_1.0.6 UCSC.utils_1.0.0 Biostrings_2.72.1
[21] httr2_1.0.6 cli_3.6.3 rlang_1.1.4 crayon_1.5.3
[25] dbplyr_2.5.0 XVector_0.44.0 Biobase_2.64.0 bit64_4.5.2
[29] withr_3.0.2 cachem_1.1.0 BiocBaseUtils_1.6.0 tools_4.4.1
[33] memoise_2.0.1 httpcache_1.2.0 GenomeInfoDbData_1.2.12 filelock_1.0.3
[37] curl_6.0.0 rjsoncons_1.3.1 vctrs_0.6.5 R6_2.5.1
[41] png_0.1-8 stats4_4.4.1 lifecycle_1.0.4 BiocFileCache_2.12.0
[45] zlibbioc_1.50.0 KEGGREST_1.44.1 stringr_1.5.1 S4Vectors_0.42.1
[49] IRanges_2.38.1 bit_4.5.0 pkgconfig_2.0.3 pillar_1.9.0
[53] glue_1.8.0 tibble_3.2.1 tidyselect_1.2.1 rstudioapi_0.17.1
[57] compiler_4.4.1 prettyunits_1.2.0

Also after running BiocManager::valid().:

BiocManager::valid() 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/

R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS 15.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago tzcode source: internal

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

other attached packages: [1] jsonlite_1.8.9 httr_1.4.7 UniProt.ws_2.44.0 RSQLite_2.3.7 BiocGenerics_0.50.0 [6] readxl_1.4.3 dplyr_1.1.4 biomaRt_2.60.1

loaded via a namespace (and not attached): [1] rappdirs_0.3.3 utf8_1.2.4 generics_0.1.3 xml2_1.3.6
[5] stringi_1.8.4 hms_1.1.3 digest_0.6.37 magrittr_2.0.3
[9] fastmap_1.2.0 blob_1.2.4 cellranger_1.1.0 progress_1.2.3
[13] AnnotationDbi_1.66.0 GenomeInfoDb_1.40.1 DBI_1.2.3 BiocManager_1.30.25
[17] purrr_1.0.2 fansi_1.0.6 UCSC.utils_1.0.0 Biostrings_2.72.1
[21] httr2_1.0.6 cli_3.6.3 rlang_1.1.4 crayon_1.5.3
[25] dbplyr_2.5.0 XVector_0.44.0 Biobase_2.64.0 bit64_4.5.2
[29] withr_3.0.2 cachem_1.1.0 BiocBaseUtils_1.6.0 tools_4.4.1
[33] memoise_2.0.1 httpcache_1.2.0 GenomeInfoDbData_1.2.12 filelock_1.0.3
[37] curl_6.0.0 rjsoncons_1.3.1 vctrs_0.6.5 R6_2.5.1
[41] png_0.1-8 stats4_4.4.1 lifecycle_1.0.4 BiocFileCache_2.12.0
[45] zlibbioc_1.50.0 KEGGREST_1.44.1 stringr_1.5.1 S4Vectors_0.42.1
[49] IRanges_2.38.1 bit_4.5.0 pkgconfig_2.0.3 pillar_1.9.0
[53] glue_1.8.0 tibble_3.2.1 tidyselect_1.2.1 rstudioapi_0.17.1
[57] compiler_4.4.1 prettyunits_1.2.0

Bioconductor version '3.19'

create a valid installation with

BiocManager::install("Cairo", update = TRUE, ask = FALSE, force = TRUE)

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

Warning message: 0 packages out-of-date; 1 packages too new

CreLox commented 1 day ago

Please make sure that you have the latest packages installed by doing BiocManager::valid(). I have asked Hervé @hpages if he knows more about the error. I suspect that a subset of packages are out of date or need to be re-installed.

BiocManager::valid() 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.uni-muenster.de [1] TRUE