sergeant
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Published
20 hours ago •
hrbrmstr
hrbrmstr
drill_up fails (maybe due to Docker Toolkit?)
I am eager to try out what described in the blog post about 0.8.0 version, but after having installed as instructed
devtools::install_git("https://git.sr.ht/~hrbrmstr/sergeant", ref="0.8.0")
and then running the code below, I got a failure:
> library(sergeant)
> library(tidyverse)
── Attaching packages ───────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0 ✔ purrr 0.2.5
✔ tibble 2.0.1 ✔ dplyr 0.7.8
✔ tidyr 0.8.2 ✔ stringr 1.3.1
✔ readr 1.3.1 ✔ forcats 0.3.0
── Conflicts ──────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
> # start Docker in terminal, then open
> dr <- drill_up(data_dir = here::here("data-raw"))
Drill container started. Waiting for the service to become active (this may take up to 30s).
Error in drill_up(data_dir = here::here("data-raw")) :
Could not connect to Drill container.
>
I have been able to have drill running manually and mapping the local file system to my directory of interest.
On the Docker side I have an old MBP, so I have Docker Toolkit.
(That maybe is the reason for the failure.)
If I run drill image from the command line I get the following:
> docker run drill/apache-drill (master|✚2✭)
Jan 27, 2019 2:25:49 PM org.jline.utils.Log logr
WARNING: Unable to create a system terminal, creating a dumb terminal (enable debug logging for more information)
Apache Drill 1.15.0
"The only truly happy people are children, the creative minority and Drill users."
0: jdbc:drill:zk=local> Closing: org.apache.drill.jdbc.impl.DrillConnectionImpl
I tried to hello_world Docker example using stevedore package and it works...so somewhat Docker (at least the easy bit) seems to work.
I then decided to dig into drill_up implementation and executed line by line to debug.
> docker <- stevedore::docker_client()
> (drill <- docker$container$run(image = "drill/apache-drill:1.15.0", name = "drill", cmd = "/usr/local/bin/bash", volumes = sprintf("%s:/data", here::here("data-raw"))))
E> Jan 27, 2019 3:01:03 PM org.jline.utils.Log logr
E> WARNING: Unable to create a system terminal, creating a dumb terminal (enable debug logging for more information)
E> Apache Drill 1.15.0
E> "Say hello to my little Drill."
E> Closing: org.apache.drill.jdbc.impl.DrillConnectionImpl
O> 0: jdbc:drill:zk=local> <docker_run_output>
$container:
<docker_container>
id: 2db3d96f27f55d35017dd0361531b37e25c80fbbe9e01cf731654c15adb1a773
name: drill
$logs:
Jan 27, 2019 3:01:03 PM org.jline.utils.Log logr
WARNING: Unable to create a system terminal, creating a dumb terminal (enable debug logging for more information)
Apache Drill 1.15.0
"Say hello to my little Drill."
Closing: org.apache.drill.jdbc.impl.DrillConnectionImpl
0: jdbc:drill:zk=local>
>
Then the 30 attempts of drill_active fail...(here I just show one manual try :-) )
> (drill_con <- drill_connection("localhost"))
<Drill REST API Direct Connection to localhost:8047>
> drill_active(drill_con)
[1] FALSE
I am out of ideas to try to make it work...any directions is welcome.
Thanks for the amazing problem write-up! Can you dump the session info on that system? I may be able to replicate your environment (I have a few old macs around with various macOSes on them).
Here is the relevant info out of a restarted session:
> library(sergeant)
> library(tidyverse)
── Attaching packages ───────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0 ✔ purrr 0.2.5
✔ tibble 2.0.1 ✔ dplyr 0.7.8
✔ tidyr 0.8.2 ✔ stringr 1.3.1
✔ readr 1.3.1 ✔ forcats 0.3.0
── Conflicts ──────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
> # start Docker in terminal, then open
> dr <- drill_up(data_dir = here::here("data-raw"))
Drill container started. Waiting for the service to become active (this may take up to 30s).
Error in drill_up(data_dir = here::here("data-raw")) :
Could not connect to Drill container.
> devtools::session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────────
setting value
version R version 3.5.2 (2018-12-20)
os OS X El Capitan 10.11.6
system x86_64, darwin15.6.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Brussels
date 2019-01-27
─ Packages ─────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
askpass 1.1 2019-01-13 [1] CRAN (R 3.5.2)
assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.5.0)
backports 1.1.3 2018-12-14 [1] CRAN (R 3.5.1)
bindr 0.1.1 2018-03-13 [1] CRAN (R 3.5.0)
bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.5.0)
bit 1.1-14 2018-05-29 [1] CRAN (R 3.5.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 3.5.0)
broom 0.5.1 2018-12-05 [1] CRAN (R 3.5.0)
callr 3.1.1 2018-12-21 [1] CRAN (R 3.5.1)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 3.5.0)
cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.0)
colorspace 1.4-0 2019-01-13 [1] CRAN (R 3.5.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.0)
curl 3.3 2019-01-10 [1] CRAN (R 3.5.2)
DBI 1.0.0.9001 2019-01-27 [1] Github (r-dbi/DBI@be695e2)
dbplyr 1.3.0 2019-01-09 [1] CRAN (R 3.5.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.0)
devtools 2.0.1 2018-10-26 [1] CRAN (R 3.5.2)
digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.0)
dplyr * 0.7.8 2018-11-10 [1] CRAN (R 3.5.0)
forcats * 0.3.0 2018-02-19 [1] CRAN (R 3.5.0)
fs 1.2.6 2018-08-23 [1] CRAN (R 3.5.0)
generics 0.0.2 2018-11-29 [1] CRAN (R 3.5.0)
ggplot2 * 3.1.0 2018-10-25 [1] CRAN (R 3.5.0)
glue 1.3.0.9000 2019-01-27 [1] Github (tidyverse/glue@8188cea)
gtable 0.2.0 2016-02-26 [1] CRAN (R 3.5.0)
haven 2.0.0 2018-11-22 [1] CRAN (R 3.5.0)
here 0.1 2017-05-28 [1] CRAN (R 3.5.0)
hms 0.4.2 2018-03-10 [1] CRAN (R 3.5.0)
htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.0)
httr 1.4.0 2018-12-11 [1] CRAN (R 3.5.0)
jsonlite 1.6 2018-12-07 [1] CRAN (R 3.5.0)
lattice 0.20-38 2018-11-04 [1] CRAN (R 3.5.0)
lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.5.0)
lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.5.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.0)
modelr 0.1.2 2018-05-11 [1] CRAN (R 3.5.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.0)
nlme 3.1-137 2018-04-07 [2] CRAN (R 3.5.2)
openssl 1.2.1 2019-01-17 [1] CRAN (R 3.5.2)
pillar 1.3.1 2018-12-15 [1] CRAN (R 3.5.0)
pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.5.0)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.0)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.5.0)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.0)
processx 3.2.1 2018-12-05 [1] CRAN (R 3.5.0)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.0)
purrr * 0.2.5 2018-05-29 [1] CRAN (R 3.5.0)
R6 2.3.0 2018-10-04 [1] CRAN (R 3.5.0)
Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.5.0)
readr * 1.3.1 2018-12-21 [1] CRAN (R 3.5.1)
readxl 1.2.0 2018-12-19 [1] CRAN (R 3.5.0)
remotes 2.0.2 2018-10-30 [1] CRAN (R 3.5.0)
rlang 0.3.1 2019-01-08 [1] CRAN (R 3.5.1)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.0)
rstudioapi 0.9.0 2019-01-09 [1] CRAN (R 3.5.1)
rvest 0.3.2 2016-06-17 [1] CRAN (R 3.5.0)
scales 1.0.0 2018-08-09 [1] CRAN (R 3.5.0)
sergeant * 0.8.0 2019-01-27 [1] git2r (@814195c)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.0)
stevedore 0.9.1 2019-01-02 [1] CRAN (R 3.5.2)
stringi 1.2.4 2018-07-20 [1] CRAN (R 3.5.0)
stringr * 1.3.1 2018-05-10 [1] CRAN (R 3.5.0)
testthat 2.0.1 2018-10-13 [1] CRAN (R 3.5.0)
tibble * 2.0.1 2019-01-12 [1] CRAN (R 3.5.2)
tidyr * 0.8.2 2018-10-28 [1] CRAN (R 3.5.0)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.0)
tidyverse * 1.2.1 2017-11-14 [1] CRAN (R 3.5.0)
usethis 1.4.0 2018-08-14 [1] CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.0)
xml2 1.2.0 2018-01-24 [1] CRAN (R 3.5.0)
yaml 2.2.0 2018-07-25 [1] CRAN (R 3.5.0)
[1] /Users/espin/r.library
[2] /Library/Frameworks/R.framework/Versions/3.5/Resources/library
Thanks!