Queries around makeOrgPackageFromNCBI
1
0
Entering edit mode
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
ADD COMMENT
2
Entering edit mode
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.

 

 

ADD COMMENT
0
Entering edit mode

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!

ADD REPLY

Login before adding your answer.

Traffic: 261 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6