I'm having a hard time trying to retrieve RoadMap resources using AnnotationHub (e.g. ah[['AH49441']] ). The download does reach a 100%, but then the process will never exit. I don't get any error message, but I left this overnight to see if it would eventually end the process but it just didn´t happen. Is there anything going on with the server? Thanks in advance
Thank you for your answers. I have now been able to retrieve 3 different resourses at most before R or RStudio gets "stuck". I actually have to terminate R since it wouldn't allow me to manually stop the process. I'm not sure if the data set I'm trying to retrieve could be too large or there's something going on with the internet connection. This is the code I'm using:
I'm still having trouble reproducing as I can run your code above with no issues. What is your output of sessionInfo()? We want to make sure you are using the most updated versions of all the packages for your version of R, you can check by using biocLite(). From the look of the snapshot date of AnnotationHub, I would guess that you are running an older version of R and AnnotationHub; I would suggest if you continue to have issues to update to the most current release. Also, you might consider checking your system's memory to make sure you have enough space to download.
I really appreciate all your collaboration. I believe that I finally found out that the issue was the network connection...I feel so ashamed. Eventhough some packages are not the most updated version, the code is being running today successfully without the need of making any update. Today's data transfer rate is still low, but at least it's allowing me to do the download. Sorry for the inconvenience; I didn't check this yesterday since I didn't really believe it could be that bad. Many thanks!!!
Thank you for your answers. I have now been able to retrieve 3 different resourses at most before R or RStudio gets "stuck". I actually have to terminate R since it wouldn't allow me to manually stop the process. I'm not sure if the data set I'm trying to retrieve could be too large or there's something going on with the internet connection. This is the code I'm using:
> ah <- AnnotationHub()snapshotDate(): 2016-10-11>> #SUBSET BROAD INSTITUTE DATA> epiRoad <- subset(ah, species=="Homo sapiens" & dataprovider=="BroadInstitute")>> #SELECT CONSOLIDATED GENOMES> epiRoad_consolidated <- query(epiRoad, c("E{1}[0-9]{3}[^0-9]", "EID_metadata"), pattern.op=`|`)>> #SELECT H3K4ME1 NARROW PEAKS> narrow.h3k4me1 <- query(epiRoad_consolidated, c("h3k4me1", "narrow ChIP-seq"))>> data.narrow.h3k4me1 <- lapply(X = names(narrow.h3k4me1), FUN = function(x){epiRoad_consolidated[[x]]})require(“rtracklayer”)downloading from ‘https://annotationhub.bioconductor.org/fetch/35299’retrieving 1 resource|==============================================================================| 100%I'm still having trouble reproducing as I can run your code above with no issues. What is your output of
sessionInfo()? We want tomake sure you are using the most updated versions of all the packages for your version of R, you can check by usingbiocLite(). From the look of the snapshot date of AnnotationHub, I would guess that you are running an older version of R and AnnotationHub; I would suggest if you continue to have issues to update to the most current release. Also, you might consider checking your system's memory to make sure you have enough space to download.I really appreciate all your collaboration. I believe that I finally found out that the issue was the network connection...I feel so ashamed. Eventhough some packages are not the most updated version, the code is being running today successfully without the need of making any update. Today's data transfer rate is still low, but at least it's allowing me to do the download. Sorry for the inconvenience; I didn't check this yesterday since I didn't really believe it could be that bad. Many thanks!!!
No problem. We've all dealt with slow network issues. Feel free to post more if you find you are having any other issues.