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lgatto / rpx

R Interface to the ProteomeXchange Repository
http://lgatto.github.io/rpx/
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FTP status was '550 Requested action not taken; file unavailable' #21

Open MonnieMcGee opened 1 year ago

MonnieMcGee commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

@ypriverol should be able to confirm this.

ypriverol commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

@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 commented 1 year ago

I wanted to use files from PX for a class that I am teaching in bioinformatics. So, yes, it’s something special. That said, I am not particular about the study data I use.

Sent from my iPhone

On Mar 7, 2023, at 5:03 AM, Yasset Perez-Riverol @.***> wrote:



[EXTERNAL SENDER]

Hi @lgattohttps://github.com/lgatto sorry for the late reply. @MonnieMcGeehttps://github.com/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?

— Reply to this email directly, view it on GitHubhttps://github.com/lgatto/rpx/issues/21#issuecomment-1457973169, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADK2IREOQU2S2LQO73FAMADW24IZHANCNFSM6AAAAAAVNSDE4M. You are receiving this because you were mentioned.Message ID: @.***>

lgatto commented 1 year ago

@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 commented 1 year ago

@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 commented 1 year ago

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

lgatto commented 1 year ago

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

MonnieMcGee commented 1 year ago

Oops. Mistyped your name. Sorry, Laurent.

Monnie McGee, PhD Associate Professor Statistical Science Southern Methodist University Office: 214-768-2462 Fax: 214-768-4035

From: McGee, Monnie Sent: Wednesday, March 8, 2023 10:39 AM To: lgatto/rpx; lgatto/rpx Cc: Mention Subject: RE: [lgatto/rpx] FTP status was '550 Requested action not taken; file unavailable' (Issue #21)

Hi, Laurant,

It's still not working. See code below. I installed "lgatto/rpx" as directed.

My university will be on spring break next week. I can come back and try this again on March 17 or 18.

Monnie

library(remotes) BiocManager::install("lgatto/rpx") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 (2022-10-31) Installing github package(s) 'lgatto/rpx' Downloading GitHub repo @.*** Running R CMD build...

  • checking for file ‘/private/var/folders/z9/tycx8gl55nz3g4ll83j03_5h0000gp/T/RtmpGhU23u/remotes1f891669d4d8/lgatto-rpx-47b861c/DESCRIPTION’ ... OK
  • preparing ‘rpx’:
  • checking DESCRIPTION meta-information ... OK
  • checking for LF line-endings in source and make files and shell scripts
  • checking for empty or unneeded directories
  • building ‘rpx_2.7.1.tar.gz’
  • installing source package ‘rpx’ ... using staged installation R byte-compile and prepare package for lazy loading help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path
  • DONE (rpx) library(rpx) my_cache <- BiocFileCache::BiocFileCache(tempfile()) /var/folders/z9/tycx8gl55nz3g4ll83j03_5h0000gp/T//RtmpGhU23u/file1f8948ade7e0 does not exist, create directory? (yes/no): yes my_cache class: BiocFileCache bfccache: /var/folders/z9/tycx8gl55nz3g4ll83j03_5h0000gp/T//RtmpGhU23u/file1f8948ade7e0 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' PXDataset("PXD031685") 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' library(lgatto/rpx) Error in library(lgatto/rpx) : 'package' must be of length 1 library("lgatto/rpx") Error in library("lgatto/rpx") : there is no package called ‘lgatto/rpx’ PXDataset("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'

Monnie McGee, PhD Associate Professor Statistical Science Southern Methodist University Office: 214-768-2462 Fax: 214-768-4035

From: Laurent Gatto @.*** Sent: Wednesday, March 8, 2023 4:58 AM To: lgatto/rpx Cc: McGee, Monnie; Mention Subject: Re: [lgatto/rpx] FTP status was '550 Requested action not taken; file unavailable' (Issue #21)

[EXTERNAL SENDER]

@MonnieMcGeehttps://github.com/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.

— Reply to this email directly, view it on GitHubhttps://github.com/lgatto/rpx/issues/21#issuecomment-1459985291, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADK2IRAL25TC3Q64D2E6OJLW3BQ4BANCNFSM6AAAAAAVNSDE4M. You are receiving this because you were mentioned.Message ID: @.***>

MonnieMcGee commented 1 year ago

Hi, Laurant,

It's still not working. See code below. I installed "lgatto/rpx" as directed.

My university will be on spring break next week. I can come back and try this again on March 17 or 18.

Monnie

library(remotes) BiocManager::install("lgatto/rpx") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 (2022-10-31) Installing github package(s) 'lgatto/rpx' Downloading GitHub repo @.*** Running R CMD build...

  • checking for file ‘/private/var/folders/z9/tycx8gl55nz3g4ll83j03_5h0000gp/T/RtmpGhU23u/remotes1f891669d4d8/lgatto-rpx-47b861c/DESCRIPTION’ ... OK
  • preparing ‘rpx’:
  • checking DESCRIPTION meta-information ... OK
  • checking for LF line-endings in source and make files and shell scripts
  • checking for empty or unneeded directories
  • building ‘rpx_2.7.1.tar.gz’
  • installing source package ‘rpx’ ... using staged installation R byte-compile and prepare package for lazy loading help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path
  • DONE (rpx) library(rpx) my_cache <- BiocFileCache::BiocFileCache(tempfile()) /var/folders/z9/tycx8gl55nz3g4ll83j03_5h0000gp/T//RtmpGhU23u/file1f8948ade7e0 does not exist, create directory? (yes/no): yes my_cache class: BiocFileCache bfccache: /var/folders/z9/tycx8gl55nz3g4ll83j03_5h0000gp/T//RtmpGhU23u/file1f8948ade7e0 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' PXDataset("PXD031685") 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' library(lgatto/rpx) Error in library(lgatto/rpx) : 'package' must be of length 1 library("lgatto/rpx") Error in library("lgatto/rpx") : there is no package called ‘lgatto/rpx’ PXDataset("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'

Monnie McGee, PhD Associate Professor Statistical Science Southern Methodist University Office: 214-768-2462 Fax: 214-768-4035

From: Laurent Gatto @.*** Sent: Wednesday, March 8, 2023 4:58 AM To: lgatto/rpx Cc: McGee, Monnie; Mention Subject: Re: [lgatto/rpx] FTP status was '550 Requested action not taken; file unavailable' (Issue #21)

[EXTERNAL SENDER]

@MonnieMcGeehttps://github.com/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.

— Reply to this email directly, view it on GitHubhttps://github.com/lgatto/rpx/issues/21#issuecomment-1459985291, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADK2IRAL25TC3Q64D2E6OJLW3BQ4BANCNFSM6AAAAAAVNSDE4M. You are receiving this because you were mentioned.Message ID: @.***>

lgatto commented 1 year ago

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