 Hi  all and M. Carlson
I am now working on an archaea, which is not a common organism. I want to
use goseq to do the GO analysis of my RNAseq data.In order to creat the
category mappings(relationship between GO and gene id), I try to use the
makeOrgPackagesFromNCBI.Now the problem comes as following:
1 using the command here,
 makeOrgPackageFromNCBI(
+            version="0.1",
+            maintainer="Pengfei Liu <liupfskygre@gmail.com>",
+            author="Pengfei Liu <liupfskygre@gmail.com>",
+            outputDir=".",
+            tax_id="1041930",
+            genus="Methanocella",
+            species="conradii",NCBIFilesDir=NULL)
Error in makeOrgPackageFromNCBI(version = "0.1", maintainer = "Pengfei Liu <
liupfskygre@gmail.com>",  :
  'NCBIFilesDir' argument needs to be a single string or NULL
2, add NCBIFilesDir=NULL, same error
makeOrgPackageFromNCBI(
+            version="0.1",
+            maintainer="Pengfei Liu <liupfskygre@gmail.com>",
+            author="Pengfei Liu <liupfskygre@gmail.com>",
+            outputDir=".",
+            tax_id="1041930",
+            genus="Methanocella",
+            species="conradii", NCBIFilesDir=NULL)
Error in makeOrgPackageFromNCBI(version = "0.1", maintainer = "Pengfei Liu <
liupfskygre@gmail.com>",  :
  'NCBIFilesDir' argument needs to be a single string or NULL
3 use following, it worked for a while
makeOrgPackageFromNCBI(
           version="0.1",
           maintainer="Pengfei Liu <liupfskygre@gmail.com>",
           author="Pengfei Liu <liupfskygre@gmail.com>",
           outputDir=".",
           tax_id="1041930",
           genus="Methanocella",
           species="conradii", NCBIFilesDir="/home/hp/liupf")

however, following appeared and stoped

Getting blast2GO data as a substitute for gene2go
Error in .tryDL(url, tmp) :
  After 3 attempts, AnnotationDbi is still not able to access the
  following URL:
  http://www.b2gfar.org/_media/species:data:1041930.annot.zip You might
  want to try again later.

Moreover, when using above command, the memeroy of my computer(8 Gb) is
nearyly fully occupied, it is my first time to use this function,
I do not know the memory requirement of this function?

so how to solve this issuse and to successfully create a db for goseq, or
is there any other way to do the same job?

Thanks!

sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] GO.db_2.10.1          RCurl_1.95-4.1        bitops_1.0-6
 [4] AnnotationForge_1.4.0 org.Hs.eg.db_2.10.1   RSQLite_0.11.4
 [7] DBI_0.2-7             AnnotationDbi_1.24.0  Biobase_2.22.0
[10] BiocGenerics_0.8.0    BiocInstaller_1.12.0

loaded via a namespace (and not attached):
[1] IRanges_1.20.4 stats4_3.0.2   tcltk_3.0.2    tools_3.0.2


-- 
Pengfei Liu, PhD Candidate

Lab of Microbial Ecology
College of Resources and Environmental Sciences
China Agricultural University
No.2 Yuanmingyuanxilu, Beijing, 100193
P.R. China

Tel: +86-10-62731358
Fax: +86-10-62731016

E-mail: liupfskygre@gmail.com

If you are afraid of tomorrow, how can you enjoy today!
Keep hungry, Keep foolish!
Moving forward!

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