[Seqinr-forum] Seqinr

[Jean Lobry]

Hi Ran,

now I'm able to reproduce the issue. There is an
entry for ACC "NC_001477" as visible here:

https://www.ncbi.nlm.nih.gov/nuccore/NC_001477

But it clearly doesn't work here:

 > library(seqinr)
 > where.is.this.acc("NC_001477")
Looking for available databases
Looking for sequence with accession number NC_001477 in the following 
ACNUC databases:
  [1] "genbank"         "embl"            "emblwgs"         "swissprot" 

  [5] "ensembl"         "hogenom"         "hogenomdna" 
"hovergendna"
  [9] "hovergen"        "hogenom5"        "hogenom5dna"     "hogenom4" 

[13] "hogenom4dna"     "homolens"        "homolensdna"     "hobacnucl"
[17] "hobacprot"       "phever2"         "phever2dna"      "refseq"
[21] "greviews"        "bacterial"       "archaeal"        "protozoan"
[25] "ensprotists"     "ensfungi"        "ensmetazoa"      "ensplants"
[29] "ensemblbacteria" "mito"            "polymorphix"     "emglib"
[33] "refseqViruses"   "ribodb"          "taxodb"

Trying to open bank with name --->genbank<--- ...... and opening was OK.
==> Trying to find sequence NC_001477 in bank genbank ...... not found here.

Trying to open bank with name --->embl<--- ...... and opening was OK.
==> Trying to find sequence NC_001477 in bank embl ...... not found here.

Trying to open bank with name --->emblwgs<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->emblwgs<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->swissprot<--- ...... and opening was OK.
==> Trying to find sequence NC_001477 in bank swissprot ...... not found 
here.

Trying to open bank with name --->ensembl<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->ensembl<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hogenom<--- ...... and opening was OK.
==> Trying to find sequence NC_001477 in bank hogenom ...... not found here.

Trying to open bank with name --->hogenomdna<--- ...... and opening was OK.
==> Trying to find sequence NC_001477 in bank hogenomdna ...... not 
found here.

Trying to open bank with name --->hovergendna<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->hovergendna<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hovergen<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->hovergen<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hogenom5<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->hogenom5<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hogenom5dna<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->hogenom5dna<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hogenom4<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->hogenom4<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hogenom4dna<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->hogenom4dna<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->homolens<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->homolens<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->homolensdna<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->homolensdna<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hobacnucl<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->hobacnucl<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hobacprot<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->hobacprot<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->phever2<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->phever2<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->phever2dna<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->phever2dna<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->refseq<--- ...Error in acnucopen(bank, 
socket) :
   Database with name -->refseq<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->greviews<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->greviews<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->bacterial<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->bacterial<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->archaeal<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->archaeal<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->protozoan<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->protozoan<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ensprotists<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->ensprotists<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ensfungi<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->ensfungi<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ensmetazoa<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->ensmetazoa<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ensplants<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->ensplants<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ensemblbacteria<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->ensemblbacteria<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->mito<--- ...Error in acnucopen(bank, 
socket) :
   Database with name -->mito<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->polymorphix<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->polymorphix<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->emglib<--- ...Error in acnucopen(bank, 
socket) :
   Database with name -->emglib<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->refseqViruses<--- ...Error in 
acnucopen(bank, socket) :
   Database with name -->refseqViruses<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ribodb<--- ...Error in acnucopen(bank, 
socket) :
   Database with name -->ribodb<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->taxodb<--- ...Error in acnucopen(bank, 
socket) :
   Database with name -->taxodb<-- is not known by server.

... opening not OK, skipping this bank.


Sequence with accesion number NC_001477 was not found in available 
databases.
  Are you sure this is an accession number and not a sequence name?
 >

Here is my sessionInfo()

 > sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

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

other attached packages:
[1] seqinr_3.4-5

loaded via a namespace (and not attached):
[1] compiler_3.4.1 ade4_1.7-6
 >



Given the number of databases that failed to open my best guess
is a problem on the server side. Not sure however.

We'll keep you in touch.

Best,

JLO

Le 08/08/2017 à 00:15, Ran Wei a écrit :
> Hi Jean,
> 
> Thank you very much for your reply. Actually there was a typo in my 
> first email. The accession number should be "NC_001477" instead of 
> "NC001477". Sorry about that, but the problem did not change. Please let 
> me know once the problem get fixed.
> 
> Thank you,
> Ran Wei