Question

Error:could not find function "DESeqDataSetFromHTSeqCount"

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bugaya1 ▴ 30

@bugaya1-23299

Last seen 4.1 years ago

Hi,

Im using DESeq2 to analyse my data. When I am trying to run this:

> library('DESeq2')
Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘glue’

I just went ahead and continued but when I ran this:

ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory,design=~condition)

The following error popped up:

Error in DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory,  : 
  could not find function "DESeqDataSetFromHTSeqCount"

Im trying to figure out why this function is not available. Hoping for your help.

Thanks. -Adrienne

deseq2 • 1.5k views

ADD COMMENT • link updated 4.1 years ago by Martin Morgan 25k • written 4.1 years ago by bugaya1 ▴ 30

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What command line did you use to install deseq2?

ADD REPLY • link 4.1 years ago swbarnes2 ★ 1.4k

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This is the one I used: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("DESeq2")

ADD REPLY • link 4.1 years ago bugaya1 ▴ 30

Martin Morgan · Answer 1 · 2020-04-09

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Martin Morgan 25k

@martin-morgan-1513

Last seen 20 days ago

United States

If loading the package fails, then the functions provided by the package won't be available. So given

> library('DESeq2')
Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘glue’

it's not surprising that

Error in DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory,  : 
  could not find function "DESeqDataSetFromHTSeqCount"

I think the problem is that an updated version of 'glue' is available, but not as a compiled binary. I'm guessing you're on a mac? So try to install just glue

BiocManager::install('glue')

if it fails or you are asked if you'd like to install from source, you could try

options(pkgType = "both")
BiocManager::install('glue')

I'm guessing that you will then be told that there is a binary version of 'glue' available, but a newer source version is available. Again, you could try to answer 'yes' to installing from source.

Depending on your computer system, you may have the tools already available to install from source, and this will just work. If it does not work, and the binary version of glue is out-of-date, the easiest choice is to take a break for a day or so and wait for the binary build of glue to catch up to the source version.

ADD COMMENT • link 4.1 years ago Martin Morgan 25k

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Hi,

I tried your suggestion and it returned the following:

The downloaded source packages are in
    ‘/private/var/folders/27/22nvsl493l901r47qh2rn1m80000gn/T/Rtmphqs9KX/downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘glue’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘lattice’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘Rcpp’ had non-zero exit status

ADD REPLY • link updated 4.1 years ago by Martin Morgan 25k • written 4.1 years ago by bugaya1 ▴ 30

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Before you clicke the 'Add comment' button, please take a second to drag over any 'code chunks' and click on the icon with the '010101' label; this will format the code so it is readable.

Look at the full output and find the first package that fails to install, probably Rcpp. Install only that

BiocManager::install("Rcpp")

and if / when it fails provide more complete output.

ADD REPLY • link 4.1 years ago Martin Morgan 25k

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Hi,

Thank you for your suggestions! Yes, I was using mac earlier. I transferred to a windows computer and everything ran smoothly. You were right at the beginning. I just have to wait for the binary versions to catch up to the source version.

Thanks again!

ADD REPLY • link 4.1 years ago bugaya1 ▴ 30