[BioC] getGEO invalid multibyte string

[Saroj Mohapatra]

Hi Tobias:

I could not reproduce the error with R 2.5.0 and GEOquery 2.0.5

 > library(GEOquery)
 > gse<-getGEO('GSE94')
trying URL 
'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE94/GSE94_family.soft.gz'
ftp data connection made, file length 100293949 bytes
opened URL
downloaded 97943Kb

File stored at:
C:\DOCUME~1\smohapat\LOCALS~1\Temp\RtmpabhBsb/GSE94.soft.gz
Parsing....
^PLATFORM = GPL218
^SAMPLE = GSM2628
^SAMPLE = GSM2629
^SAMPLE = GSM2630
^SAMPLE = GSM3514
^SAMPLE = GSM3515
^SAMPLE = GSM3516
^SAMPLE = GSM3517
^SAMPLE = GSM3518
^SAMPLE = GSM3519
^SAMPLE = GSM3520
^SAMPLE = GSM3521
^SAMPLE = GSM3522
^SAMPLE = GSM3523
^SAMPLE = GSM3524
^SAMPLE = GSM3525
^SAMPLE = GSM3526
^SAMPLE = GSM3527
^SAMPLE = GSM3528
^SAMPLE = GSM3529
^SAMPLE = GSM3530
^SAMPLE = GSM3531
^SAMPLE = GSM3532
^SAMPLE = GSM3533
^SAMPLE = GSM3534
^SAMPLE = GSM3535
^SAMPLE = GSM3536
^SAMPLE = GSM3537
^SAMPLE = GSM3538
^SAMPLE = GSM3539
^SAMPLE = GSM3540
^SAMPLE = GSM3541
^SAMPLE = GSM3542
^SAMPLE = GSM3543
^SAMPLE = GSM3544
^SAMPLE = GSM3545
^SAMPLE = GSM3546
^SAMPLE = GSM3547
^SAMPLE = GSM3548
^SAMPLE = GSM3549
^SAMPLE = GSM3550
^SAMPLE = GSM3551
^SAMPLE = GSM3552
^SAMPLE = GSM3553
^SAMPLE = GSM3554
^SAMPLE = GSM3555
^SAMPLE = GSM3556
^SAMPLE = GSM3557
^SAMPLE = GSM3558
^SAMPLE = GSM3559
^SAMPLE = GSM3560
^SAMPLE = GSM3561
^SAMPLE = GSM3562
^SAMPLE = GSM3563
^SAMPLE = GSM3564
^SAMPLE = GSM3565
^SAMPLE = GSM3566
^SAMPLE = GSM3567
^SAMPLE = GSM3568
^SAMPLE = GSM3569
^SAMPLE = GSM3570
^SAMPLE = GSM3571
^SAMPLE = GSM3572
^SAMPLE = GSM3573
^SAMPLE = GSM3574
^SAMPLE = GSM3575
^SAMPLE = GSM3576
^SAMPLE = GSM3577
^SAMPLE = GSM3578
^SAMPLE = GSM3579
^SAMPLE = GSM3580
^SAMPLE = GSM3581
^SAMPLE = GSM3582
^SAMPLE = GSM3583
^SAMPLE = GSM3584
^SAMPLE = GSM3585
^SAMPLE = GSM3586
^SAMPLE = GSM3587
^SAMPLE = GSM3588
^SAMPLE = GSM3589
^SAMPLE = GSM3590
^SAMPLE = GSM3591
^SAMPLE = GSM3592
^SAMPLE = GSM3593
^SAMPLE = GSM3594
^SAMPLE = GSM3595
^SAMPLE = GSM3596
^SAMPLE = GSM3597
^SAMPLE = GSM3598
^SAMPLE = GSM3599
^SAMPLE = GSM3600
^SAMPLE = GSM3601
^SAMPLE = GSM3602
^SAMPLE = GSM3603
^SAMPLE = GSM3604
^SAMPLE = GSM3605
^SAMPLE = GSM3606
^SAMPLE = GSM3607
^SAMPLE = GSM3608
^SAMPLE = GSM3609
^SAMPLE = GSM3610
^SAMPLE = GSM3611
^SAMPLE = GSM3612
^SAMPLE = GSM3613
^SAMPLE = GSM3614
^SAMPLE = GSM3615
^SAMPLE = GSM3616
^SAMPLE = GSM3617
^SAMPLE = GSM3618
^SAMPLE = GSM3619
^SAMPLE = GSM3620
^SAMPLE = GSM3621
^SAMPLE = GSM3622
^SAMPLE = GSM3623
^SAMPLE = GSM3624
^SAMPLE = GSM3625
^SAMPLE = GSM3626
^SAMPLE = GSM3627
^SAMPLE = GSM3628
^SAMPLE = GSM3629
^SAMPLE = GSM3630
^SAMPLE = GSM3631
^SAMPLE = GSM3632
^SAMPLE = GSM3633
^SAMPLE = GSM3634
^SAMPLE = GSM3635
^SAMPLE = GSM3636
^SAMPLE = GSM3637
^SAMPLE = GSM3638
^SAMPLE = GSM3639
^SAMPLE = GSM3640
^SAMPLE = GSM3641
^SAMPLE = GSM3642
^SAMPLE = GSM3643
^SAMPLE = GSM3644
^SAMPLE = GSM3645
^SAMPLE = GSM3646
^SAMPLE = GSM3647
^SAMPLE = GSM3648
^SAMPLE = GSM3649
^SAMPLE = GSM3650
^SAMPLE = GSM3651
^SAMPLE = GSM3652
^SAMPLE = GSM3653
^SAMPLE = GSM3654
^SAMPLE = GSM3655
^SAMPLE = GSM3656
^SAMPLE = GSM3657
^SAMPLE = GSM3658
^SAMPLE = GSM3659
^SAMPLE = GSM3660
^SAMPLE = GSM3661
^SAMPLE = GSM3662
^SAMPLE = GSM3663
^SAMPLE = GSM3664
^SAMPLE = GSM3665
^SAMPLE = GSM3666
^SAMPLE = GSM3667
^SAMPLE = GSM3668
 > sessionInfo()
R version 2.5.0 (2007-04-23)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
GEOquery
 "2.0.5"
 >

Best,

Saroj

Tobias Straub wrote:

>I tried to fetch and parse the GSE94 series from GEO using GEOquery  
>library (gse<-getGEO('GSE94')). Operation is aborted with the message:
>
>Error in make.names(as.character(names), allow_) :
>	invalid multibyte string 29
>In addition: There were 12 warnings (use warnings() to see them)
>
>is that an error of getGEO or a problem of the data set?
>
>Tobias
>
> > sessionInfo()
>R version 2.5.1 (2007-06-27)
>i386-apple-darwin8.9.1
>
>locale:
>en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>attached base packages:
>[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"   
>"methods"   "base"
>
>other attached packages:
>GEOquery
>"2.0.6"
>
>
>======================================================================
>Dr. Tobias Straub         Adolf-Butenandt-Institute, Molecular Biology
>tel: +49-89-2180 75 439         Schillerstr. 44, 80336 Munich, Germany
>
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>  
>