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ropensci / piggyback

:package: for using large(r) data files on GitHub
https://docs.ropensci.org/piggyback
GNU General Public License v3.0
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`Error in data.frame(file_name = "", size = 0L, timestamp = lubridate::as_datetime(0), : object 'x' not found` #92

Closed bschilder closed 2 years ago

bschilder commented 2 years ago

Hello,

Description

It only occurs on Windows (seen here in my GHA report)

Error in data.frame(file_name = "", size = 0L, timestamp = lubridate::as_datetime(0),  : 
  object 'x' not found
Calls: <Anonymous> ... withVisible -> eval -> eval -> <Anonymous> -> data.frame

I think this error in my function traces back to piggyback::pb_list, and more specifically the pb_info functional internally. https://github.com/ropensci/piggyback/blob/aa6e3f86a9b46e44a977d77c8c8e282be4402a09/R/pb_info.R#L126

Reprex (on Windows)

files <- piggyback::pb_list(repo = "neurogenomics/MAGMA_Celltyping",
                                tag = "latest")

Do you know what might be happening here?

Many thanks in advance, Brian

Session info

``` R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.4 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ewceData_1.4.0 ExperimentHub_2.4.0 AnnotationHub_3.4.0 BiocFileCache_2.4.0 [5] dbplyr_2.2.1 BiocGenerics_0.42.0 MAGMA.Celltyping_2.0.6 loaded via a namespace (and not attached): [1] utf8_1.2.2 R.utils_2.12.0 tidyselect_1.1.2 [4] lme4_1.1-30 RSQLite_2.2.15 AnnotationDbi_1.58.0 [7] htmlwidgets_1.5.4 grid_4.2.0 BiocParallel_1.30.3 [10] devtools_2.4.4 munsell_0.5.0 codetools_0.2-18 [13] miniUI_0.1.1.1 withr_2.5.0 colorspace_2.0-3 [16] Biobase_2.56.0 filelock_1.0.2 knitr_1.39 [19] rstudioapi_0.13 orthogene_1.3.1 stats4_4.2.0 [22] SingleCellExperiment_1.18.0 ggsignif_0.6.3 gitcreds_0.1.1 [25] labeling_0.4.2 MatrixGenerics_1.8.1 GenomeInfoDbData_1.2.8 [28] farver_2.1.1 bit64_4.0.5 rprojroot_2.0.3 [31] vctrs_0.4.1 treeio_1.20.1 generics_0.1.3 [34] xfun_0.31 R6_2.5.1 GenomeInfoDb_1.32.2 [37] bitops_1.0-7 cachem_1.0.6 gridGraphics_0.5-1 [40] DelayedArray_0.22.0 assertthat_0.2.1 promises_1.2.0.1 [43] BiocIO_1.6.0 scales_1.2.0 gtable_0.3.0 [46] processx_3.7.0 rlang_1.0.4 MungeSumstats_1.5.5 [49] splines_4.2.0 rtracklayer_1.57.0 rstatix_0.7.0 [52] lazyeval_0.2.2 gargle_1.2.0 broom_1.0.0 [55] BiocManager_1.30.18 yaml_2.3.5 reshape2_1.4.4 [58] abind_1.4-5 GenomicFeatures_1.48.3 backports_1.4.1 [61] httpuv_1.6.5 tools_4.2.0 usethis_2.1.6 [64] ggplotify_0.1.0 ggplot2_3.3.6 ellipsis_0.3.2 [67] RColorBrewer_1.1-3 ggdendro_0.1.23 sessioninfo_1.2.2 [70] Rcpp_1.0.9 plyr_1.8.7 progress_1.2.2 [73] zlibbioc_1.42.0 purrr_0.3.4 RCurl_1.98-1.8 [76] ps_1.7.1 prettyunits_1.1.1 openssl_2.0.2 [79] ggpubr_0.4.0 urlchecker_1.0.1 S4Vectors_0.34.0 [82] SummarizedExperiment_1.26.1 fs_1.5.2 magrittr_2.0.3 [85] data.table_1.14.2 gh_1.3.0 whisker_0.4 [88] matrixStats_0.62.0 pkgload_1.3.0 evaluate_0.15 [91] hms_1.1.1 patchwork_1.1.1 mime_0.12 [94] xtable_1.8-4 XML_3.99-0.10 EWCE_1.5.4 [97] IRanges_2.30.0 gridExtra_2.3 testthat_3.1.4 [100] compiler_4.2.0 biomaRt_2.52.0 credentials_1.3.2 [103] tibble_3.1.8 crayon_1.5.1 minqa_1.2.4 [106] R.oo_1.25.0 htmltools_0.5.3 ggfun_0.0.6 [109] later_1.3.0 tidyr_1.2.0 aplot_0.1.6 [112] DBI_1.1.3 gprofiler2_0.2.1 MASS_7.3-58.1 [115] rappdirs_0.3.3 boot_1.3-28 sys_3.4 [118] dlstats_0.1.5 babelgene_22.3 badger_0.2.1 [121] Matrix_1.4-1 car_3.1-0 piggyback_0.1.4 [124] brio_1.1.3 cli_3.3.0 R.methodsS3_1.8.2 [127] parallel_4.2.0 GenomicRanges_1.48.0 pkgconfig_2.0.3 [130] rvcheck_0.2.1 GenomicAlignments_1.32.1 plotly_4.10.0 [133] xml2_1.3.3 roxygen2_7.2.1 ggtree_3.4.1 [136] XVector_0.36.0 yulab.utils_0.0.5 stringr_1.4.0 [139] VariantAnnotation_1.42.1 callr_3.7.1 digest_0.6.29 [142] Biostrings_2.64.0 rmarkdown_2.14 HGNChelper_0.8.1 [145] tidytree_0.3.9 restfulr_0.0.15 curl_4.3.2 [148] shiny_1.7.2 Rsamtools_2.12.0 rjson_0.2.21 [151] nloptr_2.0.3 lifecycle_1.0.1 nlme_3.1-158 [154] jsonlite_1.8.0 carData_3.0-5 askpass_1.1 [157] desc_1.4.1 viridisLite_0.4.0 limma_3.52.2 [160] BSgenome_1.64.0 fansi_1.0.3 pillar_1.8.0 [163] lattice_0.20-45 homologene_1.4.68.19.3.27 KEGGREST_1.36.3 [166] fastmap_1.1.0 httr_1.4.3 pkgbuild_1.3.1 [169] googleAuthR_2.0.0 waldo_0.4.0 interactiveDisplayBase_1.34.0 [172] glue_1.6.2 remotes_2.4.2 RNOmni_1.0.0 [175] gert_1.6.0 png_0.1-7 BiocVersion_3.15.2 [178] bit_4.0.4 stringi_1.7.8 profvis_0.3.7 [181] blob_1.2.3 memoise_2.0.1 dplyr_1.0.9 [184] ape_5.6-2 ```
tanho63 commented 2 years ago

Hmm. Cannot immediately repro 

R> piggyback::pb_list(repo = "neurogenomics/MAGMA_Celltyping",
+++                             tag = "latest") |> dplyr::glimpse()
Rows: 33
Columns: 6
$ file_name <chr> "ctd_Aerts2018.rds", "ctd_Aerts2021.rds", "ctd_AIBS.rds"…
$ size      <int> 5789935, 22266719, 1264213, 24532199, 2633276, 7860815, …
$ timestamp <dttm> 2022-07-22 19:57:48, 2022-07-22 19:58:02, 2022-07-22 19…
$ tag       <chr> "latest", "latest", "latest", "latest", "latest", "lates…"
$ owner     <chr> "neurogenomics", "neurogenomics", "neurogenomics", "neur…"
$ repo      <chr> "MAGMA_Celltyping", "MAGMA_Celltyping", "MAGMA_Celltypin…"
R> devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.0 (2022-04-22 ucrt)
 os       Windows 10 x64 (build 19044)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_Canada.utf8
 ctype    English_Canada.utf8
 tz       America/New_York
 date     2022-08-10
 rstudio  2022.06.0-daily+477 Spotted Wakerobin (desktop)
 pandoc   NA

─ Packages ───────────────────────────────────────────────────────────────
 package     * version date (UTC) lib source
 assertthat    0.2.1   2019-03-21 [1] RSPM (R 4.2.0)
 brio          1.1.3   2021-11-30 [1] RSPM (R 4.2.0)
 cachem        1.0.6   2021-08-19 [1] RSPM (R 4.2.0)
 callr         3.7.0   2021-04-20 [1] RSPM (R 4.2.0)
 cli           3.3.0   2022-04-25 [1] RSPM (R 4.2.0)
 crayon        1.5.1   2022-03-26 [1] RSPM (R 4.2.0)
 curl          4.3.2   2021-06-23 [1] RSPM (R 4.2.0)
 DBI           1.1.2   2021-12-20 [1] RSPM (R 4.2.0)
 desc          1.4.1   2022-03-06 [1] RSPM (R 4.2.0)
 devtools    * 2.4.3   2021-11-30 [1] RSPM (R 4.2.0)
 dplyr         1.0.9   2022-04-28 [1] RSPM (R 4.2.0)
 ellipsis      0.3.2   2021-04-29 [1] RSPM (R 4.2.0)
 fansi         1.0.3   2022-03-24 [1] RSPM (R 4.2.0)
 fastmap       1.1.0   2021-01-25 [1] RSPM (R 4.2.0)
 fs            1.5.2   2021-12-08 [1] RSPM (R 4.2.0)
 generics      0.1.3   2022-07-05 [1] RSPM (R 4.2.0)
 gh            1.3.0   2021-04-30 [1] RSPM (R 4.2.0)
 gitcreds      0.1.1   2020-12-04 [1] RSPM (R 4.2.0)
 glue          1.6.2   2022-02-24 [1] RSPM (R 4.2.0)
 here          1.0.1   2020-12-13 [1] RSPM (R 4.2.0)
 httr          1.4.3   2022-05-04 [1] RSPM (R 4.2.0)
 jsonlite      1.8.0   2022-02-22 [1] RSPM (R 4.2.0)
 lattice       0.20-45 2021-09-22 [2] CRAN (R 4.2.0)
 lifecycle     1.0.1   2021-09-24 [1] RSPM (R 4.2.0)
 lubridate     1.8.0   2021-10-07 [1] RSPM (R 4.2.0)
 magrittr      2.0.3   2022-03-30 [1] RSPM (R 4.2.0)
 Matrix        1.4-1   2022-03-23 [1] RSPM (R 4.2.0)
 memoise       2.0.1   2021-11-26 [1] RSPM (R 4.2.0)
 piggyback     0.1.4   2022-07-19 [1] RSPM
 pillar        1.8.0   2022-07-18 [1] RSPM (R 4.2.0)
 pkgbuild      1.3.1   2021-12-20 [1] RSPM (R 4.2.0)
 pkgconfig     2.0.3   2019-09-22 [1] RSPM (R 4.2.0)
 pkgload       1.2.4   2021-11-30 [1] RSPM (R 4.2.0)
 png           0.1-7   2013-12-03 [1] RSPM (R 4.2.0)
 prettyunits   1.1.1   2020-01-24 [1] RSPM (R 4.2.0)
 processx      3.5.3   2022-03-25 [1] RSPM (R 4.2.0)
 ps            1.7.0   2022-04-23 [1] RSPM (R 4.2.0)
 purrr         0.3.4   2020-04-17 [1] RSPM (R 4.2.0)
 R6            2.5.1   2021-08-19 [1] RSPM (R 4.2.0)
 rappdirs      0.3.3   2021-01-31 [1] RSPM (R 4.2.0)
 Rcpp          1.0.8.3 2022-03-17 [1] RSPM (R 4.2.0)
 remotes       2.4.2   2021-11-30 [1] RSPM (R 4.2.0)
 reticulate    1.25    2022-05-11 [1] RSPM (R 4.2.0)
 rlang         1.0.4   2022-07-12 [1] RSPM
 rprojroot     2.0.3   2022-04-02 [1] RSPM (R 4.2.0)
 rstudioapi    0.13    2020-11-12 [1] RSPM (R 4.2.0)
 sessioninfo   1.2.2   2021-12-06 [1] RSPM (R 4.2.0)
 testthat      3.1.4   2022-04-26 [1] RSPM (R 4.2.0)
 tibble        3.1.7   2022-05-03 [1] RSPM (R 4.2.0)
 tidyselect    1.1.2   2022-02-21 [1] RSPM (R 4.2.0)
 usethis     * 2.1.5   2021-12-09 [1] RSPM (R 4.2.0)
 utf8          1.2.2   2021-07-24 [1] RSPM (R 4.2.0)
 vctrs         0.4.1   2022-04-13 [1] RSPM (R 4.2.0)
 withr         2.5.0   2022-03-03 [1] RSPM (R 4.2.0)

 [1] C:/Users/Tan/AppData/Local/R/win-library/4.2
 [2] C:/Program Files/R/R-4.2.0/library
bschilder commented 2 years ago

Thanks @tanho63 , is this using a gh token? I'm wondering if maybe Windows can't find the token, simply bc i know it was issue in the past #50 Not that it should matter now. But this is just a guess, and perhaps a bit of a longshot.

bschilder commented 2 years ago

Also, here is the session info from the GHA Windows VM.

The piggback version is the same, but I do notice they're using R 4.2.1 (as opposed to 4.2.0).

Run options(width = 100)
  options(width = 100)
  pkgs <- installed.packages()[, "Package"]
  if(!require("sessioninfo")) install.packages("sessioninfo")
  tryCatch({
    sessioninfo::session_info(pkgs, include_base = TRUE)
  }, error = function(x){utils::sessionInfo()})
  shell: C:\R\bin\Rscript.EXE {0}
  env:
    run_bioccheck: false
    run_crancheck: true
    has_testthat: true
    run_covr: true
    run_pkgdown: true
    has_RUnit: false
    cache-version: cache-v1
    run_docker: true
    R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
    RSPM: 
    NOT_CRAN: true
    TZ: UTC
    GITHUB_TOKEN: ***
    GITHUB_PAT: ***
    GITHUB_REPO: neurogenomics/MAGMA_Celltyping
    RGL_USE_NULL: true
    DOCKER_USERNAME: bschilder
    DOCKER_ORG: neurogenomicslab
    R_LIBS_USER: D:\a\_temp\Library
    _R_CHECK_SYSTEM_CLOCK_: FALSE
Loading required package: sessioninfo
─ Session info ───────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.[2](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:2).1 (2022-06-2[3](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:3) ucrt)
 os       Windows Server x6[4](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:4) (build 20348)
 system   x86_64, mingw32
 ui       RTerm
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       UTC
 date     2022-08-10
 pandoc   2.7.3 @ C:\\HOSTED~1\\windows\\pandoc\\270C81~1.3\\x64\\PANDOC~1.3-W\\pandoc.exe

─ Packages ───────────────────────────────────────────────────────────────────────────────────────
 package                * version        date (UTC) lib source
 abind                    1.4-[5](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:5)          201[6](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:6)-0[7](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:7)-21 [1] CRAN (R 4.2.0)
 AnnotationDbi            1.5[8](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:8).0         2022-04-26 [1] Bioconductor
 AnnotationHub            3.4.0          2022-04-26 [1] Bioconductor
 ape                      5.6-2          2022-03-02 [1] CRAN (R 4.2.1)
 aplot                    0.1.6          2022-06-03 [1] CRAN (R 4.2.1)
 askpass                  1.1            201[9](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:9)-01-13 [1] CRAN (R 4.2.1)
 assertthat               0.2.1          2019-03-21 [1] CRAN (R 4.2.1)
 babelgene                22.3           2022-03-30 [1] CRAN (R 4.2.1)
 backports                1.4.1          2021-12-13 [1] CRAN (R 4.2.0)
 badger                   0.2.1          2022-05-31 [1] CRAN (R 4.2.1)
 base                   * 4.2.1          2022-06-23 [2] local
 base64enc                0.1-3          2015-07-28 [1] CRAN (R 4.2.0)
 BH                       1.78.0-0       2021-12-15 [1] CRAN (R 4.2.0)
 Biobase                  2.56.0         2022-04-26 [1] Bioconductor
 BiocCheck                1.32.0         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
 BiocManager              1.30.18        2022-05-18 [1] CRAN (R 4.2.1)
 BiocParallel             1.30.3         2022-06-07 [1] Bioconductor
 BiocStyle                2.24.0         2022-04-26 [1] Bioconductor
 BiocVersion              3.15.2         2022-03-29 [1] Bioconductor
 biocViews                1.64.1         2022-08-02 [1] Bioconductor
 biomaRt                  2.52.0         2022-04-26 [1] Bioconductor
 Biostrings               2.64.0         2022-04-26 [1] Bioconductor
 bit                      4.0.4          2020-08-04 [1] CRAN (R 4.2.1)
 bit64                    4.0.5          2020-08-30 [1] CRAN (R 4.2.1)
 bitops                   1.0-7          2021-04-24 [1] CRAN (R 4.2.0)
 blob                     1.2.3          2022-04-[10](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:10) [1] CRAN (R 4.2.1)
 bookdown                 0.28           2022-08-09 [1] CRAN (R 4.2.1)
 boot                     1.3-28         2021-05-03 [2] CRAN (R 4.2.1)
 brio                     1.1.3          2021-[11](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:11)-30 [1] CRAN (R 4.2.1)
 broom                    1.0.0          2022-07-01 [1] CRAN (R 4.2.1)
 BSgenome                 1.64.0         2022-04-26 [1] Bioconductor
 bslib                    0.4.0          2022-07-16 [1] CRAN (R 4.2.1)
 cachem                   1.0.6          2021-08-19 [1] CRAN (R 4.2.1)
 callr                    3.7.1          2022-07-13 [1] CRAN (R 4.2.1)
 car                      3.1-0          2022-06-15 [1] CRAN (R 4.2.1)
 carData                  3.0-5          2022-01-06 [1] CRAN (R 4.2.1)
 class                    7.3-20         2022-01-16 [2] CRAN (R 4.2.1)
 cli                      3.3.0          2022-04-25 [1] CRAN (R 4.2.1)
 clipr                    0.8.0          2022-02-22 [1] CRAN (R 4.2.1)
 cluster                  2.1.3          2022-03-28 [2] CRAN (R 4.2.1)
 codetools                0.2-18         2020-11-04 [2] CRAN (R 4.2.1)
 colorspace               2.0-3          2022-02-21 [1] CRAN (R 4.2.1)
 commonmark               1.8.0          2022-03-09 [1] CRAN (R 4.2.1)
 compiler                 4.2.1          2022-06-23 [2] local
 corrplot                 0.92           2021-11-18 [1] CRAN (R 4.2.1)
 covr                     3.5.1          2020-09-16 [1] CRAN (R 4.2.1)
 cowplot                  1.1.1          2020-[12](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:12)-30 [1] CRAN (R 4.2.1)
 cpp11                    0.4.2          2021-11-30 [1] CRAN (R 4.2.1)
 crayon                   1.5.1          2022-03-26 [1] CRAN (R 4.2.1)
 credentials              1.3.2          2021-11-29 [1] CRAN (R 4.2.1)
 crosstalk                1.2.0          2021-11-04 [1] CRAN (R 4.2.1)
 curl                     4.3.2          2021-06-23 [1] CRAN (R 4.2.1)
 data.table               1.14.2         2021-09-27 [1] CRAN (R 4.2.1)
 datasets               * 4.2.1          2022-06-23 [2] local
 DBI                      1.1.3          2022-06-18 [1] CRAN (R 4.2.1)
 dbplyr                   2.2.1          2022-06-27 [1] CRAN (R 4.2.1)
 DelayedArray             0.22.0         2022-04-26 [1] Bioconductor
 DelayedMatrixStats       1.18.0         2022-04-26 [1] Bioconductor
 desc                     1.4.1          2022-03-06 [1] CRAN (R 4.2.1)
 diffobj                  0.3.5          2021-10-05 [1] CRAN (R 4.2.1)
 digest                   0.6.29         2021-12-01 [1] CRAN (R 4.2.1)
 dlstats                  0.1.5          2022-04-[13](https://github.com/neurogenomics/MAGMA_Celltyping/runs/7772528339?check_suite_focus=true#step:20:13) [1] CRAN (R 4.2.1)
 dplyr                    1.0.9          2022-04-28 [1] CRAN (R 4.2.1)
 DT                       0.24           2022-08-09 [1] CRAN (R 4.2.1)
 ellipsis                 0.3.2          2021-04-29 [1] CRAN (R 4.2.1)
 evaluate                 0.16           2022-08-09 [1] CRAN (R 4.2.1)
 EWCE                     1.4.0          2022-04-26 [1] Bioconductor
 ewceData                 1.4.0          2022-04-28 [1] Bioconductor
 ExperimentHub            2.4.0          2022-04-26 [1] Bioconductor
 fansi                    1.0.3          2022-03-24 [1] CRAN (R 4.2.1)
 farver                   2.1.1          2022-07-06 [1] CRAN (R 4.2.1)
 fastmap                  1.1.0          2021-01-25 [1] CRAN (R 4.2.1)
 filelock                 1.0.2          2018-10-05 [1] CRAN (R 4.2.1)
 fontawesome              0.3.0          2022-07-20 [1] CRAN (R 4.2.1)
 foreign                  0.8-82         2022-01-16 [2] CRAN (R 4.2.1)
 formatR                  1.12           2022-03-31 [1] CRAN (R 4.2.1)
 fs                       1.5.2          2021-12-08 [1] CRAN (R 4.2.1)
 futile.logger            1.4.3          2016-07-10 [1] CRAN (R 4.2.1)
 futile.options           1.0.1          2018-04-20 [1] CRAN (R 4.2.0)
 gargle                   1.2.0          2021-07-02 [1] CRAN (R 4.2.1)
 generics                 0.1.3          2022-07-05 [1] CRAN (R 4.2.1)
 GenomeInfoDb             1.32.2         2022-05-15 [1] Bioconductor
 GenomeInfoDbData         1.2.8          2022-08-10 [1] Bioconductor
 GenomicAlignments        1.32.1         2022-08-02 [1] Bioconductor
 GenomicFeatures          1.48.3         2022-05-31 [1] Bioconductor
 GenomicRanges            1.48.0         2022-04-26 [1] Bioconductor
 gert                     1.7.0          2022-08-07 [1] CRAN (R 4.2.1)
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 [1] D:/a/_temp/Library
 [2] C:/R/library
tanho63 commented 2 years ago

Hmm. Digging around to find where

data.frame(file_name = "", size = 0L, timestamp = lubridate::as_datetime(0),

would have occurred and found the commit where I fixed this in development version: https://github.com/ropensci/piggyback/commit/b73acf0f708610d35046ae90dc66ef8e6c5a183f

the larger question is why nrow(releases) would return 0 in the first place

tanho63 commented 2 years ago

So you have tests for get_ctd() and those pass okay. Your troubles are in trying to run the example for calculate_conditional_geneset_enrichment(), am I reading that correctly?

bschilder commented 2 years ago

That's exactly right, it's very strange that get_ctd works fine in other examples/tests: https://github.com/neurogenomics/MAGMA_Celltyping/issues/120#issuecomment-1211004184

In other examples where get_ctd is called, it's importing a different file, but that shouldn't matter since it's failing at pb_list in the beginning of the function.

tanho63 commented 2 years ago

Can you just try rerunning the failed windows job? I wonder if it's just a bad API connection. It looks like the previous windows GHAs all worked fine for that example (all examples built fine) https://github.com/neurogenomics/MAGMA_Celltyping/runs/7601918758?check_suite_focus=true#step:21:105

bschilder commented 2 years ago

Sure! That is quite possible, I find the GHA VMs can be a bit buggy with their connections in some cases. Rerunning now and will let you know if it replicates

tanho63 commented 2 years ago

Great! Not sure if this package goes to CRAN but if so I tend to wrap all of my examples in try() to prevent internet issues from triggering a BDR email

tanho63 commented 2 years ago

https://github.com/neurogenomics/MAGMA_Celltyping/runs/7774739207?check_suite_focus=true#step:21:104 Looks like examples built okay that time, so definitely a random error 🙃

Good luck with the rest of the bugs!

bschilder commented 2 years ago

Great! Not sure if this package goes to CRAN but if so I tend to wrap all of my examples in try() to prevent internet issues from triggering a BDR email

It's not quite on CRAN yet, but that is indeed the plan! try() is certainly one option, but it does make me a bit nervous that I'd miss when examples aren't working anymore. It does get a bit tricky with variable internet connection though. Perhaps I could add a tryCatch for loop that tries pb_info several times (with some delay in between) before ultimately giving an error.

https://github.com/neurogenomics/MAGMA_Celltyping/runs/7774739207?check_suite_focus=true#step:21:104 Looks like examples built okay that time, so definitely a random error 🙃

Good luck with the rest of the bugs!

Ahh, so it was! Sorry for the trouble! But thank you for your speedy help in getting to the bottom of it.

All the best, Brian