Code "open_raw_illum" not working

[MooseAntler]

I am trying to use the guide found here: [https://bioconductor.org/packages/devel/bioc/vignettes/crossmeta/inst/doc/crossmeta-vignette.html]
It says that I need to use open_raw_illum(illum_names, data_dir), but this command does not exist in this package. How can work around it or get it?

[RamRS]

@MooseAntler open_raw_illum a function, not a command. @alexvpickering Some more info: I looked through the entire repo and the function is only mentioned in the vignette and in a documentation (roxygen) comment on a function.

@MooseAntler I'd recommend adding the output of sessionInfo() so Alex knows more about your environment.

[alexvpickering]

Hi @MooseAntler and @RamRS,

I can't recall exactly why it was removed. It may have been that I simply felt the auto-correction of illumina headers had improved enough that it wasn't useful. Irrespective, I should have also updated the vignette and docs.

I have restored it in the latest commit. All it does is open raw illumina text micro-array files so that you can inspect the headers and fix them so crossmeta can auto-detect the appropriate columns.

To get the latest version with open_raw_illum restored:

install.packages('remotes')
remotes::install_github('alexvpickering/crossmeta')

[zx8754]

Related Biostars post: Trouble using crossmeta

[MooseAntler]

@alexvpickering @RamRS @zx8754 Thank you for your responses - I am very new to R and barely know what I am doing. I tried downloading the latest version and it loaded okay, but it still wouldn't let me use the open_raw_illum function.

`> install.packages('remotes')
Error in install.packages : Updating loaded packages

remotes::install_github('alexvpickering/crossmeta')
Downloading GitHub repo alexvpickering/crossmeta@HEAD
Skipping 28 packages ahead of CRAN: limma, S4Vectors, IRanges, Biobase, annotate, AnnotationDbi, BiocGenerics, zlibbioc, XVector, DelayedArray, GenomeInfoDb, affyio, Biostrings, SummarizedExperiment, GenomicRanges, multtest, edgeR, BiocParallel, genefilter, preprocessCore, affxparser, oligoClasses, ccdata, sva, oligo, GEOquery, ccmap, affy
√ checking for file 'C:\Users\miria\AppData\Local\Temp\RtmpAtS92q\remotes685c494c77fd\alexvpickering-crossmeta-0bd8aa6/DESCRIPTION' (740ms)

• preparing 'crossmeta': (429ms)
  checking DESCRIPTION meta-information ...
  Restarting R session...

`> install.packages("remotes")
Installing package into ‘C:/Users/miria/Desktop/R’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/remotes_2.2.0.zip'
Content type 'application/zip' length 388915 bytes (379 KB)
downloaded 379 KB

package ‘remotes’ successfully unpacked and MD5 sums checked

But I still got the same error:

`> library(crossmeta)

library(remotes)
open_raw_illum(illum_names, data_dir)
Error in open_raw_illum(illum_names, data_dir) :
could not find function "open_raw_illum"`

Here is the session info:

`R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils
[5] datasets methods base

other attached packages:
[1] crossmeta_1.15.0 remotes_2.2.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 compiler_4.0.2
[3] pillar_1.4.6 later_1.1.0.1
[5] rngtools_1.5 iterators_1.0.12
[7] tools_4.0.2 digest_0.6.25
[9] viridisLite_0.3.0 jsonlite_1.7.0
[11] lifecycle_0.2.0 tibble_3.0.3
[13] gtable_0.3.0 doRNG_1.8.2
[15] pkgconfig_2.0.3 rlang_0.4.7
[17] foreach_1.5.0 shiny_1.5.0
[19] cli_2.0.2 rstudioapi_0.11
[21] parallel_4.0.2 fastmap_1.0.1
[23] httr_1.4.2 dplyr_1.0.0
[25] htmlwidgets_1.5.1 generics_0.0.2
[27] vctrs_0.3.2 tidyselect_1.1.0
[29] grid_4.0.2 glue_1.4.1
[31] data.table_1.12.8 Biobase_2.49.0
[33] R6_2.4.1 fansi_0.4.1
[35] plotly_4.9.2.1 tidyr_1.1.0
[37] purrr_0.3.4 ggplot2_3.3.2
[39] magrittr_1.5 codetools_0.2-16
[41] scales_1.1.1 promises_1.1.1
[43] htmltools_0.5.0 ellipsis_0.3.1
[45] BiocGenerics_0.35.4 assertthat_0.2.1
[47] mime_0.9 xtable_1.8-4
[49] colorspace_1.4-1 httpuv_1.5.4
[51] miniUI_0.1.1.1 lazyeval_0.2.2
[53] munsell_0.5.0 crayon_1.3.4 `

[RamRS]

I don't understand - the repository has version 1.11.11 but your sessionInfo() says you have version 1.15.0. Maybe try remove.packages(crossmeta) followed by remotes::install_github('alexvpickering/crossmeta)?

[MooseAntler]

@RamRS That did the trick. Thank you so much to all of you for your help!