Entering edit mode
babak.loghmani
▴
20
@babakloghmani-23075
Last seen 4.1 years ago
Hi,
I made a package for Streptococcus pyogenes using makeOrgPackageFromNCBI() function. The process finished without giving an error, but only a list of warnings, which probably are not very critical. The problem is that I cannot use this package. I tried to install it using several functions, but it always returns the same error:
> install.packages("org.Spyogenes.eg.sqlite")
Installing package into ‘/Users/babak/Library/R/3.6/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘org.Spyogenes.eg.sqlite’ is not available (for R version 3.6.2)
> install.packages("./org.Spyogenes.eg.sqlite")
Installing package into ‘/Users/babak/Library/R/3.6/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘./org.Spyogenes.eg.sqlite’ is not available (for R version 3.6.2)
can anyone help me by this issue?
I have to mention that I would like to use this package for Gene ontology (GO) and pathway analysis in edgeR package. So if there are better alternatives, please let me know
Cheers, Babak
Thanks for your answer,
I tried this and I faced this error:
Error : Invalid DESCRIPTION file
Malformed maintainer field.
See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual.
ERROR: installing package DESCRIPTION failed for package ‘org.Spyogenes.eg.db’
I checked the description file and the maintainer field is filled in a correct format. I created the package again but the error message remained the same. Do you have any idea about the source of the problem?
Could you show the line of code you used to create the OrgDb?
See also here, and the post above (since I also struggled with this a bit before): https://support.bioconductor.org/p/85687/#86971
This is the line. shall I change anything?
Thanks Guido, I found that the maintainer and author line were not complete written in the beginning. I edited the line and created the package again at it worked.
Cheers
For completeness, this should be
Where the critical part is that the maintainer should be Firstname Lastname <email>
This is so important and cool. It saved me from tons of pain! Thank you for existing guys