Problem with installing packages made by makeOrgPackageFromNCBI
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@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

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@james-w-macdonald-5106
Last seen 17 hours ago
United States
install.packages("./org.Spyogenes.eg.sqlite", repos = NULL)


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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?

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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

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>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?

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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

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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>