Closed kmosi0 closed 4 years ago
Hi, I got the same problem. Do you fix this problem yet?
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>)
@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.
I try with correct maintainer and author and it worked , thanks very much !
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.
thanks very much !
Hi,I successfuly bulit the org.db package ,but got a Error when I install the package ;here is my code:
Any one got this error too ?hope for your reply !