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Chunk options #+echo not correctly parsed #532
Description
Symptom
Running the demo data I got errors:
Pipeline_SampleAnnotation_R:
processing file: /tmp/Rtmp4HVNRw/file1b74e41ef83803/SampleAnnotation.spin.Rmd
|............................... | 33%
Quitting from lines at lines 2-36 (/tmp/Rtmp4HVNRw/file1b74e41ef83803/SampleAnnotation.spin.Rmd)
Error:
! object 'sa' not found
MonoallelicExpression_pipeline_MAE_Results_R:
processing file: /tmp/RtmpxJMIWB/file1d4052152736d3/Results.spin.Rmd
|................................. | 36% [unnamed-chunk-2]
Quitting from lines at lines 160-164 [unnamed-chunk-2] (/tmp/RtmpxJMIWB/file1d4052152736d3/Results.spin.Rmd)
Error:
! object 'melt_dt' not found
Backtrace:
1. ggplot2::ggplot(melt_dt, aes(variable, value))
Debugging
Investigating I noticed these errors were directly downstream of #+echo=F.
Manually converting the R script using knitr:spin I noticed that this accidentally gets converted into:
{recho=F}
```
## Proposed solution
Add a space between `#+` and `echo`: all `#+echo` comments with `#+ echo`
## Environment
```
R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 23.10
Matrix products: default
BLAS/LAPACK: /home/vitoz/mambaforge/envs/drop_env/lib/libopenblasp-r0.3.27.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_CH.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_CH.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_CH.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Zurich
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitr_1.46 tidyr_1.3.1 magrittr_2.0.3 data.table_1.15.2
loaded via a namespace (and not attached):
[1] utf8_1.2.4 R6_2.5.1 tidyselect_1.2.0 xfun_0.43
[5] glue_1.7.0 tibble_3.2.1 pkgconfig_2.0.3 dplyr_1.1.4
[9] generics_0.1.3 lifecycle_1.0.4 cli_3.6.2 fansi_1.0.6
[13] vctrs_0.6.5 compiler_4.3.3 purrr_1.0.2 tools_4.3.3
[17] evaluate_0.23 pillar_1.9.0 yaml_2.3.8 rlang_1.1.3
```
Activity
Adds space between `#+` and `echo`
vyepez88 commentedon Apr 15, 2024
Many thanks! I also noticed this on Friday. I'm meeting the rest of the development meeting later today to address this today!
fix #532 knitr parsing
fix issue gagneurlab#532
Freeze version (gagneurlab#544)