Problem with installing packages made by makeOrgPackageFromNCBI
1
0
Entering edit mode
@babakloghmani-23075
Last seen 2.3 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

AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis • 384 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 17 hours ago
United States
install.packages("./org.Spyogenes.eg.sqlite", repos = NULL)

ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
>makeOrgPackageFromNCBI(version = "0.1",tax_id = "160490",author = "babak.loghmani@bioquant.uni-heidelberg.de",maintainer = "babak.loghmani@bioquant.uni-heidelberg.de",genus = "streptococcus",species = "pyogenes")

This is the line. shall I change anything?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

For completeness, this should be

makeOrgPackageFromNCBI(version = "0.1",tax_id = "160490",author = "Babak Loghmani",maintainer = "Babak Loghmani <babak.loghmani@bioquant.uni-heidelberg.de>",genus = "streptococcus",species = "pyogenes")

Where the critical part is that the maintainer should be Firstname Lastname <email>

ADD REPLY

Login before adding your answer.

Traffic: 183 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