Error in xj[i] : only 0's may be mixed with negative subscripts about geoquery HOT 4 CLOSED

I am getting the same error:

> library(GEOquery)
> eset <- getGEO("GSE50841")

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50841/matrix/
Found 1 file(s)
GSE50841_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50841/matrix/GSE50841_series_matrix.txt.gz'
ftp data connection made, file length 4729722 bytes
==================================================
downloaded 4.5 MB

File stored at: 
/tmp/RtmpjvWXtU/GPL10558.soft
Error in xj[i] : only 0's may be mixed with negative subscripts

> sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8       
 [4] LC_COLLATE=en_CA.UTF-8     LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GEOquery_2.36.0     Biobase_2.30.0      BiocGenerics_0.16.1

loaded via a namespace (and not attached):
[1] tools_3.2.4    RCurl_1.95-4.8 bitops_1.0-6   XML_3.98-1.4 

from geoquery.

This error has been solved. I guess it had something to do with their servers as this issue describes.
However, while the servers were down, I observed a particular thing - the http servers weren't down and I was able to download data from my web browser.

@seandavi Can the function be modified such that we can input an argument ftp or http to it so that when one is down, we can download it via the other?

from geoquery.

Late reply, but GEOquery uses https only now.

from geoquery.

ERROR: configuration failed for package ‘openssl’

• removing ‘/home/avantika/R/x86_64-pc-linux-gnu-library/4.1/openssl’
  ERROR: dependency ‘openssl’ is not available for package ‘httr’
• removing ‘/home/avantika/R/x86_64-pc-linux-gnu-library/4.1/httr’
  ERROR: dependency ‘httr’ is not available for package ‘GEOquery’
• removing ‘/home/avantika/R/x86_64-pc-linux-gnu-library/4.1/GEOquery’
• The downloaded source packages are in
  ‘/tmp/Rtmp4ls7uu/downloaded_packages’
  Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
  boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS,
  Matrix, mgcv, nlme, nnet, rpart, spatial, survival
  Warning messages:
  1: In install.packages(...) :
  installation of package ‘openssl’ had non-zero exit status
  2: In install.packages(...) :
  installation of package ‘httr’ had non-zero exit status
  3: In install.packages(...) :
  installation of package ‘GEOquery’ had non-zero exit status
  This is the result I get when I install BiocManager GEO query package. But when I try to run the command of library(GEOquery I always get this error.)

library(GEOquery)
Error in library(GEOquery) : there is no package called ‘GEOquery’

I am using latest ubuntu version and R 4.1.2 version

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