pxfiles() and pxget(): Server denied you to change the given directory

[simonroome]

Hi,

I'm getting errors running this code from the vignette. I tried several times and I'm not sure if it's something wrong on my end like a missing package, or something wrong on the EBI server end.

> px1 <- PXDataset("PXD000001")
> pxfiles(px1)
Error in function (type, msg, asError = TRUE)  : 
  Server denied you to change to the given directory
> mztab <- pxget(px1, "PXD000001_mztab.txt")
Error in function (type, msg, asError = TRUE)  : 
  Server denied you to change to the given directory

This is my sessionInfo.

> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252    LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
[5] LC_TIME=English_Canada.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RforProteomics_1.20.0       MSnbase_2.8.3               ProtGenerics_1.14.0         mzR_2.16.2                  Rcpp_1.0.0                 
 [6] curl_3.3                    rpx_1.18.1                  SummarizedExperiment_1.12.0 DelayedArray_0.8.0          BiocParallel_1.16.6        
[11] GenomicRanges_1.34.0        GenomeInfoDb_1.18.2         DEP_1.4.1                   GSEABase_1.44.0             graph_1.60.0               
[16] annotate_1.60.0             XML_3.98-1.18               bindrcpp_0.2.2              shinycssloaders_0.2.0       V8_2.0                     
[21] ReactomePA_1.26.0           DOSE_3.8.2                  clusterProfiler_3.10.1      shinyjs_1.0                 wordcloud2_0.2.2           
[26] rintrojs_0.2.0              checkmate_1.9.1             KEGGREST_1.22.0             DT_0.5                      shinydashboard_0.7.1       
[31] forcats_0.3.0               dplyr_0.7.8                 purrr_0.3.0                 readr_1.3.1                 tidyr_0.8.2                
[36] tibble_2.0.1                tidyverse_1.2.1             plyr_1.8.4                  visNetwork_2.0.5            igraph_1.2.2               
[41] jsonlite_1.6                data.table_1.12.0           xml2_1.2.0                  stringr_1.3.1               heatmaply_0.15.2           
[46] viridis_0.5.1               viridisLite_0.3.0           plotly_4.9.0                ggplot2_3.2.1               org.Hs.eg.db_3.7.0         
[51] org.Mm.eg.db_3.7.0          AnnotationDbi_1.44.0        IRanges_2.16.0              S4Vectors_0.20.1            Biobase_2.42.0             
[56] BiocGenerics_0.28.0         matrixStats_0.54.0          dendextend_1.9.0            httr_1.4.0                  shiny_1.2.0                

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.1         prabclus_2.2-7         R.methodsS3_1.7.1      bit64_0.9-7            R.utils_2.8.0          RCurl_1.95-4.12       
  [7] doParallel_1.0.14      generics_0.0.2         snow_0.4-3             preprocessCore_1.44.0  cowplot_0.9.4          RSQLite_2.1.1         
 [13] europepmc_0.3          bit_1.1-14             enrichplot_1.2.0       webshot_0.5.1          lubridate_1.7.4        httpuv_1.4.5.1        
 [19] assertthat_0.2.0       hms_0.4.2              promises_1.0.1         TSP_1.1-6              DEoptimR_1.0-8         progress_1.2.0        
 [25] caTools_1.17.1.1       readxl_1.3.0           DBI_1.0.0              htmlwidgets_1.3        crosstalk_1.0.0        backports_1.1.3       
 [31] trimcluster_0.1-2.1    imputeLCMD_2.0         Cairo_1.5-9            withr_2.1.2            ggforce_0.1.3          triebeard_0.3.0       
 [37] robustbase_0.93-3      gclus_1.3.2            prettyunits_1.0.2      mclust_5.4.2           cluster_2.0.7-1        lazyeval_0.2.1        
 [43] crayon_1.3.4           pkgconfig_2.0.2        labeling_0.3           units_0.6-2            tweenr_1.0.1           nlme_3.1-137          
 [49] seriation_1.2-3        nnet_7.3-12            bindr_0.1.1            rlang_0.3.1            diptest_0.75-7         sandwich_2.5-1        
 [55] registry_0.5-1         affyio_1.52.0          modelr_0.1.4           cellranger_1.1.0       Matrix_1.2-15          urltools_1.7.2        
 [61] zoo_1.8-4              whisker_0.3-2          ggridges_0.5.1         GlobalOptions_0.1.0    png_0.1-7              rjson_0.2.20          
 [67] bitops_1.0-6           R.oo_1.22.0            KernSmooth_2.23-15     Biostrings_2.50.2      blob_1.1.1             shape_1.4.4           
 [73] qvalue_2.14.1          gridGraphics_0.3-0     tmvtnorm_1.4-10        reactome.db_1.66.0     scales_1.0.0           memoise_1.1.0         
 [79] graphite_1.28.2        magrittr_1.5           gplots_3.0.1.1         gdata_2.18.0           zlibbioc_1.28.0        compiler_3.5.3        
 [85] RColorBrewer_1.1-2     pcaMethods_1.74.0      cli_1.0.1              affy_1.60.0            XVector_0.22.0         MASS_7.3-51.1         
 [91] tidyselect_0.2.5       vsn_3.50.0             stringi_1.3.1          yaml_2.2.0             GOSemSim_2.8.0         norm_1.0-9.5          
 [97] MALDIquant_1.19.2      ggrepel_0.8.0          biocViews_1.50.10      grid_3.5.3             fastmatch_1.1-0        tools_3.5.3           
[103] circlize_0.4.6         rstudioapi_0.9.0       foreach_1.4.4          gridExtra_2.3          farver_1.1.0           mzID_1.20.1           
[109] ggraph_1.0.2           digest_0.6.18          rvcheck_0.1.3          BiocManager_1.30.4     fpc_2.1-11.1           broom_0.5.1           
[115] later_0.8.0            ncdf4_1.16.1           ComplexHeatmap_1.20.0  kernlab_0.9-27         colorspace_1.4-0       rvest_0.3.2           
[121] splines_3.5.3          RBGL_1.58.2            gmm_1.6-2              ggplotify_0.0.3        flexmix_2.3-15         xtable_1.8-3          
[127] UpSetR_1.3.3           modeltools_0.2-22      RUnit_0.4.32           R6_2.4.0               pillar_1.3.1           htmltools_0.3.6       
[133] mime_0.6               glue_1.3.0             class_7.3-15           codetools_0.2-16       fgsea_1.8.0            mvtnorm_1.0-10        
[139] lattice_0.20-38        gtools_3.8.1           GO.db_3.7.0            limma_3.38.3           munsell_0.5.0          DO.db_2.9             
[145] GetoptLong_0.1.7       GenomeInfoDbData_1.2.0 iterators_1.0.10       impute_1.56.0          haven_2.1.0            reshape2_1.4.3        
[151] gtable_0.2.0      

Any advice would be much appreciated!

[lgatto]

Hi @simonroome - Very annoyingly, there have been disruptive changes on the PRIDE servers (see #5), and it's unclear what (if anything) is done on their side. To be able to work around these changes, you will need a more recent version of rpx.

Ideally, you would update your R, that is already quite old, and you will be able to update/reinstall your packages to get the latest versions. Otherwise, you could try to force installation of a recent version with

BiocManager::install("lgatto/rpx")

but you might run into installation conflicts, by running old and new packages.

[lgatto]

I'm closing this issue but feel free to re-open it if necessary.