warning for gsutil_requesterpays when reading from gsutil_pipe
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Entering edit mode
@stephanie-m-gogarten-5121
Last seen 8 weeks ago
University of Washington

When I read from a file in AnVIL with gsutil_pipe(), I get a warning message, though the file does read correctly:

famfile <- 'gs://fc-secure-6c0eb33e-f3d2-46a5-b409-f45d5948bb6f/hapmap3_r3_b37_fwd.consensus.qc.poly_Ilmn1M.fam'
fampipe <- gsutil_pipe(famfile, "rb")
fam <- read_table(fampipe)

Warning message:
“'gsutil_requesterpays()' returned an error:
  'gsutil -u terra-50ae4b25 requesterpays get' failed:
  CommandException: The requesterpays command requires at least 2 arguments. Usage:

      gsutil requesterpays set (on|off) gs://<bucket_name>...
      gsutil requesterpays get gs://<bucket_name>...

    For additional help run:
      gsutil help requesterpays
  exit status: 1”

sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] forcats_0.5.1   stringr_1.4.0   purrr_0.3.4     readr_2.1.1    
 [5] tidyr_1.1.4     tibble_3.1.6    ggplot2_3.3.5   tidyverse_1.3.1
 [9] AnVIL_1.6.2     dplyr_1.0.7    

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8           lubridate_1.8.0      assertthat_0.2.1    
 [4] digest_0.6.29        utf8_1.2.2           IRdisplay_1.1       
 [7] R6_2.5.1             cellranger_1.1.0     repr_1.1.4          
[10] futile.options_1.0.1 backports_1.4.1      reprex_2.0.1        
[13] rapiclient_0.1.3     evaluate_0.14        httr_1.4.2          
[16] pillar_1.6.4         rlang_0.4.12         uuid_1.0-3          
[19] readxl_1.3.1         rstudioapi_0.13      munsell_0.5.0       
[22] broom_0.7.11         compiler_4.1.2       modelr_0.1.8        
[25] pkgconfig_2.0.3      base64enc_0.1-3      htmltools_0.5.2     
[28] tidyselect_1.1.1     fansi_1.0.2          crayon_1.4.2        
[31] tzdb_0.2.0           dbplyr_2.1.1         withr_2.4.3         
[34] grid_4.1.2           jsonlite_1.7.3       gtable_0.3.0        
[37] lifecycle_1.0.1      DBI_1.1.2            magrittr_2.0.1      
[40] formatR_1.11         scales_1.1.1         cli_3.1.0           
[43] stringi_1.7.6        fs_1.5.2             xml2_1.3.3          
[46] futile.logger_1.4.3  ellipsis_0.3.2       generics_0.1.1      
[49] vctrs_0.3.8          IRkernel_1.3         lambda.r_1.2.4      
[52] tools_4.1.2          glue_1.6.0           hms_1.1.1           
[55] parallel_4.1.2       fastmap_1.1.0        yaml_2.2.1          
[58] colorspace_2.0-2     BiocManager_1.30.16  rvest_1.0.2         
[61] pbdZMQ_0.3-6         haven_2.4.3
AnVIL • 167 views
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Entering edit mode
@martin-morgan-1513
Last seen 5 days ago
United States

Thanks Stephanie; I didn't see this post earlier. This should be fixed in AnVIL 1.6.6 / 1.7.12.

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