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length of NULL cannot be changed using readr::read_tsv (readr v1.1.1) #750

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stianlagstad opened this issue Nov 25, 2017 · 10 comments
Closed

length of NULL cannot be changed using readr::read_tsv (readr v1.1.1) #750

stianlagstad opened this issue Nov 25, 2017 · 10 comments
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bug an unexpected problem or unintended behavior

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@stianlagstad
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col_types_defuse = readr::cols_only(
  "cluster_id" = readr::col_character(),
  "splitr_sequence" = readr::col_character(),
  "splitr_count" = readr::col_integer(),
  "gene1" = readr::col_character(),
  "gene2" = readr::col_character(),
  "gene_chromosome1" = readr::col_character(),
  "gene_chromosome2" = readr::col_character(),
  "gene_name1" = readr::col_character(),
  "gene_name2" = readr::col_character(),
  "gene_strand1" = readr::col_character(),
  "gene_strand2" = readr::col_character(),
  "genomic_break_pos1" = readr::col_integer(),
  "genomic_break_pos2" = readr::col_integer(),
  "span_count" = readr::col_integer(),
  "orf" = readr::col_character(),
  "probability" = readr::col_number()
)
readr::read_tsv(
  file = "defuse_833ke_results.filtered.tsv",
  col_types = col_types_defuse
)

This leads to a lot of warning messages:

Warning messages:
1: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
2: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
...

Is there something I'm doing wrong? I'm doing this from the rocker/rstudio:devel docker image.

defuse_833ke_results.filtered.tsv.tar.gz
@cderv
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cderv commented Nov 26, 2017

to provide more feedback, I tried to reproduce this on my computer. No warning. I did not test it on R rocker/rstudio:devel or R devel version, which can be the issue cause. Just on R 3.4.2 with readr 1.1.1.
A full reprex to help test it further:

reprex::reprex_info()
#> Created by the reprex package v0.1.1.9000 on 2017-11-26

# Download the file in temp folder
url <- "https://github.com/tidyverse/readr/files/1503502/defuse_833ke_results.filtered.tsv.tar.gz"
tmp_file <- tempfile()
download.file(url, tmp_file)
tmp_dir <- tempfile("untar-dir-")
untar(tmp_file, list = T)
#> [1] "defuse_833ke_results.filtered.tsv"
untar(tmp_file, exdir = tmp_dir)
file_name <- list.files(tmp_dir)
path_to_file <- file.path(tmp_dir, file_name)

# Define col types
col_types_defuse = readr::cols_only(
  "cluster_id" = readr::col_character(),
  "splitr_sequence" = readr::col_character(),
  "splitr_count" = readr::col_integer(),
  "gene1" = readr::col_character(),
  "gene2" = readr::col_character(),
  "gene_chromosome1" = readr::col_character(),
  "gene_chromosome2" = readr::col_character(),
  "gene_name1" = readr::col_character(),
  "gene_name2" = readr::col_character(),
  "gene_strand1" = readr::col_character(),
  "gene_strand2" = readr::col_character(),
  "genomic_break_pos1" = readr::col_integer(),
  "genomic_break_pos2" = readr::col_integer(),
  "span_count" = readr::col_integer(),
  "orf" = readr::col_character(),
  "probability" = readr::col_number()
)

# read the file with custom col type
readr::read_tsv(
  file = path_to_file,
  col_types = col_types_defuse
)
#> # A tibble: 17 x 16
#>    cluster_id
#>         <chr>
#>  1       5267
#>  2      12586
#>  3         58
#>  4       2406
#>  5       8264
#>  6       3085
#>  7       2416
#>  8      11901
#>  9       2546
#> 10       8250
#> 11      11758
#> 12       9493
#> 13       8958
#> 14       2374
#> 15      11759
#> 16      11946
#> 17      15540
#> # ... with 15 more variables: splitr_sequence <chr>, splitr_count <int>,
#> #   gene1 <chr>, gene2 <chr>, gene_chromosome1 <chr>,
#> #   gene_chromosome2 <chr>, gene_name1 <chr>, gene_name2 <chr>,
#> #   gene_strand1 <chr>, gene_strand2 <chr>, genomic_break_pos1 <int>,
#> #   genomic_break_pos2 <int>, orf <chr>, span_count <int>,
#> #   probability <dbl>

# delete tmp file
unlink(tmp_dir, recursive = T)
unlink(tmp_file)

Thanks for providing the file.

@stianlagstad
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Thank you for replying. It works without issue on R 3.4.2 for me as well.

@stianlagstad
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stianlagstad commented Nov 26, 2017 •
edited

To make it a bit easier to reproduce I created a docker image.

Dockerfile:

from rocker/rstudio:devel

COPY defuse_833ke_results.filtered.tsv /tmp/defuse_833ke_results.filtered.tsv
COPY script.R /tmp/script.R
RUN chmod u+x /tmp/script.R

RUN R -e 'install.packages("readr")'
RUN ./tmp/script.R

script.R:

#!/usr/bin/env Rscript
setwd("/tmp")
col_types_defuse = readr::cols_only(
  "cluster_id" = readr::col_character(),
  "splitr_sequence" = readr::col_character(),
  "splitr_count" = readr::col_integer(),
  "gene1" = readr::col_character(),
  "gene2" = readr::col_character(),
  "gene_chromosome1" = readr::col_character(),
  "gene_chromosome2" = readr::col_character(),
  "gene_name1" = readr::col_character(),
  "gene_name2" = readr::col_character(),
  "gene_strand1" = readr::col_character(),
  "gene_strand2" = readr::col_character(),
  "genomic_break_pos1" = readr::col_integer(),
  "genomic_break_pos2" = readr::col_integer(),
  "span_count" = readr::col_integer(),
  "orf" = readr::col_character(),
  "probability" = readr::col_number()
)
readr::read_tsv(
  file = "defuse_833ke_results.filtered.tsv",
  col_types = col_types_defuse
)
warnings()

Building the image (docker build . -t readrtest) should give the warnings:

...
46: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :                                         
  length of NULL cannot be changed                   
47: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :                                         
  length of NULL cannot be changed                   
48: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :                                         
  length of NULL cannot be changed                   
49: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :                                         
  length of NULL cannot be changed                   
50: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :                                         
  length of NULL cannot be changed                   
 ---> 350e29a74bee                                   
Removing intermediate container b016e1b46252         
Successfully built 350e29a74bee                      
Successfully tagged readrtest:latest

I've added the dockerfile, the script and the .tsv file in readr-error.tar.gz.

Changing the dockerfile from saying from rocker/rstudio:devel to saying from rocker/rstudio will not reproduce the warnings.

@jimhester jimhester added the bug an unexpected problem or unintended behavior label Dec 11, 2017
@jimhester
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Using the current devel version of readr ddbb5f4 and R-devel r73889 I am able to run the code in a rocker/rstudio:devel container without warnings.

So either a change in R or a change in the package seems to have fixed this.

@stianlagstad
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stianlagstad commented Dec 12, 2017 •
edited

A rerun of that dockerfile reproduced the warnings (I made sure to delete all my local containers and images before rebuilding), so I guess I'm not getting the latest version of readr (sessionInfo() within the container tells me it's readr_1.1.1). Should I install readr by other means to avoid the error? (Or just wait a few days?)

@batpigandme
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I believe Jim is referring to the dev. version of readr which you can install using:

# install.packages("devtools")
devtools::install_github("tidyverse/readr")

@stianlagstad
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stianlagstad commented Dec 12, 2017 •
edited

Now I tried installing it from github with the same error, though. This is the Dockerfile:

from rocker/rstudio:devel

RUN sudo apt-get update
RUN sudo apt-get install libssl-dev zlib1g-dev -y

COPY defuse_833ke_results.filtered.tsv /tmp/defuse_833ke_results.filtered.tsv
COPY script.R /tmp/script.R
RUN chmod u+x /tmp/script.R

RUN R -e 'install.packages("git2r")'
RUN R -e 'install.packages("devtools")'
RUN R -e 'library(devtools);devtools::install_github("tidyverse/readr")'
RUN ./tmp/script.R

Building that with docker rm $(docker ps -a -q) && docker rmi $(docker images -q) && docker build --no-cache=true . -t readrtest produced the following:

...
Step 10/10 : RUN ./tmp/script.R
 ---> Running in 9286c2bf0a13
There were 50 or more warnings (use warnings() to see the first 50)
# A tibble: 17 x 16
   cluster_id
        <chr>
 1       5267
 2      12586
 3         58
 4       2406
 5       8264
 6       3085
 7       2416
 8      11901
 9       2546
10       8250
11      11758
12       9493
13       8958
14       2374
15      11759
16      11946
17      15540
# ... with 15 more variables: splitr_sequence <chr>, splitr_count <int>,
#   gene1 <chr>, gene2 <chr>, gene_chromosome1 <chr>, gene_chromosome2 <chr>,
#   gene_name1 <chr>, gene_name2 <chr>, gene_strand1 <chr>, gene_strand2 <chr>,
#   genomic_break_pos1 <int>, genomic_break_pos2 <int>, orf <chr>,
#   span_count <int>, probability <dbl>
Warning messages:
1: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
2: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
3: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
4: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
5: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
6: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
7: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
8: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
9: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
10: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
11: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
12: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
13: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
14: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
15: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
16: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
17: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
18: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
19: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
20: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
21: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
22: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
23: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
24: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
25: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
26: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
27: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
28: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
29: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
30: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
31: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
32: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
33: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
34: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
35: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
36: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
37: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
38: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
39: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
40: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
41: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
42: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
43: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
44: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
45: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
46: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
47: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
48: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
49: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
50: In read_tokens_(data, tokenizer, col_specs, col_names,  ... :
  length of NULL cannot be changed
 ---> cea2e539f359
Removing intermediate container 9286c2bf0a13
Successfully built cea2e539f359
Successfully tagged readrtest:latest

Since I now installed readr from github and made sure I pulled the latest rstudio/rocker image, I shoouuld have the latest of both, right?

@stianlagstad
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Could you try building the Dockerfile I posted above, @jimhester? I'm still seeing this issue.

@jimhester jimhester mentioned this issue Apr 25, 2018
Closed
jimhester added a commit that referenced this issue Apr 30, 2018
@jimhester
Do not try to resize skipped columns
47ea858 
These are represented as NULL values, and trying to resize `R_NilValue`
throws a warning in R 3.5+

Fixes #750, #833
@nevrome nevrome mentioned this issue May 5, 2018
Closed
@stianlagstad stianlagstad mentioned this issue May 22, 2018
Closed
@stianlagstad
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I can confirm that this issue has been resolved by 47ea858. (Ref #833)

@nevrome nevrome mentioned this issue May 23, 2018
Closed
@jennybc jennybc mentioned this issue May 30, 2018
Closed
stianlagstad added a commit to stianlagstad/chimeraviz that referenced this issue Sep 16, 2018
@stianlagstad
Avoid readr because of tidyverse/readr#750
bd3f6fd
stianlagstad added a commit to stianlagstad/chimeraviz that referenced this issue Sep 16, 2018
@stianlagstad
Avoid readr because of tidyverse/readr#750
76a069f
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lock bot commented Nov 18, 2018

This old issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with reprex) and link to this issue. https://reprex.tidyverse.org/

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@jimhester @batpigandme @stianlagstad @cderv