Error in using examples

[benjin44]

Hello,

Firstly, thank you for your tool. It totally answers what I want to represent. So, I wanted to test it. But unfortunately, I can not run the sample datasets. For example, the following command returns the error:

logomaker (sequence, type = "Logo") Error in logomaker (sequence, type = "Logo"):    unused argument (type = "Logo")

In addition, the sample datasets seem to be missing.

data ("seqlogo_example") Warning message: In data ("seqlogo_example"): dataset 'seqlogo_example' not found

I can not solve the various problems for the moment. Could you help me ?

My R session information is as follows: Version:1.0 StartHTML:0000000107 EndHTML:0000001863 StartFragment:0000000127 EndFragment:0000001845 R version 3.4.4 (2018-03-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252

attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets methods
[10] base

other attached packages: [1] Logolas_1.2.0 BiocInstaller_1.28.0 Biostrings_2.46.0 XVector_0.18.0
[5] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0

loaded via a namespace (and not attached): [1] Rcpp_0.12.16 plyr_1.8.4 gtable_0.2.0 scales_0.5.0 ggplot2_2.2.1
[6] pillar_1.2.2 zlibbioc_1.24.0 rlang_0.2.0 lazyeval_0.2.1 tools_3.4.4
[11] munsell_0.4.3 yaml_2.1.19 compiler_3.4.4 colorspace_1.3-2 tibble_1.4.2

Thanking you in advance,

Benjamin N

[pcarbo]

@benjin44 Thank you for the feedback.

@kkdey I am also getting these errors when installing Logolas from Bioconductor. Looks like you will need to update the Logolas package on Bioconductor. Let me know if you need any help in resolving these issues.

[kkdey]

So, the latest updated version of Logolas is in Bioconductor 3.7, which needs the latest R version - R 3.5.0. It worked for me on R 3.5.0. I will try to fix it for R 3.4 and Bioc 3.6 users, but can you check if it works for you on the updated R?

[benjin44]

Thank you for your quick return. Indeed, everything works with the latest version of R. I had tested an older one, but had not thought to test the most recent.I will be able to begin the discovery of your package. Indeed, I am trying to highlight mutated positions in large sequence groups. Thank you very much

[kkdey]

Thanks @benjin44 for checking it out. We are looking into how best to fix the broken old version. So, I will keep this issue open.