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lgatto / rpx

R Interface to the ProteomeXchange Repository
http://lgatto.github.io/rpx/
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Error in fix_issue_17(x) #24

Closed GermanFernandezz closed 1 year ago

GermanFernandezz commented 1 year ago

Hello! I am doing the tutorial http://bioconductor.org/packages/3.10/bioc/vignettes/proteoQC/inst/doc/proteoQC.html But i get the following error

px <- PXDataset("PXD000864") Querying ProteomeXchange for PXD000864. Error in fix_issue_17(x) : Can't access URL(s): ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/03/PXD000864 ftp://ftp.pride.ebi.ac.uk/pride-archive/2014/03/PXD000864

lgatto commented 1 year ago

What is your sessionInfo()? I suspect you need to update your R/Bioc.

I works here with the latest versions of R and rpx.

> library(rpx)
> px <- PXDataset("PXD000864")
Querying ProteomeXchange for PXD000864.
> px
Project PXD000864 with 218 files
 Resource ID BFC1254 in cache in /home/lgatto/.cache/R/rpx.
 [1] 'README.txt' ... [218] 'TTE2010.zip'
 Use 'pxfiles(.)' to see all files.
> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3;  LAPACK version 3.10.0

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

time zone: Europe/Brussels
tzcode source: system (glibc)

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

other attached packages:
[1] rpx_2.8.0

loaded via a namespace (and not attached):
 [1] vctrs_0.6.2         httr_1.4.6          cli_3.6.1          
 [4] rlang_1.1.1         DBI_1.1.3           BiocFileCache_2.8.0
 [7] purrr_1.0.1         generics_0.1.3      jsonlite_1.8.4     
[10] glue_1.6.2          bit_4.0.5           RCurl_1.98-1.12    
[13] dbplyr_2.3.2        fansi_1.0.4         filelock_1.0.2     
[16] tibble_3.2.1        bitops_1.0-7        fastmap_1.1.1      
[19] lifecycle_1.0.3     memoise_2.0.1       BiocManager_1.30.20
[22] compiler_4.3.0      dplyr_1.1.2         RSQLite_2.3.1      
[25] blob_1.2.4          pkgconfig_2.0.3     R6_2.5.1           
[28] tidyselect_1.2.0    utf8_1.2.3          curl_5.0.0         
[31] pillar_1.9.0        magrittr_2.0.3      withr_2.5.0        
[34] tools_4.3.0         bit64_4.0.5         xml2_1.3.4         
[37] cachem_1.0.8
GermanFernandezz commented 1 year ago

Hi Laurent, Thank foy your answer My sessioninfo() is sessionInfo() R version 4.3.0 (2023-04-21 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

time zone: America/Buenos_Aires tzcode source: internal

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

other attached packages: [1] rpx_2.8.0

loaded via a namespace (and not attached): [1] vctrs_0.6.2 httr_1.4.6 cli_3.6.1
[4] rlang_1.1.1 DBI_1.1.3 BiocFileCache_2.8.0 [7] purrr_1.0.1 generics_0.1.3 jsonlite_1.8.4
[10] glue_1.6.2 bit_4.0.5 RCurl_1.98-1.12
[13] dbplyr_2.3.2 fansi_1.0.4 filelock_1.0.2
[16] tibble_3.2.1 bitops_1.0-7 fastmap_1.1.1
[19] lifecycle_1.0.3 memoise_2.0.1 BiocManager_1.30.20 [22] compiler_4.3.0 dplyr_1.1.2 RSQLite_2.3.1
[25] blob_1.2.4 pkgconfig_2.0.3 R6_2.5.1
[28] tidyselect_1.2.0 utf8_1.2.3 curl_5.0.0
[31] pillar_1.9.0 magrittr_2.0.3 withr_2.5.0
[34] tools_4.3.0 bit64_4.0.5 xml2_1.3.4
[37] cachem_1.0.8

lgatto commented 1 year ago

Could you then try again in a new session. I checked again and I can't reproduce your error.

GermanFernandezz commented 1 year ago

Could it be a problem with the proxies?

lgatto commented 1 year ago

Yes. Can you open this URL in your browser

http://ftp.pride.ebi.ac.uk/pride/data/archive/2014/03/PXD000864/

GermanFernandezz commented 1 year ago

Yes

GermanFernandezz commented 1 year ago

Hi, ii is something with my work connection. I will tried to solve it. Thanks for your help.

lgatto commented 1 year ago

Closing for now, but feel free to re-open if necessary.