Queries around makeOrgPackageFromNCBI
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laural710 • 0
@laural710-14567
Last seen 2.5 years ago

Hi All

I'm new to using this particular package but i have great hopes for it. I work on a model organism which is not currently supported. I have build a package using the following code:

makeOrgPackageFromNCBI(version="0.1",
author="my name <myname@gmail.com>",
maintainer="my name <myname@gmail.com>",
outputDir="C:/Program Files/R/R-3.4.3/library",
tax_id="8022",
genus="Oncorhynchus",
species="mykiss")

There is a lovely folder in my R directory (i've also tried setting this up in another location), but when i go to install the package using install.package("org.Omykiss.eg.db") (with and without repos=NULL or type="source"), i just get error messages such as Warning in install.packages :package ‘org.Omykiss.eg.db’ is not available (for R version 3.4.3) or

Warning: invalid package 'org.Omykiss.eg.db'
Error: ERROR: no packages specified
In R CMD INSTALL
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" CMD INSTALL -l "..\Documents\R\win-library\3.4" "org.Omykiss.eg.db"' had status 1
Warning in install.packages :
installation of package ‘org.Omykiss.eg.db’ had non-zero exit status

Any help on this would be greatly appreciated. I have looked at the file with select function etc and undersand that it has all the GO information i require for some proteomics analysis of which this is a central to the final bit of work, but i have to admit i'm stumped. Its probably something small, so any help would be very much appreicated.

R software error annotationforge • 603 views
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Guido Hooiveld ★ 3.2k
@guido-hooiveld-2020
Last seen 10 hours ago
Wageningen University, Wageningen, the …

In the past I also struggled a bit with this... See the thread on how I got it working C: problem with makeOrgPackageFromNCBI when making an annotation package.

Could it be you are calling the install.packages() function without being in the proper directory, and as a result the created OrgDb files cannot be found and installed?
I usually 'set' the working directory using setwd("c:\\bla\\bla") before running the function makeOrgPackageFromNCBI(). All required files will then be downloaded in that directory, and the parsed files will be automatically put in a sub-directory named after your species + genus. Installation will then also work without the need to specify the correct (sub-)directory.

Also, if I were you I would create the OrgDb in another directory than the c/program files/... you used now.

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Dear Guido

Many thanks for the link to your thread. I have now gotten it to work by setting up a completely new folder and placing all important files into it while building the new organism package (instead of what i was doing which was just having files in one directory but building in another). Much thanks!