Question: Annotation package built with pdInfoBuilder cannot be installed
0
gravatar for alakatos
4.6 years ago by
alakatos110
United States
alakatos110 wrote:

Hello,

I followed a workflow (Draft support for HTA 2.0 with oligo) using  pdInfoBuilder to build an annotation package for my MTA10 array. Unfortunately, I cannot install the package.  In my directory, there is a folder named "pd.mta.1.0" but not a zip file.  

 I am wondering if someone have found a solution to this issue.

Thank you in advance.

Anita

code:

> library(pdInfoBuilder)
> p <- new("AffyHTAPDInfoPkgSeed", clfFile = "MTA-1_0.r3.clf", pgfFile = "MTA-1_0.r3.pgf", coreMps = "MTA-1_0.r3.Psrs.mps", transFile = "MTA-1_0.na34.1.mm10.transcript.csv", probeFile = "MTA-1_0.na34.1.mm10.probeset.csv", author = "alakatos", email = "alakatos@uci.edu", version = "1.0.r3")
> makePdInfoPackage(p, destDir = ".")
==================================================================================================================================================
Building annotation package for Affymetrix HTA Array
PGF.........: MTA-1_0.r3.pgf
CLF.........: MTA-1_0.r3.clf
Probeset....: MTA-1_0.na34.1.mm10.probeset.csv
Transcript..: MTA-1_0.na34.1.mm10.transcript.csv
Core MPS....: MTA-1_0.r3.Psrs.mps
==================================================================================================================================================
Parsing file: MTA-1_0.r3.pgf... OK
Parsing file: MTA-1_0.r3.clf... OK
Creating initial table for probes... OK
Creating dictionaries... OK
Parsing file: MTA-1_0.na34.1.mm10.probeset.csv... OK
Parsing file: MTA-1_0.r3.Psrs.mps... OK
Creating package in ./pd.mta.1.0 
Inserting 594 rows into table chrom_dict... OK
Inserting 5 rows into table level_dict... OK
Inserting 17 rows into table type_dict... OK
Inserting 444001 rows into table core_mps... OK
Inserting 734916 rows into table featureSet... OK
Inserting 6142582 rows into table pmfeature... OK
Inserting 711 rows into table mmfeature... OK
Counting rows in chrom_dict
Counting rows in core_mps
Counting rows in featureSet
Counting rows in level_dict
Counting rows in mmfeature
Counting rows in pmfeature
Counting rows in type_dict
Creating index idx_pmfsetid on pmfeature... OK
Creating index idx_pmfid on pmfeature... OK
Creating index idx_fsfsetid on featureSet... OK
Creating index idx_core_meta_fsetid on core_mps... OK
Creating index idx_core_fsetid on core_mps... OK
Creating index idx_mmfsetid on mmfeature... OK
Creating index idx_mmfid on mmfeature... OK
Saving DataFrame object for PM.
Saving DataFrame object for MM.
Saving NetAffx Annotation... OK
Done.
> install.packages("pd.mta.1.0", repos = NULL, type = "source")
Installing package into ‘C:/Users/alakatos/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
* installing *source* package 'pd.mta.1.0' ...
Error : Invalid DESCRIPTION file

Malformed package version.

See the information on DESCRIPTION files in section 'Creating R
packages' of the 'Writing R Extensions' manual.

ERROR: installing package DESCRIPTION failed for package 'pd.mta.1.0'
* removing 'C:/Users/alakatos/Documents/R/win-library/3.1/pd.mta.1.0'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\alakatos\Documents\R\win-library\3.1" "pd.mta.1.0"' had status 1
Warning in install.packages :
  installation of package ‘pd.mta.1.0’ had non-zero exit status
sessionInfo()
attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pdInfoBuilder_1.30.6 oligo_1.30.0         Biostrings_2.34.1    XVector_0.6.0       
 [5] IRanges_2.0.1        S4Vectors_0.4.0      oligoClasses_1.28.0  affxparser_1.38.0   
 [9] RSQLite_1.0.0        DBI_0.3.1            Biobase_2.26.0       BiocGenerics_0.12.1 
annotation pdinfobuilder • 980 views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by alakatos110
Answer: Annotation package built with pdInfoBuilder cannot be installed
0
gravatar for James W. MacDonald
4.6 years ago by
United States
James W. MacDonald51k wrote:

I think the error message is pretty clear:

Error : Invalid DESCRIPTION file

Malformed package version.

See the information on DESCRIPTION files in section 'Creating R
packages' of the 'Writing R Extensions' manual.

So you need to follow the recommendation that was given to you and figure out what is wrong with your package version.


 

ADD COMMENTlink written 4.6 years ago by James W. MacDonald51k
Answer: Annotation package built with pdInfoBuilder cannot be installed
0
gravatar for alakatos
4.6 years ago by
alakatos110
United States
alakatos110 wrote:

I see. Thank you.

Anita 

 

ADD COMMENTlink written 4.6 years ago by alakatos110
Answer: Annotation package built with pdInfoBuilder cannot be installed
0
gravatar for alakatos
4.6 years ago by
alakatos110
United States
alakatos110 wrote:

Hi James,

Description:

Package: pd.mta.1.0

Title: Platform Design Info for Affymetrix MTA-1_0

Description: Platform Design Info for Affymetrix MTA-1_0

Version: 1.0.r3

Author: alakatos

Maintainer: alakatos <alakatos@uci.edu>

LazyLoad: yes

Depends: R (>= 3.1.0),

Biostrings (>= 2.33.14),

methods,

RSQLite (>= 1.0.0),

oligoClasses (>= 1.27.2),

oligo (>= 1.29.1),

DBI (>= 0.3.1),

IRanges (>= 1.99.31),

S4Vectors (>= 0.2.5)

License: Artistic-2.0

biocViews: AnnotationData

ZipData: no

 

I went through both packages. Package "pdInfoBuilder" does not have the option to make 'zip' file .

http://www.bioconductor.org/packages/release/bioc/news/pdInfoBuilder/NEWS
BUG FIXES
    o   Added 'ZipData: no' to the template, which caused problems on Windows system

> showClass("AffyHTAPDInfoPkgSeed")
Class "AffyHTAPDInfoPkgSeed" [package "pdInfoBuilder"]

Slots:
                                                                                                                                                                                                      
Name:        probeFile       transFile         coreMps         fullMps     extendedMps       geneArray         pgfFile         clfFile         version         license          author           email
Class: ScalarCharacter ScalarCharacter ScalarCharacter ScalarCharacter ScalarCharacter         logical ScalarCharacter ScalarCharacter       character       character       character       character
                                                                                                                      
Name:        biocViews        chipName    manufacturer             url     genomebuild        organism         species
Class:       character       character       character       character       character       character       character

Extends: 
Class "AffySTPDInfoPkgSeed", directly
Class "AffyGeneric1PDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance 2
Class "AffymetrixPDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance 3
Class "PDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance 4

In the 'Writing R Extensions' manual:

http://www.hep.by/gnu/r-patched/r-exts/R-exts_4.html

 ## The `Package', `Version', `License', `Description', `Title', `Author', and `Maintainer' fields are mandatory, all other fields are optional

I have all the fields in the descriptions file.

##The `LazyData' logical field controls whether the R datasets use lazy-loading. A `LazyLoad' field was used in versions prior to 2.14.0, but now is ignored.

###The `ZipData' logical field used to control whether the automatic Windows build would zip up the data directory or not: set this to `no' if your package will not work with a zipped data directory. (Setting to any other value is deprecated, and it is unused from R 2.13.0: but it might still be needed if the package can be installed under earlier versions of R.)

Since  I am not a programmer ; therefore, I am not sure how to fix it.

install.packages("pd.mta.1.0/", repos = NULL) -- looks for a zip file.
install.packages("pd.mta.1.0/", repos = NULL, type = "source") does not like the "Description"

In the 'Writing R Extensions' manual:" The `Type' field specifies the type of the package: see section Package types". However, there is no slot name for "type".  

invalid name for slot of class “AffyHTAPDInfoPkgSeed”: type.

Would you please advise?

Thank you,

Anita

ADD COMMENTlink written 4.6 years ago by alakatos110
Answer: Annotation package built with pdInfoBuilder cannot be installed
0
gravatar for James W. MacDonald
4.6 years ago by
United States
James W. MacDonald51k wrote:

My intent was to give you the information you needed to figure this out yourself, and allow you to do so. This is something you WILL have to learn how to do if you plan on using R/Bioconductor. The upside of Open Source software is that you get it for free, it's updated really regularly, lots of people contribute, etc.

The downside is that the software doesn't come with a tech support license, so you either have to figure things out yourself, or ask for help on forums like this. Unfortunately, the amount of help you receive is inversely proportional to the amount of effort you appear to be putting in yourself, so the more questions you ask, and the simpler they are, the less help you will tend to get. So it's in your best interest to try to figure things out on your own, and only ask if you are stuck.

So, enough of the lecturing and on to the helping. One thing you will have to learn about R is that the help and messages are often terse, but they usually tell you everything you need to know. You just have to pay attention. So let's look at the error message again:

Error : Invalid DESCRIPTION file

Malformed package version.

See the information on DESCRIPTION files in section 'Creating R
packages' of the 'Writing R Extensions' manual.

The first line tells you there is a problem with your DESCRIPTION file, and the second line tells you what the problem is, and the third line tells you where to find the answer.

So let's consider exactly what the second line is saying. It says that the package version is malformed, right? Now if you look at the description file, do you see anything in there that might be the package version? I do. It's this line:

Version: 1.0.r3

So let's go to the manual and see what they say about the version field:

The mandatory ‘Version’ field gives the version of the package. This is a sequence of at least two (and usually three) non-negative integers separated by single ‘.’ or ‘-’ characters. The canonical form is as shown in the example, and a version such as ‘0.01’ or ‘0.01.0’ will be handled as if it were ‘0.1-0’. It is not a decimal number, so for example 0.9 < 0.75 since 9 < 75.

Is your version a 'sequence of at least two non-negative integers'?

ADD COMMENTlink written 4.6 years ago by James W. MacDonald51k
Answer: Annotation package built with pdInfoBuilder cannot be installed
0
gravatar for alakatos
4.6 years ago by
alakatos110
United States
alakatos110 wrote:

Hi James,

Thank you. It worked.

Please lecture me any time! 

I am in the learning process, so I am grateful for any advice on how to navigate in this world.

I appreciate your help.

Anita

ADD COMMENTlink written 4.6 years ago by alakatos110
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