Temporary file not found
AurelieMLB opened this issue · comments
Hello,
I am trying your package. Thanks for your work.
I tried the example code:
(https://cran.r-project.org/web/packages/msaR/vignettes/msaR.html)
library(msaR)
seqfile <- system.file("sequences","AHBA.aln", package="msaR")
msaR(seqfile, menu=F, overviewbox = F)
At this point my browser (firefox) opened and told me:
"file not found: /tmp/Rtmpw64fvO/viewhtml31c94594a835/index.html."
I work on a Linux environment. I have double checked the /tmp is open in writing and reading for all.
Would you have an idea of what is happening and how to fix this please?
Many thanks
Hello,
Update:
I removed some the packages that I was importing "by default" and now I am passed that issue.
But, I have another issue: the html file that opens is all blank...
For reference (I do not know if it is related), I have a similar issue with d3Heatmap. I have the x and y axis but all the grid is blank. Heatmaply works perfectly though.
Any idea of what is happening please?
Any help would be really appreciated.
Many thanks
Hello again,
Apologies for spamming.
May I ask which version of R is necessary for Rmsa please?
Thank you!
Hi Aureliemb,
I'm away so I can't properly troubleshoot this until the end of the week. But everything should work. If you are getting a partial load in the browser you may not be passing in any data. Did you try with your own sequences?
Zach cp
Hello,
Thanks for your answer.
I have used the sequences provided in the package. I got them by doing:
seqfile <- system.file("sequences","AHBA.aln", package="msaR")
I just checked. There is data in this file.
But the plot still comes back blank.... even though msaR gives no error/warning at all.
I did also tried with my sequences and the outcome is the same.
I am interested in any help, even next week :)
For reference, here are my session info:
sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)
locale:
[1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB
[4] LC_COLLATE=en_GB LC_MONETARY=en_GB LC_MESSAGES=en_GB
[7] LC_PAPER=en_GB LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] msaR_0.2.0
loaded via a namespace (and not attached):
[1] htmlwidgets_0.9 parallel_3.3.1 htmltools_0.3.6 yaml_2.1.14
[5] Rcpp_0.12.12 nlme_3.1-131 ape_4.1 grid_3.3.1
[9] jsonlite_1.5 digest_0.6.12 lattice_0.20-35
Many thanks
Aurelie
Aurelie,
This works fine for me. Do you have a Javascript blocker in your browser by any chance? Are you using Rstudio (this should definitely display)? If you open up your browser's development tools do you get an error? I am guessing that your browser is blocking javascript or that there is a browser-incompatability problem although this works fine for me in Chrome/Safari/Firefox.
zach cp
Hello Zach,
Thank you so much for looking into this!
I will check the browser development tools. I will definitely keep you updated if I find something.
Best
Aurelie
Aurelie,
Did you figure this out? I'm closing this -please reopen a new issue if you still have a problem.
zach cp
Hello,
No sorry...
I ended up using R studio with the last version of R and it works there but I have not persisted on Linux.
Many thanks for asking.
Aurelie