Frequently Asked Questions
This is the FAQ for the Bioconductor support site; also visit the Bioconductor project FAQ.
What questions should I post to this site?
This site is for questions related to Bioconductor packages. General questions about high-throughput sequencing or software unrelated to Bioconductor can be asked on biostars or seqanswers. General R questions can be asked on the R-help mailing list, or on StackOverflow. If you are seeking guidance on developing a Bioconductor package, post to the bioc-devel mailing list.
How can I contact you?
Those of us who maintain this site read the posts that are made here. So users who wish to contact us are encouraged to post to this site. Having trouble posting to the support site? Consider opening an issue at the github repository for the support site.
How do I write good posts?
One of the biggest things that new users struggle with is how to ask questions in a way that allows people to answer them. So if you are unfamiliar please have a look at the posting guide for some great advice.
If a Bioconductor package reports an error that you cannot diagnose
BiocInstaller::biocValid()reports that your packages are of the correct version
- To record the output of
traceback()immediately after the error occurs
- Include the output of
How do I format source code in a post?
Community members prefer that questions containing source code have properly formatted code snippets. To create formatted code snippets, a post author can use the text formatting tools on the new post form (at the top of the text area). One workflow that you may like to accomplish formatted code, is as follows :
- Write all of your non-code content first, omitting the space for code to be inserted
- Come back to the spot where you'd like to insert a chunk of code
- Place your cursor in the placeholder position and paste the code
- Select the entire code block
- Click the "Styles" drop down (at the top of the text area) to select a different text style and choose either "Code" under Block Styles for code blocks or "Inline Code" under Inline Styles for inline code.
How do I put images into my posts?
You can also put images and plots into your posts. All you need to do is create (or login to) a free account with http://imgur.com and upload any images or plots that you want to share. Then you can enter the imgur generated 'Direct Link' url into the 'URL' location that is available when you click on the 'image' button in the text editor. The plot will be embedded right into your post. To "attach" other files to your posts, upload them to Dropbox or another similar site and include the URL in your post. Make sure the URL is publicly accessible.
How do I write a reproducible example?
The best way to describe a problem is to provide a short, easy-to-reproduce code chunk. The code chunk should use data that everyone has available, maybe from examples in the package that you are having problems with, or from one of the Experiment Data packages. The code chunk should be as short as possible, just a couple of lines. Work hard to remove any unnecessary code -- this often helps you to spot the problem, and makes it easy for those trying to help to get right to the issue. StackOverflow has addition suggestions.
How do I change my avatar (icon)?
Go to Gravatar and create an account using the same email address you used to register here. Then set your default avatar on the Gravatar site.
How can I keep track of topics that interest me?
Add tags that you want tracked in your user profile. 'My Tags' will put posts that match your tagging criteria into the 'My: tags' tab that you can check whenever you log in. Posts tagged with 'Watched Tags' send email to you. Use 'Notifications' to control how updates to the site are reported to you, e.g., via site messages or email.
How do I merge multiple previous accounts?
So perhaps you have been using the Bioconductor mailing list for a long time and during that time you have been using multiple different aliases. And now you would like to consolidate things so that you can get credit for actually being only one person. What should you do? Well 1st of all you should get set up with the account that you normally use. If you have not logged in before this may mean going straight to password recovery.
Once you can log in, you will want to click on your name and then go to the little blue button that is called 'Social Login'. Here you should be able to link in other social accounts that you may have used before (such as gmail) to your primary account email.
If it turns out that your previous aliases are not listed as optional social logins (as may happen if they were associated with different academic institutions) then you will need to email us at email@example.com and send us a file. This file needs to contain a single line that looks like this: email1 email2 email3 etc. Essentially, this file should contain one email for each account you wish to merge (separated by white space). And the very first email that it lists must be the one that you want to regularly use as your primary account for this site.
What if I find a bug or want to suggest a new feature?
No site is perfect and you may come across things that are not working as they should be or could be improved. This site is based on a fork of Biostars so we have the power to correct many problems as they are discovered. If you find a problem with this website, we ask that you please post such questions as to our github issues.
What about offensive content?
Users posting content that does not belong to the site will be notified and required to edit their content. Users may post job postings to the 'Jobs' section as long as the topic aligns with the main focus of this site. Users posting obvious spam will be immediately suspended.
The number next to a user's name is the sum of up-votes and accepted answers that user has collected. Up-votes boost your reputation on the site.
How is this site different from a mailing list?
There are several important differences. Posts made to this site can be edited long into the future, and people who ask similar questions can be directed to carefully maintained and easily discovered answers. This site allows flexible email notification when new posts (questions and answers) are made to this site, and email replies are associated with the appropriate post (the entire contents of the email will be added to the thread, so be sure and trim out the original message when you reply). Email clients do not thread all posts correctly, comments and edits to posts do not trigger email notifications, and new threads cannot be started by email.
What does a moderator do?
Moderators can both edit and moderate posts. Editing allows you to change the text of a post (perhaps cleaning up formatting) and add/remove tags to a post. Moderation allows you to do the following tasks:
- Open a closed or deleted post
- Move post to an answer
- Move post to a comment on the top level post
- Duplicated post (top level)
- Cross posted at other site
- Close post (top level)
- Delete post
Who can become a moderator?
Moderators are selected by Bioconductor core team members. The responsibility of moderating posts is given to long-term trusted users.
What are the rules of being a moderator?
Do not delete posts unless they are obviously spam. The purpose of moderation should be to make the discussion clearer and more relevant to all. If you have any doubts about whether to moderate, don't do it; ask the site maintainers for guidance. If you edit a post, add a (polite) comment describing what you did. This will help all users to write better posts and will keep people from repeating the same mistakes.
How do I post NEWS or JOBS or TUTORIALS?
Follow the 'ASK QUESTION' link and choose 'News Event' or 'Job Ad' or 'Tutorial' as post type. The post will appear under 'Latest' with 'News:' or 'Job:' or 'Tutorial:' prefixed to title, and will also appear under corresponding link at the top of the support site page.