Entering edit mode
Stephanie M. Gogarten
▴
870
@stephanie-m-gogarten-5121
Last seen 5 months 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