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LieberInstitute / recount3

Explore and download data from the recount3 project
http://lieberinstitute.github.io/recount3
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recount3_url' is not a valid supported URL #23

Closed xiangwei6963 closed 2 years ago

xiangwei6963 commented 2 years ago

Hi authors: It comes to an error when I run recount3 as follows: Error: 'recount3_url' is not a valid supported URL since it's missing the URL//homes_index text file or 'recount3_url' is not an existing directory in your file system. So what should I do? Thank you!

lcolladotor commented 2 years ago

Hi,

Can you provide a reproducible example using the reprex R package? https://reprex.tidyverse.org/

Thank you!

Best, Leo

xiangwei6963 commented 2 years ago

Hi, I run the code as follows: 

recount3::create_rse_manual(
  project = "THYROID",
  project_home = "data_sources/gtex",
  organism = "human",
  annotation = "gencode_v26",
  type = "gene"
)
#> Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.

Created on 2022-07-04 by the reprex package (v2.0.1)

lcolladotor commented 2 years ago

Thanks for the reprex and sorry for the delay. I just tried it out and it does work for me. What recount3 version are you using?

Maybe it was a temporary issue with duffel? Can you try it again and see if it works now?

Thanks!

```R > x <- recount3::create_rse_manual( + project = "THYROID", + project_home = "data_sources/gtex", + organism = "human", + annotation = "gencode_v26", + type = "gene" + ) 2022-08-16 12:59:41 downloading and reading the metadata. 2022-08-16 12:59:46 caching file gtex.gtex.THYROID.MD.gz. adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/ID/THYROID/gtex.gtex.THYROID.MD.gz' |======================================================================| 100% 2022-08-16 12:59:48 caching file gtex.recount_project.THYROID.MD.gz. adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/ID/THYROID/gtex.recount_project.THYROID.MD.gz' |======================================================================| 100% 2022-08-16 12:59:49 caching file gtex.recount_qc.THYROID.MD.gz. adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/ID/THYROID/gtex.recount_qc.THYROID.MD.gz' |======================================================================| 100% 2022-08-16 12:59:52 caching file gtex.recount_seq_qc.THYROID.MD.gz. adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/ID/THYROID/gtex.recount_seq_qc.THYROID.MD.gz' |======================================================================| 100% 2022-08-16 12:59:53 downloading and reading the feature information. 2022-08-16 12:59:54 caching file human.gene_sums.G026.gtf.gz. 2022-08-16 12:59:54 downloading and reading the counts: 706 samples across 63856 features. 2022-08-16 12:59:56 caching file gtex.gene_sums.THYROID.G026.gz. adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/gene_sums/ID/THYROID/gtex.gene_sums.THYROID.G026.gz' |======================================================================| 100% 2022-08-16 13:00:03 construcing the RangedSummarizedExperiment (rse) object. > options(width = 120) > sessioninfo::session_info() ─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.2.1 (2022-06-23) os macOS Monterey 12.5 system aarch64, darwin20 ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/New_York date 2022-08-16 pandoc 2.17.1.1 @ /opt/homebrew/bin/pandoc ─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── package * version date (UTC) lib source assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0) Biobase 2.56.0 2022-04-26 [1] Bioconductor BiocFileCache 2.4.0 2022-04-26 [1] Bioconductor BiocGenerics 0.42.0 2022-04-26 [1] Bioconductor BiocIO 1.6.0 2022-04-26 [1] Bioconductor BiocParallel 1.30.3 2022-06-05 [1] Bioconductor Biostrings 2.64.0 2022-04-26 [1] Bioconductor bit 4.0.4 2020-08-04 [1] CRAN (R 4.2.0) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.0) bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0) blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.0) brio 1.1.3 2021-11-30 [1] CRAN (R 4.2.0) cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0) callr 3.7.1 2022-07-13 [1] CRAN (R 4.2.1) cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.0) codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.1) colorout 1.2-2 2022-03-01 [1] Github (jalvesaq/colorout@79931fd) crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0) curl 4.3.2 2021-06-23 [1] CRAN (R 4.2.0) data.table 1.14.2 2021-09-27 [1] CRAN (R 4.2.0) DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0) dbplyr 2.2.1 2022-06-27 [1] CRAN (R 4.2.0) DelayedArray 0.22.0 2022-04-26 [1] Bioconductor devtools * 2.4.4 2022-07-20 [1] CRAN (R 4.2.0) digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0) dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.2.0) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0) fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) filelock 1.0.2 2018-10-05 [1] CRAN (R 4.2.0) fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0) generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0) GenomeInfoDb 1.32.2 2022-05-15 [1] Bioconductor GenomeInfoDbData 1.2.8 2022-04-28 [1] Bioconductor GenomicAlignments 1.32.1 2022-07-24 [1] Bioconductor GenomicRanges 1.48.0 2022-04-26 [1] Bioconductor glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0) htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.2.0) httpuv 1.6.5 2022-01-05 [1] CRAN (R 4.2.0) httr 1.4.3 2022-05-04 [1] CRAN (R 4.2.0) IRanges 2.30.0 2022-04-26 [1] Bioconductor later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0) lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.1) lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.2.1) MatrixGenerics 1.8.1 2022-06-26 [1] Bioconductor matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.2.0) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0) mime 0.12 2021-09-28 [1] CRAN (R 4.2.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0) pillar 1.8.0 2022-07-18 [1] CRAN (R 4.2.0) pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 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RSQLite 2.2.15 2022-07-17 [1] CRAN (R 4.2.0) rsthemes 0.3.1 2022-03-01 [1] Github (gadenbuie/rsthemes@bbe73ca) rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0) rtracklayer 1.56.1 2022-06-23 [1] Bioconductor S4Vectors 0.34.0 2022-04-26 [1] Bioconductor sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) shiny 1.7.2 2022-07-19 [1] CRAN (R 4.2.0) stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1) stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0) SummarizedExperiment 1.26.1 2022-04-29 [1] Bioconductor testthat * 3.1.4 2022-04-26 [1] CRAN (R 4.2.0) tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1) tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.0) urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0) usethis * 2.1.6 2022-05-25 [1] CRAN (R 4.2.0) utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0) vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0) XML 3.99-0.10 2022-06-09 [1] CRAN (R 4.2.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0) XVector 0.36.0 2022-04-26 [1] Bioconductor yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0) zlibbioc 1.42.0 2022-04-26 [1] Bioconductor [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ```
Florencia-DeLillo commented 2 years ago

Hi!!

I'm getting the same error too. In my case, I 'm running the example code in your documentation page (https://rna.recount.bio/docs/quick-access.html#quick-recount3)

Error: 'recount3_url' is not a valid supported URL since it's missing the URL//homes_index text file or 'recount3_url' is not an existing directory in your file system.

Thanks!

lcolladotor commented 2 years ago

Can you provide the output of options(width = 120); sessioninfo::session_info()? Also try using reprex https://reprex.tidyverse.org/. Thanks!

Florencia-DeLillo commented 2 years ago

Hi!!!

options(width = 120); sessioninfo::session_info()
#> - Session info -------------------------------------------------------------------------------------------------------
#>  setting  value
#>  version  R version 4.1.2 (2021-11-01)
#>  os       Windows 10 x64 (build 19044)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  Spanish_Argentina.1252
#>  ctype    Spanish_Argentina.1252
#>  tz       America/Buenos_Aires
#>  date     2022-08-19
#>  pandoc   2.18 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> - Packages -----------------------------------------------------------------------------------------------------------
#>  package     * version date (UTC) lib source
#>  cli           3.3.0   2022-04-25 [1] CRAN (R 4.1.3)
#>  digest        0.6.29  2021-12-01 [1] CRAN (R 4.1.2)
#>  evaluate      0.16    2022-08-09 [1] CRAN (R 4.1.3)
#>  fansi         1.0.3   2022-03-24 [1] CRAN (R 4.1.3)
#>  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.1.2)
#>  fs            1.5.2   2021-12-08 [1] CRAN (R 4.1.2)
#>  glue          1.6.2   2022-02-24 [1] CRAN (R 4.1.2)
#>  highr         0.9     2021-04-16 [1] CRAN (R 4.1.2)
#>  htmltools     0.5.3   2022-07-18 [1] CRAN (R 4.1.3)
#>  knitr         1.39    2022-04-26 [1] CRAN (R 4.1.3)
#>  lifecycle     1.0.1   2021-09-24 [1] CRAN (R 4.1.2)
#>  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.1.3)
#>  pillar        1.8.1   2022-08-19 [1] CRAN (R 4.1.2)
#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.1.2)
#>  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.1.2)
#>  R.cache       0.16.0  2022-07-21 [1] CRAN (R 4.1.3)
#>  R.methodsS3   1.8.2   2022-06-13 [1] CRAN (R 4.1.3)
#>  R.oo          1.25.0  2022-06-12 [1] CRAN (R 4.1.3)
#>  R.utils       2.12.0  2022-06-28 [1] CRAN (R 4.1.3)
#>  reprex        2.0.2   2022-08-17 [1] CRAN (R 4.1.2)
#>  rlang         1.0.4   2022-07-12 [1] CRAN (R 4.1.3)
#>  rmarkdown     2.15    2022-08-16 [1] CRAN (R 4.1.2)
#>  rstudioapi    0.13    2020-11-12 [1] CRAN (R 4.1.2)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.1.3)
#>  stringi       1.7.6   2021-11-29 [1] CRAN (R 4.1.2)
#>  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.1.2)
#>  styler        1.7.0   2022-03-13 [1] CRAN (R 4.1.3)
#>  tibble        3.1.8   2022-07-22 [1] CRAN (R 4.1.3)
#>  utf8          1.2.2   2021-07-24 [1] CRAN (R 4.1.2)
#>  vctrs         0.4.1   2022-04-13 [1] CRAN (R 4.1.3)
#>  withr         2.5.0   2022-03-03 [1] CRAN (R 4.1.2)
#>  xfun          0.32    2022-08-10 [1] CRAN (R 4.1.3)
#>  yaml          2.3.5   2022-02-21 [1] CRAN (R 4.1.2)
#> 
#>  [1] C:/Users/flord/OneDrive/Documentos/R/win-library/4.1
#>  [2] C:/Program Files/R/R-4.1.2/library
#> 
#> ----------------------------------------------------------------------------------------------------------------------

Created on 2022-08-19 with reprex v2.0.2

I attach the output as an image as well, since when using reprex not all of them are printed (sorry, I don't know why that happens)

image

lcolladotor commented 2 years ago

Hi again,

reprex

When using reprex, you have to specify what code you want to run in a new clean R session. Sounds like you only had the sessioninfo code selected when you ran reprex::reprex() and forgot to include the recount3 code, hence why your list of packages is smaller.

For example, to generate

recount3::create_rse_manual(
  project = "THYROID",
  project_home = "data_sources/gtex",
  organism = "human",
  annotation = "gencode_v26",
  type = "gene"
)
#> 2022-08-19 10:08:03 downloading and reading the metadata.
#> 2022-08-19 10:08:06 caching file gtex.gtex.THYROID.MD.gz.
#> 2022-08-19 10:08:06 caching file gtex.recount_project.THYROID.MD.gz.
#> 2022-08-19 10:08:06 caching file gtex.recount_qc.THYROID.MD.gz.
#> 2022-08-19 10:08:07 caching file gtex.recount_seq_qc.THYROID.MD.gz.
#> 2022-08-19 10:08:07 downloading and reading the feature information.
#> 2022-08-19 10:08:09 caching file human.gene_sums.G026.gtf.gz.
#> 2022-08-19 10:08:09 downloading and reading the counts: 706 samples across 63856 features.
#> 2022-08-19 10:08:10 caching file gtex.gene_sums.THYROID.G026.gz.
#> 2022-08-19 10:08:14 construcing the RangedSummarizedExperiment (rse) object.
#> class: RangedSummarizedExperiment 
#> dim: 63856 706 
#> metadata(8): time_created recount3_version ... annotation recount3_url
#> assays(1): raw_counts
#> rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ...
#>   ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y
#> rowData names(10): source type ... havana_gene tag
#> colnames(706): GTEX-T5JW-1226-SM-3GACY.1 GTEX-WXYG-0226-SM-3NB2Y.1 ...
#>   GTEX-1MJK2-0826-SM-DTXE8.1 GTEX-1NUQO-0926-SM-DTXEX.1
#> colData names(198): rail_id external_id ... recount_seq_qc.errq
#>   BigWigURL

options(width = 120)
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.1 (2022-06-23)
#>  os       macOS Monterey 12.5
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2022-08-19
#>  pandoc   2.17.1.1 @ /opt/homebrew/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package              * version   date (UTC) lib source
#>  assertthat             0.2.1     2019-03-21 [1] CRAN (R 4.2.0)
#>  Biobase                2.56.0    2022-04-26 [1] Bioconductor
#>  BiocFileCache          2.4.0     2022-04-26 [1] Bioconductor
#>  BiocGenerics           0.42.0    2022-04-26 [1] Bioconductor
#>  BiocIO                 1.6.0     2022-04-26 [1] Bioconductor
#>  BiocParallel           1.30.3    2022-06-05 [1] Bioconductor
#>  Biostrings             2.64.0    2022-04-26 [1] Bioconductor
#>  bit                    4.0.4     2020-08-04 [1] CRAN (R 4.2.0)
#>  bit64                  4.0.5     2020-08-30 [1] CRAN (R 4.2.0)
#>  bitops                 1.0-7     2021-04-24 [1] CRAN (R 4.2.0)
#>  blob                   1.2.3     2022-04-10 [1] CRAN (R 4.2.0)
#>  cachem                 1.0.6     2021-08-19 [1] CRAN (R 4.2.0)
#>  cli                    3.3.0     2022-04-25 [1] CRAN (R 4.2.0)
#>  codetools              0.2-18    2020-11-04 [1] CRAN (R 4.2.1)
#>  crayon                 1.5.1     2022-03-26 [1] CRAN (R 4.2.0)
#>  curl                   4.3.2     2021-06-23 [1] CRAN (R 4.2.0)
#>  data.table             1.14.2    2021-09-27 [1] CRAN (R 4.2.0)
#>  DBI                    1.1.3     2022-06-18 [1] CRAN (R 4.2.0)
#>  dbplyr                 2.2.1     2022-06-27 [1] CRAN (R 4.2.0)
#>  DelayedArray           0.22.0    2022-04-26 [1] Bioconductor
#>  digest                 0.6.29    2021-12-01 [1] CRAN (R 4.2.0)
#>  dplyr                  1.0.9     2022-04-28 [1] CRAN (R 4.2.0)
#>  ellipsis               0.3.2     2021-04-29 [1] CRAN (R 4.2.0)
#>  evaluate               0.16      2022-08-09 [1] CRAN (R 4.2.0)
#>  fansi                  1.0.3     2022-03-24 [1] CRAN (R 4.2.0)
#>  fastmap                1.1.0     2021-01-25 [1] CRAN (R 4.2.0)
#>  filelock               1.0.2     2018-10-05 [1] CRAN (R 4.2.0)
#>  fs                     1.5.2     2021-12-08 [1] CRAN (R 4.2.0)
#>  generics               0.1.3     2022-07-05 [1] CRAN (R 4.2.0)
#>  GenomeInfoDb           1.32.3    2022-08-09 [1] Bioconductor
#>  GenomeInfoDbData       1.2.8     2022-04-28 [1] Bioconductor
#>  GenomicAlignments      1.32.1    2022-07-24 [1] Bioconductor
#>  GenomicRanges          1.48.0    2022-04-26 [1] Bioconductor
#>  glue                   1.6.2     2022-02-24 [1] CRAN (R 4.2.0)
#>  highr                  0.9       2021-04-16 [1] CRAN (R 4.2.0)
#>  htmltools              0.5.3     2022-07-18 [1] CRAN (R 4.2.0)
#>  httr                   1.4.4     2022-08-17 [1] CRAN (R 4.2.0)
#>  IRanges                2.30.0    2022-04-26 [1] Bioconductor
#>  knitr                  1.39      2022-04-26 [1] CRAN (R 4.2.0)
#>  lattice                0.20-45   2021-09-22 [1] CRAN (R 4.2.1)
#>  lifecycle              1.0.1     2021-09-24 [1] CRAN (R 4.2.0)
#>  magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.2.0)
#>  Matrix                 1.4-1     2022-03-23 [1] CRAN (R 4.2.1)
#>  MatrixGenerics         1.8.1     2022-06-26 [1] Bioconductor
#>  matrixStats            0.62.0    2022-04-19 [1] CRAN (R 4.2.0)
#>  memoise                2.0.1     2021-11-26 [1] CRAN (R 4.2.0)
#>  pillar                 1.8.0     2022-07-18 [1] CRAN (R 4.2.0)
#>  pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.2.0)
#>  purrr                  0.3.4     2020-04-17 [1] CRAN (R 4.2.0)
#>  R.cache                0.16.0    2022-07-21 [1] CRAN (R 4.2.0)
#>  R.methodsS3            1.8.2     2022-06-13 [1] CRAN (R 4.2.0)
#>  R.oo                   1.25.0    2022-06-12 [1] CRAN (R 4.2.0)
#>  R.utils                2.12.0    2022-06-28 [1] CRAN (R 4.2.0)
#>  R6                     2.5.1     2021-08-19 [1] CRAN (R 4.2.0)
#>  rappdirs               0.3.3     2021-01-31 [1] CRAN (R 4.2.0)
#>  Rcpp                   1.0.9     2022-07-08 [1] CRAN (R 4.2.1)
#>  RCurl                  1.98-1.8  2022-07-30 [1] CRAN (R 4.2.0)
#>  recount3               1.6.0     2022-04-26 [1] Bioconductor
#>  reprex                 2.0.1     2021-08-05 [1] CRAN (R 4.2.0)
#>  restfulr               0.0.15    2022-06-16 [1] CRAN (R 4.2.0)
#>  rjson                  0.2.21    2022-01-09 [1] CRAN (R 4.2.0)
#>  rlang                  1.0.4     2022-07-12 [1] CRAN (R 4.2.1)
#>  rmarkdown              2.14      2022-04-25 [1] CRAN (R 4.2.0)
#>  Rsamtools              2.12.0    2022-04-26 [1] Bioconductor
#>  RSQLite                2.2.16    2022-08-17 [1] CRAN (R 4.2.0)
#>  rtracklayer            1.56.1    2022-06-23 [1] Bioconductor
#>  S4Vectors              0.34.0    2022-04-26 [1] Bioconductor
#>  sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.2.0)
#>  stringi                1.7.8     2022-07-11 [1] CRAN (R 4.2.1)
#>  stringr                1.4.0     2019-02-10 [1] CRAN (R 4.2.0)
#>  styler                 1.7.0     2022-03-13 [1] CRAN (R 4.2.0)
#>  SummarizedExperiment   1.26.1    2022-04-29 [1] Bioconductor
#>  tibble                 3.1.8     2022-07-22 [1] CRAN (R 4.2.1)
#>  tidyselect             1.1.2     2022-02-21 [1] CRAN (R 4.2.0)
#>  utf8                   1.2.2     2021-07-24 [1] CRAN (R 4.2.0)
#>  vctrs                  0.4.1     2022-04-13 [1] CRAN (R 4.2.0)
#>  withr                  2.5.0     2022-03-03 [1] CRAN (R 4.2.0)
#>  xfun                   0.32      2022-08-10 [1] CRAN (R 4.2.0)
#>  XML                    3.99-0.10 2022-06-09 [1] CRAN (R 4.2.0)
#>  XVector                0.36.0    2022-04-26 [1] Bioconductor
#>  yaml                   2.3.5     2022-02-21 [1] CRAN (R 4.2.0)
#>  zlibbioc               1.42.0    2022-04-26 [1] Bioconductor
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Created on 2022-08-19 by the reprex package (v2.0.1)

I first wrote on a new script the following R code:

recount3::create_rse_manual(
  project = "THYROID",
  project_home = "data_sources/gtex",
  organism = "human",
  annotation = "gencode_v26",
  type = "gene"
)

options(width = 120)
sessioninfo::session_info()

then I copied it to, then I ran reprex::reprex().

JHPCE

I also can run the code without reproducing the error at JHPCE, our local HPC system.

```R > recount3::create_rse_manual( + project = "THYROID", + project_home = "data_sources/gtex", + organism = "human", + annotation = "gencode_v26", + type = "gene" + ) 2022-08-19 10:11:03 downloading and reading the metadata. 2022-08-19 10:11:04 caching file gtex.gtex.THYROID.MD.gz. adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/ID/THYROID/gtex.gtex.THYROID.MD.gz' |======================================================================| 100% 2022-08-19 10:11:05 caching file gtex.recount_project.THYROID.MD.gz. adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/ID/THYROID/gtex.recount_project.THYROID.MD.gz' |======================================================================| 100% 2022-08-19 10:11:07 caching file gtex.recount_qc.THYROID.MD.gz. adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/ID/THYROID/gtex.recount_qc.THYROID.MD.gz' |======================================================================| 100% 2022-08-19 10:11:08 caching file gtex.recount_seq_qc.THYROID.MD.gz. adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/ID/THYROID/gtex.recount_seq_qc.THYROID.MD.gz' |======================================================================| 100% 2022-08-19 10:11:09 downloading and reading the feature information. 2022-08-19 10:11:09 caching file human.gene_sums.G026.gtf.gz. adding rname 'http://duffel.rail.bio/recount3/human/annotations/gene_sums/human.gene_sums.G026.gtf.gz' |======================================================================| 100% 2022-08-19 10:11:11 downloading and reading the counts: 706 samples across 63856 features. 2022-08-19 10:11:11 caching file gtex.gene_sums.THYROID.G026.gz. adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/gene_sums/ID/THYROID/gtex.gene_sums.THYROID.G026.gz' |======================================================================| 100% 2022-08-19 10:11:24 construcing the RangedSummarizedExperiment (rse) object. class: RangedSummarizedExperiment dim: 63856 706 metadata(8): time_created recount3_version ... annotation recount3_url assays(1): raw_counts rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ... ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y rowData names(10): source type ... havana_gene tag colnames(706): GTEX-T5JW-1226-SM-3GACY.1 GTEX-WXYG-0226-SM-3NB2Y.1 ... GTEX-1MJK2-0826-SM-DTXE8.1 GTEX-1NUQO-0926-SM-DTXEX.1 colData names(198): rail_id external_id ... recount_seq_qc.errq BigWigURL > > options(width = 120) > sessioninfo::session_info() ─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R Under development (unstable) (2021-11-06 r81149) os CentOS Linux 7 (Core) system x86_64, linux-gnu ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz US/Eastern date 2022-08-19 pandoc 2.11.0.4 @ /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-devel/bin/pandoc ─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────── package * version date (UTC) lib source assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.1.0) Biobase 2.56.0 2022-04-26 [1] Bioconductor BiocFileCache 2.4.0 2022-04-26 [2] Bioconductor BiocGenerics 0.42.0 2022-04-26 [2] Bioconductor BiocIO 1.6.0 2022-04-26 [2] Bioconductor BiocParallel 1.30.3 2022-06-05 [2] Bioconductor Biostrings 2.64.0 2022-04-26 [2] Bioconductor bit 4.0.4 2020-08-04 [2] CRAN (R 4.1.0) bit64 4.0.5 2020-08-30 [2] CRAN (R 4.1.0) bitops 1.0-7 2021-04-24 [2] CRAN (R 4.2.0) blob 1.2.3 2022-04-10 [2] CRAN (R 4.2.0) cachem 1.0.6 2021-08-19 [2] CRAN (R 4.2.0) cli 3.3.0 2022-04-25 [2] CRAN (R 4.2.0) codetools 0.2-18 2020-11-04 [3] CRAN (R 4.2.0) colorout 1.2-2 2022-03-04 [1] Github (jalvesaq/colorout@79931fd) colorspace 2.0-3 2022-02-21 [2] CRAN (R 4.2.0) crayon 1.5.1 2022-03-26 [2] CRAN (R 4.2.0) curl 4.3.2 2021-06-23 [2] CRAN (R 4.2.0) data.table 1.14.2 2021-09-27 [2] CRAN (R 4.2.0) DBI 1.1.3 2022-06-18 [2] CRAN (R 4.2.0) dbplyr 2.2.1 2022-06-27 [2] CRAN (R 4.2.0) DelayedArray 0.22.0 2022-04-26 [2] Bioconductor digest 0.6.29 2021-12-01 [2] CRAN (R 4.2.0) dplyr 1.0.9 2022-04-28 [2] CRAN (R 4.2.0) ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.2.0) fansi 1.0.3 2022-03-24 [2] CRAN (R 4.2.0) fastmap 1.1.0 2021-01-25 [2] CRAN (R 4.1.0) filelock 1.0.2 2018-10-05 [2] CRAN (R 4.1.0) generics 0.1.3 2022-07-05 [2] CRAN (R 4.2.0) GenomeInfoDb 1.32.3 2022-08-09 [1] Bioconductor GenomeInfoDbData 1.2.8 2022-04-16 [2] Bioconductor GenomicAlignments 1.32.1 2022-07-24 [2] Bioconductor GenomicRanges 1.48.0 2022-04-26 [2] Bioconductor ggplot2 3.3.6 2022-05-03 [2] CRAN (R 4.2.0) glue 1.6.2 2022-02-24 [2] CRAN (R 4.2.0) gtable 0.3.0 2019-03-25 [2] CRAN (R 4.1.0) htmltools 0.5.3 2022-07-18 [2] CRAN (R 4.2.0) htmlwidgets 1.5.4 2021-09-08 [2] CRAN (R 4.2.0) httpuv 1.6.5 2022-01-05 [2] CRAN (R 4.2.0) httr 1.4.4 2022-08-17 [2] CRAN (R 4.2.0) IRanges 2.30.0 2022-04-26 [2] Bioconductor jsonlite 1.8.0 2022-02-22 [2] CRAN (R 4.2.0) later 1.3.0 2021-08-18 [2] CRAN (R 4.2.0) lattice 0.20-45 2021-09-22 [3] CRAN (R 4.2.0) lifecycle 1.0.1 2021-09-24 [2] CRAN (R 4.2.0) magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.2.0) Matrix 1.4-1 2022-03-23 [3] CRAN (R 4.2.0) MatrixGenerics 1.8.1 2022-06-26 [2] Bioconductor matrixStats 0.62.0 2022-04-19 [2] CRAN (R 4.2.0) memoise 2.0.1 2021-11-26 [2] CRAN (R 4.2.0) munsell 0.5.0 2018-06-12 [2] CRAN (R 4.1.0) pillar 1.8.1 2022-08-19 [2] CRAN (R 4.2.0) pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.1.0) png 0.1-7 2013-12-03 [2] CRAN (R 4.1.0) promises 1.2.0.1 2021-02-11 [2] CRAN (R 4.1.0) purrr 0.3.4 2020-04-17 [2] CRAN (R 4.1.0) R.methodsS3 1.8.2 2022-06-13 [2] CRAN (R 4.2.0) R.oo 1.25.0 2022-06-12 [2] CRAN (R 4.2.0) R.utils 2.12.0 2022-06-28 [2] CRAN (R 4.2.0) R6 2.5.1 2021-08-19 [2] CRAN (R 4.2.0) rappdirs 0.3.3 2021-01-31 [2] CRAN (R 4.1.0) Rcpp 1.0.9 2022-07-08 [2] CRAN (R 4.2.0) RCurl 1.98-1.8 2022-07-30 [2] CRAN (R 4.2.0) recount3 1.6.0 2022-04-26 [2] Bioconductor restfulr 0.0.15 2022-06-16 [2] CRAN (R 4.2.0) rjson 0.2.21 2022-01-09 [2] CRAN (R 4.2.0) rlang 1.0.4 2022-07-12 [2] CRAN (R 4.2.0) rmote 0.3.4 2022-03-04 [1] Github (cloudyr/rmote@fbce611) Rsamtools 2.12.0 2022-04-26 [2] Bioconductor RSQLite 2.2.16 2022-08-17 [2] CRAN (R 4.2.0) rtracklayer 1.56.1 2022-06-23 [2] Bioconductor S4Vectors 0.34.0 2022-04-26 [2] Bioconductor scales 1.2.0 2022-04-13 [2] CRAN (R 4.2.0) servr 0.24 2021-11-16 [1] CRAN (R 4.2.0) sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.2.0) SummarizedExperiment 1.26.1 2022-04-29 [2] Bioconductor tibble 3.1.8 2022-07-22 [2] CRAN (R 4.2.0) tidyselect 1.1.2 2022-02-21 [2] CRAN (R 4.2.0) utf8 1.2.2 2021-07-24 [2] CRAN (R 4.2.0) vctrs 0.4.1 2022-04-13 [2] CRAN (R 4.2.0) xfun 0.32 2022-08-10 [2] CRAN (R 4.2.0) XML 3.99-0.10 2022-06-09 [2] CRAN (R 4.2.0) XVector 0.36.0 2022-04-26 [2] Bioconductor yaml 2.3.5 2022-02-21 [2] CRAN (R 4.2.0) zlibbioc 1.42.0 2022-04-26 [2] Bioconductor [1] /users/lcollado/R/devel [2] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-devel/R/devel/lib64/R/site-library [3] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-devel/R/devel/lib64/R/library ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── > ```

Speculation

In any case, from your screenshot, I see that you are using R 4.1 (the current release is 4.2) and recount3 version 1.4.0. The latest release version is 1.6.0, which isn't very different from 1.4.0 as you can see at https://github.com/LieberInstitute/recount3/commits/master. Technically speaking, your and my R setup are different because although we are using very similar recount3 versions, dependencies are different. In general, it's best to use the latest stable release of R to have access to the latest tested tools.

Having said that, I don't think that this particular error shouldn't be related to other dependencies. But without any other leads on how to reproduce the error, I would encourage you to give it a try with R 4.2 and recount3 version 1.6.0 (aka, try it with an R session info as close to the ones I reported successful runs).

I don't know if it's a time of day or something related to duffel. To test the time of day component, you could try running the code at different times one day. To test the duffel part, you could use recount3_url = "http://idies.jhu.edu/recount3/data".

And well, make sure you are running exactly the same code I'm running (hence why I asked for the full reprex initially, so I could help you check that).

Best, Leo

lcolladotor commented 2 years ago

By the way, regarding time of day, I don't that's the issue since well, Bioconductor checks the package daily on both release and devel, each on 3 operating systems. So well, I would have gotten emails about errors if that was the case.

Regarding duffel, I don't think that's the issue either. But well, you never know I guess. Like, whenever we have an issue with duffel (like forgetting to pay for it), we see errors across all computers.

So yeah, that's why upgrading to R 4.2 and using recount3 1.6.0 is the only lead right now.

Florencia-DeLillo commented 2 years ago

I Just upgraded R and re-install recount 3... It worked!!!

Thank you very much and sorry for the inconvenience. Have a nice day :) Florencia

lcolladotor commented 2 years ago

Awesome! Thanks for the info @Florencia-DeLillo =)

lcolladotor commented 1 year ago

Hi again,

If you are a Windows user, duffel now fully works on that operating system. That is, the duffel access issue has now been addressed by the internal switch from RCurl::url.exists() to httr::http_error(). You can gain access to these updates by installing recount3 version 1.10.2 (bioc-release aka 3.17) or 1.11.2 (bioc-devel aka 3.18).

duffel currently points to https://registry.opendata.aws/recount/ instead of IDIES.

Best, Leo