I can't reproduce this error at the moment. I've made a modified version of your example script available at https://gist.github.com/grimbough/09d150bff2b07ec032de4d47cf201215
The main changes were to remove all the comment out lines so it was easier for me to read, automated the downloading & unzipping of the files, and modified line 24 as I think my directory structure is slightly different from what the script was expecting.
The code runs without error for me and prints out the following:
[1] "Plate: 2; Well: A5; Position: 00001; Time:2018-11-19 18:29:39"
[1] "Plate: 2; Well: A5; Position: 00002; Time:2018-11-19 18:30:02"
[1] "Plate: 2; Well: A5; Position: 00003; Time:2018-11-19 18:30:19"
[1] "Plate: 2; Well: A5; Position: 00004; Time:2018-11-19 18:30:35"
[1] "Plate: 2; Well: A5; Position: 00005; Time:2018-11-19 18:30:53"
[1] "Plate: 2; Well: A5; Position: 00006; Time:2018-11-19 18:31:24"
[1] "Plate: 2; Well: A5; Position: 00007; Time:2018-11-19 18:31:50"
[1] "Plate: 2; Well: A5; Position: 00008; Time:2018-11-19 18:32:07"
[1] "Plate: 2; Well: A5; Position: 00009; Time:2018-11-19 18:32:22"
and produces some CSV files:
> list.files(pattern = '.csv')
[1] "IF015_noSpeck_p--2_w--A5_pos--00001.csv"
[2] "IF015_noSpeck_p--2_w--A5_pos--00002.csv"
[3] "IF015_noSpeck_p--2_w--A5_pos--00003.csv"
[4] "IF015_noSpeck_p--2_w--A5_pos--00004.csv"
[5] "IF015_noSpeck_p--2_w--A5_pos--00005.csv"
[6] "IF015_noSpeck_p--2_w--A5_pos--00006.csv"
[7] "IF015_noSpeck_p--2_w--A5_pos--00007.csv"
[8] "IF015_noSpeck_p--2_w--A5_pos--00008.csv"
[9] "IF015_noSpeck_p--2_w--A5_pos--00009.csv"
You can source it directly with the following command. If it runs for you then take a look at the differences between the two scripts, if not then report back here & we can keep hunting
source('https://gist.githubusercontent.com/grimbough/09d150bff2b07ec032de4d47cf201215/raw/4ba02b5645e67a3ec937efe16feb4412fc30ac93/IF015_example.R')
Here's my sessionInfo()
for reference:
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19
Matrix products: default
BLAS: /home/msmith/Applications/R/R-3.5.1/lib/libRblas.so
LAPACK: /home/msmith/Applications/R/R-3.5.1/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bindrcpp_0.2.2 forcats_0.3.0 stringr_1.3.1 dplyr_0.7.8 purrr_0.2.5
[6] readr_1.1.1 tidyr_0.8.2 tibble_1.4.2 ggplot2_3.1.0 tidyverse_1.2.1
[11] EBImage_4.24.0
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 locfit_1.5-9.1 haven_1.1.2 lattice_0.20-38
[5] colorspace_1.3-2 htmltools_0.3.6 yaml_2.2.0 rlang_0.3.0.1
[9] pillar_1.3.0 withr_2.1.2 glue_1.3.0 BiocGenerics_0.28.0
[13] modelr_0.1.2 readxl_1.1.0 jpeg_0.1-8 bindr_0.1.1
[17] plyr_1.8.4 munsell_0.5.0 gtable_0.2.0 cellranger_1.1.0
[21] rvest_0.3.2 htmlwidgets_1.3 parallel_3.5.1 broom_0.5.0
[25] Rcpp_1.0.0 backports_1.1.2 scales_1.0.0 jsonlite_1.5
[29] abind_1.4-5 hms_0.4.2 png_0.1-7 digest_0.6.18
[33] stringi_1.2.4 tiff_0.1-5 grid_3.5.1 cli_1.0.1
[37] tools_3.5.1 bitops_1.0-6 magrittr_1.5 RCurl_1.95-4.11
[41] lazyeval_0.2.1 crayon_1.3.4 pkgconfig_2.0.2 xml2_1.2.0
[45] lubridate_1.7.4 assertthat_0.2.0 httr_1.3.1 rstudioapi_0.8
[49] R6_2.3.0 fftwtools_0.9-8 nlme_3.1-137 compiler_3.5.1
Can you update your post to include the output of the command
sessionInfo()
, so we can see the exact versions you're using. I've don't get this error when I run through your script (with a few changes to fix the plate number to 2).Hi Mike,
Sure I can provide this information: