Error : Invalid DESCRIPTION file

[kmosi0]

Hi，I successfuly bulit the org.db package ，but got a Error when I install the package ；here is my code：

> makeOrgPackage(gene_info=gene_info,
+                go=gene2go,
+                #ko=gene2ko,
+                #pathway=gene2pathway,
+                version="0.11",
+                outputDir = "./test",
+                tax_id="11",
+                maintainer ="<a>",
+                author="<a>",
+                genus="test",
+                species="test",
+                goTable="go"
+                )
Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating go table:
go table filled
table metadata filled
'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
'select()' returned many:1 mapping between keys and columns
Populating go_all table:
go_all table filled
Creating package in ./test/org.Ttest.eg.db 
Now deleting temporary database file
[1] "./test/org.Ttest.eg.db"
There were 37 warnings (use warnings() to see them)
> install.packages("./test/org.Ttest.eg.db", repos=NULL,type='source',unlink=TRUE)
* installing *source* package 'org.Ttest.eg.db' ...
** using staged installation
Error : Invalid DESCRIPTION file

<U+00BB><fb><d0><ce><U+03AC><d0><de><c8><cb><U+0531><d3><f2>.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

ERROR: installing package DESCRIPTION failed for package 'org.Ttest.eg.db'
* removing 'D:/R-3.5.1/R-3.6.0/library/org.Ttest.eg.db'
Warning in install.packages :
  installation of package ‘./test/org.Ttest.eg.db’ had non-zero exit status

Any one got this error too ？hope for your reply ！

[Hua-CM]

Hi, I got the same problem. Do you fix this problem yet?

[mtmorgan]

ask support questions on https://support.bioconductor.org.

If the package has been successfully built, then what does the DESCRIPTION file in the package look like? Can you read it with read.dcf(<path/to/DESCRIPTION>)

[Kayla-Morrell]

@kmosi0 and @Hua-CM - if this is still an issue it would be helpful to know what the DESCRIPTION file looks like (as @mtmorgan stated). I tried building and installing a package similar to yours (using an example from an AnnotationForge vignette), and when I tried to install it I got:

* installing *source* package ‘org.Tguttata.eg.db’ ...
** using staged installation
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.Tguttata.eg.db’

The DESCRIPTION file then looks like this:

> read.dcf("./org.Tguttata.eg.db/DESCRIPTION")
     Package              Title
[1,] "org.Tguttata.eg.db" "Genome wide annotation for Taeniopygia guttata"
     Description
[1,] "Genome wide annotation for Taeniopygia guttata, primarily based on mapping using Entrez Gene identifiers."
     Version Author Maintainer
[1,] "0.1"   "<a>"  "<a>"
     Depends                                            Suggests
[1,] "R (>= 2.7.0), methods, AnnotationDbi (>= 1.50.0)" "DBI, annotate, RUnit"
     Imports                  License        organism
[1,] "methods, AnnotationDbi" "Artistic-2.0" "Taeniopygia guttata"
     species               biocViews
[1,] "Taeniopygia guttata" "OrgDb, annotation"

Which leads me to believe the way that you define the maintainer and author are incorrect. I tried build the package again with a name and proper email in these fields and I was able to install it with no problem.

> install.packages("./org.Tguttata.eg.db", repos=NULL,type="source",unlink=TRUE)
Installing package into ‘/Users/ka36530_ca/R-stuff/bin/R-4-0/4.0-Bioc-3.11/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘org.Tguttata.eg.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (org.Tguttata.eg.db)
> read.dcf("./org.Tguttata.eg.db/DESCRIPTION")
     Package              Title
[1,] "org.Tguttata.eg.db" "Genome wide annotation for Taeniopygia guttata"
     Description
[1,] "Genome wide annotation for Taeniopygia guttata, primarily based on mapping using Entrez Gene identifiers."
     Version Author
[1,] "0.1"   "Kayla Interdonato <kayla.morrell@roswellpark.org>"
     Maintainer
[1,] "Kayla Interdonato <kayla.morrell@roswellpark.org>"
     Depends                                            Suggests
[1,] "R (>= 2.7.0), methods, AnnotationDbi (>= 1.50.0)" "DBI, annotate, RUnit"
     Imports                  License        organism
[1,] "methods, AnnotationDbi" "Artistic-2.0" "Taeniopygia guttata"
     species               biocViews
[1,] "Taeniopygia guttata" "OrgDb, annotation"
>

Please try this and let me know if it fixes your issue.

[kmosi0]

I try with correct maintainer and author and it worked , thanks very much !

[Hua-CM]

I try with correct maintainer and author and it worked , thanks very much !

You are right. I found that "_" could not be included in the author or maintainer.

[qingcloudhx]

thanks very much !