Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

FTP status was '550 Requested action not taken; file unavailable' #21

Open
MonnieMcGee opened this issue Mar 2, 2023 · 14 comments
Open

FTP status was '550 Requested action not taken; file unavailable' #21

MonnieMcGee opened this issue Mar 2, 2023 · 14 comments

Comments

@MonnieMcGee
Copy link

I ran the following code using rpx for Bioc 3.16 running R 4.2.2 on an Intel Mac running OS 12.6. Errors are shown within the code. Note that I had no trouble loading the example data set. Other data sets (just 3 so far) that I have tried give me the same error as in the subject line.

library(rpx)
my_cache <- BiocFileCache::BiocFileCache(tempfile())
using temporary cache /var/folders/z9/tycx8gl55nz3g4ll83j03_5h0000gp/T//RtmpfvV2EA/BiocFileCache
my_cache
class: BiocFileCache
bfccache: /var/folders/z9/tycx8gl55nz3g4ll83j03_5h0000gp/T//RtmpfvV2EA/BiocFileCache
bfccount: 0
For more information see: bfcinfo() or bfcquery()
px <- PXDataset2("PXD031685", cache = my_cache)
Querying ProteomeXchange for PXD031685.
Error in file(file, "rt") :
cannot open the connection to 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/11/PXD031685/README.txt'
In addition: Warning message:
In file(file, "rt") :
cannot open URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/11/PXD031685/README.txt': FTP status was '550 Requested action not taken; file unavailable'
px <- PXDataset2("PXD000001", cache = my_cache)
Querying ProteomeXchange for PXD000001.
my_cache
class: BiocFileCache
bfccache: /var/folders/z9/tycx8gl55nz3g4ll83j03_5h0000gp/T//RtmpfvV2EA/BiocFileCache
bfccount: 1
For more information see: bfcinfo() or bfcquery()

Clearly R can find my_cache because the example data set can be download (bfccount = 1).

Thanks for your attention to this! I'm teaching a bioinformatics course and I would really love for the students to be able to use rpx when we analyze flow data!

Monnie
@lgatto
Copy link
Owner

lgatto commented Mar 2, 2023

Thank you for the report. The problem comes for a missing README.txt file in that PX project. I believe that every PX project/directory should have one.

@ypriverol - could you confirm/comment?

@MonnieMcGee
Copy link
Author

If every PX project/directory should have a README file, then why doesn't this one?

And it isn't just this one. I tried two or three others (I don't have the accession numbers written down).

How can I make sure to use PX projects with README files?

@lgatto
Copy link
Owner

lgatto commented Mar 3, 2023

@ypriverol should be able to confirm this.

@ypriverol
Copy link

Hi @lgatto sorry for the late reply. @MonnieMcGee is right. Not all the PX contains a README file, a README was created in the past by PRIDE pipelines, was not use by anyone and at some time we stop generating them. Do you need them for something special?

@lgatto
Copy link
Owner

lgatto commented Mar 7, 2023

That is exactly the recurring problem:

a README was created in the past by PRIDE pipelines, was not use by anyone and at some time we stop generating them

It is impossible to make any assumptions because things change and break out of the blue. And this has happened several times in the past.

@lgatto
Copy link
Owner

lgatto commented Mar 7, 2023

@MonnieMcGee - I'll have to fix this. I don't think it is difficult to do, but I have very limited time. Will keep you posted here. Thank you for highlighting this issue!

@MonnieMcGee
Copy link
Author

MonnieMcGee commented Mar 7, 2023 via email

@lgatto
Copy link
Owner

lgatto commented Mar 8, 2023

@ypriverol - the random changes to the PRIDE infrastructure are a pain in my backside. The number of issues in this repo show it. The day somebody at PRIDE understands backward compatibility will be a great relief. But I don't hold my breath...

lgatto added a commit that referenced this issue Mar 8, 2023
@lgatto
fix: don't reply on project's README file (discontinued) - see issue #21
29f226e
@lgatto
Copy link
Owner

lgatto commented Mar 8, 2023

@MonnieMcGee - this should be fixed now:

> library(rpx)
> packageVersion("rpx")
[1] ‘2.6.1’
> PXDataset("PXD031685")
Querying ProteomeXchange for PXD031685.
Project PXD031685 with 39 files
 Resource ID BFC1235 in cache in /home/lgatto/.cache/R/rpx.
 [1] 'LUM2_1023541.mzML' ... [39] 'LUM2_803367.raw'
 Use 'pxfiles(.)' to see all files.

You can install the latest version right away with.

BiocManager::install("lgatto/rpx")

I'll push the change to Bioconductor later today.

@lgatto
Copy link
Owner

lgatto commented Mar 8, 2023

I'm closing the issue, but feel free to re-open it if you still have any issues.

@lgatto lgatto closed this as completed Mar 8, 2023
@lgatto
Copy link
Owner

lgatto commented Mar 8, 2023

FYI - version on Github is 2.7.1. This will also be the devel version. Release version will be 2.6.1.

@MonnieMcGee
Copy link
Author

MonnieMcGee commented Mar 8, 2023 via email

@MonnieMcGee
Copy link
Author

MonnieMcGee commented Mar 8, 2023 via email

@lgatto lgatto reopened this Mar 8, 2023
@lgatto
Copy link
Owner

lgatto commented Mar 8, 2023

Have you restarted your R session? Here's what I have in a new one:

> BiocManager::install("lgatto/rpx")
*** output flushed ***
> packageVersion("rpx")
[1] ‘2.7.1’
> library("rpx")
> my_cache <- BiocFileCache::BiocFileCache(tempfile())
/tmp/RtmpdvUHQ6/file93a92903ee7
  does not exist, create directory? (yes/no): yes
> px <- PXDataset2("PXD031685", cache = my_cache)
Querying ProteomeXchange for PXD031685.
> px
Project PXD031685 with 39 files
 Resource ID BFC1 in cache in /tmp/RtmpdvUHQ6/file93a92903ee7.
 [1] 'LUM2_1023541.mzML' ... [39] 'LUM2_803367.raw'
 Use 'pxfiles(.)' to see all files.

If you still have an error with the code above, in a new session, please also provide you session information, as shown below:

> sessionInfo()
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 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

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       

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

other attached packages:
[1] rpx_2.7.1

loaded via a namespace (and not attached):
 [1] compiler_4.2.2      pillar_1.8.1        BiocManager_1.30.20
 [4] dbplyr_2.3.1        bitops_1.0-7        prettyunits_1.1.1  
 [7] remotes_2.4.2       tools_4.2.2         pkgbuild_1.4.0     
[10] bit_4.0.5           jsonlite_1.8.4      BiocFileCache_2.6.1
[13] RSQLite_2.3.0       memoise_2.0.1       lifecycle_1.0.3    
[16] tibble_3.1.8        pkgconfig_2.0.3     rlang_1.0.6        
[19] DBI_1.1.3           cli_3.6.0           filelock_1.0.2     
[22] curl_5.0.0          fastmap_1.1.1       xml2_1.3.3         
[25] withr_2.5.0         dplyr_1.1.0         httr_1.4.5         
[28] rappdirs_0.3.3      desc_1.4.2          generics_0.1.3     
[31] vctrs_0.5.2         rprojroot_2.0.3     bit64_4.0.5        
[34] tidyselect_1.2.0    glue_1.6.2          R6_2.5.1           
[37] processx_3.8.0      fansi_1.0.4         purrr_1.0.1        
[40] callr_3.7.3         blob_1.2.3          magrittr_2.0.3     
[43] ps_1.7.2            utf8_1.2.3          RCurl_1.98-1.10    
[46] cachem_1.0.7        crayon_1.5.2

@lgatto lgatto mentioned this issue Mar 9, 2023
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@ypriverol @lgatto @MonnieMcGee