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mvdbeek / usegalaxy-tests

Run tests against usegalaxy.org
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test pathview 1.34.0+galaxy0 #66

Closed jennaj closed 1 year ago

jennaj commented 1 year ago

toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

State Count
Total 4
Passed 0
Error 0
Failure 4
Skipped 0
Failed s *
❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #1)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/9/d/6/dataset_9d668cb2-76b2-41e8-afba-419f932a6e63.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 104665252, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #2)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/9/d/6/dataset_9d668cb2-76b2-41e8-afba-419f932a6e63.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 104665252, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "true", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #3)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Output collection 'multiple_kegg_native': expected to have 2 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id_fp [1] "/corral4/main/objects/f/b/1/dataset_fb1d9b45-8cec-4f3d-828b-e8555fc234d9.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/9/d/6/dataset_9d668cb2-76b2-41e8-afba-419f932a6e63.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 104665248, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 104665252, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #4)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Output collection 'multiple_graphviz': expected to have 2 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id_fp [1] "/corral4/main/objects/f/b/1/dataset_fb1d9b45-8cec-4f3d-828b-e8555fc234d9.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/9/d/6/dataset_9d668cb2-76b2-41e8-afba-419f932a6e63.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] FALSE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 104665248, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 104665252, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "false", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.24.0+galaxy0

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

State Count
Total 4
Passed 4
Error 0
Failure 0
Skipped 0
Passed s *
✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #1)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Downloading png files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/046/700/46700757/working Info: Writing image file dme00010.pathview.png ``` **Standard Output:** * ```console R version 3.6.2 (2019-12-12) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-2cf70d41d6f77f52fd82bcc11c23352d038782e2655597c8cc832856e04ad6a5/lib/libopenblasp-r0.3.7.so locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] optparse_1.6.2 pathview_1.24.0 org.Hs.eg.db_3.8.2 [4] AnnotationDbi_1.46.0 IRanges_2.18.2 S4Vectors_0.22.0 [7] Biobase_2.44.0 BiocGenerics_0.30.0 loaded via a namespace (and not attached): [1] graph_1.62.0 Rcpp_1.0.3 KEGGgraph_1.44.0 XVector_0.24.0 [5] zlibbioc_1.30.0 getopt_1.20.3 bit_1.1-15.1 R6_2.4.1 [9] rlang_0.4.4 httr_1.4.1 blob_1.2.1 tools_3.6.2 [13] grid_3.6.2 png_0.1-7 DBI_1.1.0 bit64_0.9-7 [17] digest_0.6.23 Rgraphviz_2.28.0 vctrs_0.2.2 bitops_1.0-6 [21] KEGGREST_1.24.0 RCurl_1.98-1.1 memoise_1.1.0 RSQLite_2.1.5 [25] compiler_3.6.2 Biostrings_2.52.0 XML_3.99-0.3 pkgconfig_2.0.3 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/8/4/0/dataset_840ff72d-c80b-4686-9afe-c8544d034c8b.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 3876 of 17559 unique input IDs unmapped." conda_activate.log dme00010.pathview.png dme00010.png dme00010.xml ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 104666461, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "tabular" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #2)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/046/700/46700759/working Info: Writing image file dme00010.pathview.pdf Warning message: In .local(from, to, graph) : edges replaced: '139|61', '139|62', '118|117' ``` **Standard Output:** * ```console R version 3.6.2 (2019-12-12) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-2cf70d41d6f77f52fd82bcc11c23352d038782e2655597c8cc832856e04ad6a5/lib/libopenblasp-r0.3.7.so locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] optparse_1.6.2 pathview_1.24.0 org.Hs.eg.db_3.8.2 [4] AnnotationDbi_1.46.0 IRanges_2.18.2 S4Vectors_0.22.0 [7] Biobase_2.44.0 BiocGenerics_0.30.0 loaded via a namespace (and not attached): [1] graph_1.62.0 Rcpp_1.0.3 KEGGgraph_1.44.0 XVector_0.24.0 [5] zlibbioc_1.30.0 getopt_1.20.3 bit_1.1-15.1 R6_2.4.1 [9] rlang_0.4.4 httr_1.4.1 blob_1.2.1 tools_3.6.2 [13] grid_3.6.2 png_0.1-7 DBI_1.1.0 bit64_0.9-7 [17] digest_0.6.23 Rgraphviz_2.28.0 vctrs_0.2.2 bitops_1.0-6 [21] KEGGREST_1.24.0 RCurl_1.98-1.1 memoise_1.1.0 RSQLite_2.1.5 [25] compiler_3.6.2 Biostrings_2.52.0 XML_3.99-0.3 pkgconfig_2.0.3 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/8/4/0/dataset_840ff72d-c80b-4686-9afe-c8544d034c8b.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 3876 of 17559 unique input IDs unmapped." conda_activate.log dme00010.pathview.pdf dme00010.xml ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 104666461, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "true", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "tabular" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #3)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Downloading png files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/046/700/46700752/working Info: Writing image file dme00010.pathview.png 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00480, 1/1 pathways.. Info: Downloading png files for dme00480, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/046/700/46700752/working Info: Writing image file dme00480.pathview.png ``` **Standard Output:** * ```console R version 3.6.2 (2019-12-12) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-2cf70d41d6f77f52fd82bcc11c23352d038782e2655597c8cc832856e04ad6a5/lib/libopenblasp-r0.3.7.so locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] optparse_1.6.2 pathview_1.24.0 org.Hs.eg.db_3.8.2 [4] AnnotationDbi_1.46.0 IRanges_2.18.2 S4Vectors_0.22.0 [7] Biobase_2.44.0 BiocGenerics_0.30.0 loaded via a namespace (and not attached): [1] graph_1.62.0 Rcpp_1.0.3 KEGGgraph_1.44.0 XVector_0.24.0 [5] zlibbioc_1.30.0 getopt_1.20.3 bit_1.1-15.1 R6_2.4.1 [9] rlang_0.4.4 httr_1.4.1 blob_1.2.1 tools_3.6.2 [13] grid_3.6.2 png_0.1-7 DBI_1.1.0 bit64_0.9-7 [17] digest_0.6.23 Rgraphviz_2.28.0 vctrs_0.2.2 bitops_1.0-6 [21] KEGGREST_1.24.0 RCurl_1.98-1.1 memoise_1.1.0 RSQLite_2.1.5 [25] compiler_3.6.2 Biostrings_2.52.0 XML_3.99-0.3 pkgconfig_2.0.3 $pathway_id_fp [1] "/corral4/main/objects/5/3/6/dataset_53630d98-dbec-4eca-a98b-91608e418b40.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/8/4/0/dataset_840ff72d-c80b-4686-9afe-c8544d034c8b.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 3876 of 17559 unique input IDs unmapped." [1] "Note: 3876 of 17559 unique input IDs unmapped." conda_activate.log dme00010.pathview.png dme00010.png dme00010.xml dme00480.pathview.png dme00480.png dme00480.xml ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 104666457, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 104666461, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "tabular" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #4)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/046/700/46700758/working Info: Writing image file dme00010.pathview.pdf 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00480, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/046/700/46700758/working Info: Writing image file dme00480.pathview.pdf Warning messages: 1: In .local(from, to, graph) : edges replaced: '139|61', '139|62', '118|117' 2: In .local(from, to, graph) : edges replaced: '66|53' ``` **Standard Output:** * ```console R version 3.6.2 (2019-12-12) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-2cf70d41d6f77f52fd82bcc11c23352d038782e2655597c8cc832856e04ad6a5/lib/libopenblasp-r0.3.7.so locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] optparse_1.6.2 pathview_1.24.0 org.Hs.eg.db_3.8.2 [4] AnnotationDbi_1.46.0 IRanges_2.18.2 S4Vectors_0.22.0 [7] Biobase_2.44.0 BiocGenerics_0.30.0 loaded via a namespace (and not attached): [1] graph_1.62.0 Rcpp_1.0.3 KEGGgraph_1.44.0 XVector_0.24.0 [5] zlibbioc_1.30.0 getopt_1.20.3 bit_1.1-15.1 R6_2.4.1 [9] rlang_0.4.4 httr_1.4.1 blob_1.2.1 tools_3.6.2 [13] grid_3.6.2 png_0.1-7 DBI_1.1.0 bit64_0.9-7 [17] digest_0.6.23 Rgraphviz_2.28.0 vctrs_0.2.2 bitops_1.0-6 [21] KEGGREST_1.24.0 RCurl_1.98-1.1 memoise_1.1.0 RSQLite_2.1.5 [25] compiler_3.6.2 Biostrings_2.52.0 XML_3.99-0.3 pkgconfig_2.0.3 $pathway_id_fp [1] "/corral4/main/objects/5/3/6/dataset_53630d98-dbec-4eca-a98b-91608e418b40.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/8/4/0/dataset_840ff72d-c80b-4686-9afe-c8544d034c8b.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] FALSE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 3876 of 17559 unique input IDs unmapped." [1] "Note: 3876 of 17559 unique input IDs unmapped." conda_activate.log dme00010.pathview.pdf dme00010.xml dme00480.pathview.pdf dme00480.xml ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 104666457, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 104666461, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "false", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "tabular" ` |

jennaj commented 1 year ago

https://github.com/galaxyproject/tools-iuc/issues/4901

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

State Count
Total 4
Passed 0
Error 0
Failure 4
Skipped 0
Failed s *
❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #1)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/b/a/4/dataset_ba48eb1c-8dc4-4a45-9d7e-2e40f59f28df.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 105174089, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #2)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/b/a/4/dataset_ba48eb1c-8dc4-4a45-9d7e-2e40f59f28df.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 105174089, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "true", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #3)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Output collection 'multiple_kegg_native': expected to have 2 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id_fp [1] "/corral4/main/objects/5/d/a/dataset_5da90eb2-2e53-436e-a658-f943276994f5.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/b/a/4/dataset_ba48eb1c-8dc4-4a45-9d7e-2e40f59f28df.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 105174083, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 105174089, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #4)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Output collection 'multiple_graphviz': expected to have 2 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id_fp [1] "/corral4/main/objects/5/d/a/dataset_5da90eb2-2e53-436e-a658-f943276994f5.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/b/a/4/dataset_ba48eb1c-8dc4-4a45-9d7e-2e40f59f28df.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] FALSE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 105174083, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 105174089, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "false", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

State Count
Total 4
Passed 0
Error 0
Failure 4
Skipped 0
Failed s *
❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #1)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/1/4/d/dataset_14d92690-9695-4c14-9460-456263bd096a.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 105568213, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #2)
    **Problems**: * ``` HTTPSConnectionPool(host='usegalaxy.org', port=443): Max retries exceeded with url: /api/jobs/bbd44e69cb8906b5f0d8fd24810b1c43 (Caused by SSLError(SSLError(1, '[SSL: KRB5_S_TKT_NYV] unexpected eof while reading (_ssl.c:1091)'))) ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/1/4/d/dataset_14d92690-9695-4c14-9460-456263bd096a.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 105568213, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "true", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #3)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Output collection 'multiple_kegg_native': expected to have 2 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id_fp [1] "/corral4/main/objects/8/d/8/dataset_8d8388a7-9fe8-4faa-b921-69cd77c04201.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/1/4/d/dataset_14d92690-9695-4c14-9460-456263bd096a.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 105568210, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 105568213, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #4)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Output collection 'multiple_graphviz': expected to have 2 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id_fp [1] "/corral4/main/objects/8/d/8/dataset_8d8388a7-9fe8-4faa-b921-69cd77c04201.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/1/4/d/dataset_14d92690-9695-4c14-9460-456263bd096a.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] FALSE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 105568210, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 105568213, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "false", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.24.0+galaxy0

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

State Count
Total 4
Passed 0
Error 0
Failure 4
Skipped 0
Failed s *
❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #1)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/b/7/a/dataset_b7acb1c9-b5c1-48ef-a329-594f6a130ef1.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 106998386, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #2)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/b/7/a/dataset_b7acb1c9-b5c1-48ef-a329-594f6a130ef1.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 106998386, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "true", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #3)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Output collection 'multiple_kegg_native': expected to have 2 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id_fp [1] "/corral4/main/objects/3/e/6/dataset_3e699a86-8630-46a1-bfe9-772bb17dc31d.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/b/7/a/dataset_b7acb1c9-b5c1-48ef-a329-594f6a130ef1.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 106998382, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 106998386, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #4)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> . ``` * ``` Output collection 'multiple_graphviz': expected to have 2 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: run_pathview ... request_fetch -> request_fetch.write_memory -> ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id_fp [1] "/corral4/main/objects/3/e/6/dataset_3e699a86-8630-46a1-bfe9-772bb17dc31d.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/b/7/a/dataset_b7acb1c9-b5c1-48ef-a329-594f6a130ef1.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] FALSE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 106998382, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 106998386, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "false", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

State Count
Total 4
Passed 4
Error 0
Failure 0
Skipped 0
Passed s *
✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #1)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Downloading png files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/047/758/47758837/working Info: Writing image file dme00010.pathview.png ``` **Standard Output:** * ```console R version 3.6.2 (2019-12-12) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-2cf70d41d6f77f52fd82bcc11c23352d038782e2655597c8cc832856e04ad6a5/lib/libopenblasp-r0.3.7.so locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] optparse_1.6.2 pathview_1.24.0 org.Hs.eg.db_3.8.2 [4] AnnotationDbi_1.46.0 IRanges_2.18.2 S4Vectors_0.22.0 [7] Biobase_2.44.0 BiocGenerics_0.30.0 loaded via a namespace (and not attached): [1] graph_1.62.0 Rcpp_1.0.3 KEGGgraph_1.44.0 XVector_0.24.0 [5] zlibbioc_1.30.0 getopt_1.20.3 bit_1.1-15.1 R6_2.4.1 [9] rlang_0.4.4 httr_1.4.1 blob_1.2.1 tools_3.6.2 [13] grid_3.6.2 png_0.1-7 DBI_1.1.0 bit64_0.9-7 [17] digest_0.6.23 Rgraphviz_2.28.0 vctrs_0.2.2 bitops_1.0-6 [21] KEGGREST_1.24.0 RCurl_1.98-1.1 memoise_1.1.0 RSQLite_2.1.5 [25] compiler_3.6.2 Biostrings_2.52.0 XML_3.99-0.3 pkgconfig_2.0.3 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/0/b/e/dataset_0be78a6a-99f4-43a9-a579-a582a3b497c1.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 3876 of 17559 unique input IDs unmapped." conda_activate.log dme00010.pathview.png dme00010.png dme00010.xml ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 106998392, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "auto" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #2)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/047/758/47758889/working Info: Writing image file dme00010.pathview.pdf Warning message: In .local(from, to, graph) : edges replaced: '139|61', '139|62', '118|117' ``` **Standard Output:** * ```console R version 3.6.2 (2019-12-12) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-2cf70d41d6f77f52fd82bcc11c23352d038782e2655597c8cc832856e04ad6a5/lib/libopenblasp-r0.3.7.so locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] optparse_1.6.2 pathview_1.24.0 org.Hs.eg.db_3.8.2 [4] AnnotationDbi_1.46.0 IRanges_2.18.2 S4Vectors_0.22.0 [7] Biobase_2.44.0 BiocGenerics_0.30.0 loaded via a namespace (and not attached): [1] graph_1.62.0 Rcpp_1.0.3 KEGGgraph_1.44.0 XVector_0.24.0 [5] zlibbioc_1.30.0 getopt_1.20.3 bit_1.1-15.1 R6_2.4.1 [9] rlang_0.4.4 httr_1.4.1 blob_1.2.1 tools_3.6.2 [13] grid_3.6.2 png_0.1-7 DBI_1.1.0 bit64_0.9-7 [17] digest_0.6.23 Rgraphviz_2.28.0 vctrs_0.2.2 bitops_1.0-6 [21] KEGGREST_1.24.0 RCurl_1.98-1.1 memoise_1.1.0 RSQLite_2.1.5 [25] compiler_3.6.2 Biostrings_2.52.0 XML_3.99-0.3 pkgconfig_2.0.3 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/0/b/e/dataset_0be78a6a-99f4-43a9-a579-a582a3b497c1.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 3876 of 17559 unique input IDs unmapped." conda_activate.log dme00010.pathview.pdf dme00010.xml ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 106998392, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "true", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "auto" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #3)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Downloading png files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/047/758/47758892/working Info: Writing image file dme00010.pathview.png 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00480, 1/1 pathways.. Info: Downloading png files for dme00480, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/047/758/47758892/working Info: Writing image file dme00480.pathview.png ``` **Standard Output:** * ```console R version 3.6.2 (2019-12-12) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-2cf70d41d6f77f52fd82bcc11c23352d038782e2655597c8cc832856e04ad6a5/lib/libopenblasp-r0.3.7.so locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] optparse_1.6.2 pathview_1.24.0 org.Hs.eg.db_3.8.2 [4] AnnotationDbi_1.46.0 IRanges_2.18.2 S4Vectors_0.22.0 [7] Biobase_2.44.0 BiocGenerics_0.30.0 loaded via a namespace (and not attached): [1] graph_1.62.0 Rcpp_1.0.3 KEGGgraph_1.44.0 XVector_0.24.0 [5] zlibbioc_1.30.0 getopt_1.20.3 bit_1.1-15.1 R6_2.4.1 [9] rlang_0.4.4 httr_1.4.1 blob_1.2.1 tools_3.6.2 [13] grid_3.6.2 png_0.1-7 DBI_1.1.0 bit64_0.9-7 [17] digest_0.6.23 Rgraphviz_2.28.0 vctrs_0.2.2 bitops_1.0-6 [21] KEGGREST_1.24.0 RCurl_1.98-1.1 memoise_1.1.0 RSQLite_2.1.5 [25] compiler_3.6.2 Biostrings_2.52.0 XML_3.99-0.3 pkgconfig_2.0.3 $pathway_id_fp [1] "/corral4/main/objects/5/d/3/dataset_5d3f15e8-186c-48d0-89d9-a15d532a834d.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/0/b/e/dataset_0be78a6a-99f4-43a9-a579-a582a3b497c1.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 3876 of 17559 unique input IDs unmapped." [1] "Note: 3876 of 17559 unique input IDs unmapped." conda_activate.log dme00010.pathview.png dme00010.png dme00010.xml dme00480.pathview.png dme00480.png dme00480.xml ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 106998389, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 106998392, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": "true", "out": "TRUE", "same_layer": "true"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "tabular" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #4)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/047/758/47758890/working Info: Writing image file dme00010.pathview.pdf 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00480, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/047/758/47758890/working Info: Writing image file dme00480.pathview.pdf Warning messages: 1: In .local(from, to, graph) : edges replaced: '139|61', '139|62', '118|117' 2: In .local(from, to, graph) : edges replaced: '66|53' ``` **Standard Output:** * ```console R version 3.6.2 (2019-12-12) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-2cf70d41d6f77f52fd82bcc11c23352d038782e2655597c8cc832856e04ad6a5/lib/libopenblasp-r0.3.7.so locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] optparse_1.6.2 pathview_1.24.0 org.Hs.eg.db_3.8.2 [4] AnnotationDbi_1.46.0 IRanges_2.18.2 S4Vectors_0.22.0 [7] Biobase_2.44.0 BiocGenerics_0.30.0 loaded via a namespace (and not attached): [1] graph_1.62.0 Rcpp_1.0.3 KEGGgraph_1.44.0 XVector_0.24.0 [5] zlibbioc_1.30.0 getopt_1.20.3 bit_1.1-15.1 R6_2.4.1 [9] rlang_0.4.4 httr_1.4.1 blob_1.2.1 tools_3.6.2 [13] grid_3.6.2 png_0.1-7 DBI_1.1.0 bit64_0.9-7 [17] digest_0.6.23 Rgraphviz_2.28.0 vctrs_0.2.2 bitops_1.0-6 [21] KEGGREST_1.24.0 RCurl_1.98-1.1 memoise_1.1.0 RSQLite_2.1.5 [25] compiler_3.6.2 Biostrings_2.52.0 XML_3.99-0.3 pkgconfig_2.0.3 $pathway_id_fp [1] "/corral4/main/objects/5/d/3/dataset_5d3f15e8-186c-48d0-89d9-a15d532a834d.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/0/b/e/dataset_0be78a6a-99f4-43a9-a579-a582a3b497c1.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] FALSE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 3876 of 17559 unique input IDs unmapped." [1] "Note: 3876 of 17559 unique input IDs unmapped." conda_activate.log dme00010.pathview.pdf dme00010.xml dme00480.pathview.pdf dme00480.xml ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": "false", "nb": "multiple", "tabular": {"values": [{"id": 106998389, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": "false", "idtype": "ensembl", "tabular": {"values": [{"id": 106998392, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` "true" ` | | match\_data | ` "true" ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": "false", "out": "FALSE", "same_layer": "false", "sign_pos": "bottomright", "split_group": "false"}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "auto" ` |

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

State Count
Total 4
Passed 4
Error 0
Failure 0
Skipped 0
Passed s *
✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #1)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Downloading png files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/050/973/50973026/working Info: Writing image file dme00010.pathview.png ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.21.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] compiler_4.1.3 GenomeInfoDb_1.30.1 XVector_0.34.0 [4] bitops_1.0-7 tools_4.1.3 zlibbioc_1.40.0 [7] bit_4.0.5 RSQLite_2.3.1 memoise_2.0.1 [10] pkgconfig_2.0.3 png_0.1-8 rlang_1.1.1 [13] KEGGgraph_1.54.0 graph_1.72.0 DBI_1.1.3 [16] cli_3.6.1 Rgraphviz_2.38.0 fastmap_1.1.1 [19] GenomeInfoDbData_1.2.7 httr_1.4.6 Biostrings_2.62.0 [22] S4Vectors_0.32.4 vctrs_0.6.2 IRanges_2.28.0 [25] stats4_4.1.3 bit64_4.0.5 grid_4.1.3 [28] getopt_1.20.3 Biobase_2.54.0 R6_2.5.1 [31] AnnotationDbi_1.56.2 XML_3.99-0.14 blob_1.2.4 [34] org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 KEGGREST_1.34.0 [37] RCurl_1.98-1.12 cachem_1.0.8 crayon_1.5.2 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/8/9/a/dataset_89abdb4a-fdb4-4019-9c72-4f9ec4a38a0c.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." dme00010.pathview.png dme00010.png dme00010.xml ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": false, "idtype": "ensembl", "tabular": {"values": [{"id": 113091076, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` true ` | | match\_data | ` true ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": true, "out": "TRUE", "same_layer": true}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #2)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/050/973/50973027/working Info: Writing image file dme00010.pathview.pdf Warning message: In .local(from, to, graph) : edges replaced: '139|61', '139|62', '118|117' ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.21.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] compiler_4.1.3 GenomeInfoDb_1.30.1 XVector_0.34.0 [4] bitops_1.0-7 tools_4.1.3 zlibbioc_1.40.0 [7] bit_4.0.5 RSQLite_2.3.1 memoise_2.0.1 [10] pkgconfig_2.0.3 png_0.1-8 rlang_1.1.1 [13] KEGGgraph_1.54.0 graph_1.72.0 DBI_1.1.3 [16] cli_3.6.1 Rgraphviz_2.38.0 fastmap_1.1.1 [19] GenomeInfoDbData_1.2.7 httr_1.4.6 Biostrings_2.62.0 [22] S4Vectors_0.32.4 vctrs_0.6.2 IRanges_2.28.0 [25] stats4_4.1.3 bit64_4.0.5 grid_4.1.3 [28] getopt_1.20.3 Biobase_2.54.0 R6_2.5.1 [31] AnnotationDbi_1.56.2 XML_3.99-0.14 blob_1.2.4 [34] org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 KEGGREST_1.34.0 [37] RCurl_1.98-1.12 cachem_1.0.8 crayon_1.5.2 $pathway_id [1] "00010" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/8/9/a/dataset_89abdb4a-fdb4-4019-9c72-4f9ec4a38a0c.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." dme00010.pathview.pdf dme00010.xml ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 0, "nb": "one", "one_id": "00010"} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": false, "idtype": "ensembl", "tabular": {"values": [{"id": 113091076, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` true ` | | match\_data | ` true ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": false, "out": "FALSE", "same_layer": true, "sign_pos": "bottomright", "split_group": false}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #3)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Downloading png files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/050/973/50973038/working Info: Writing image file dme00010.pathview.png 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00480, 1/1 pathways.. Info: Downloading png files for dme00480, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/050/973/50973038/working Info: Writing image file dme00480.pathview.png ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.21.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] compiler_4.1.3 GenomeInfoDb_1.30.1 XVector_0.34.0 [4] bitops_1.0-7 tools_4.1.3 zlibbioc_1.40.0 [7] bit_4.0.5 RSQLite_2.3.1 memoise_2.0.1 [10] pkgconfig_2.0.3 png_0.1-8 rlang_1.1.1 [13] KEGGgraph_1.54.0 graph_1.72.0 DBI_1.1.3 [16] cli_3.6.1 Rgraphviz_2.38.0 fastmap_1.1.1 [19] GenomeInfoDbData_1.2.7 httr_1.4.6 Biostrings_2.62.0 [22] S4Vectors_0.32.4 vctrs_0.6.2 IRanges_2.28.0 [25] stats4_4.1.3 bit64_4.0.5 grid_4.1.3 [28] getopt_1.20.3 Biobase_2.54.0 R6_2.5.1 [31] AnnotationDbi_1.56.2 XML_3.99-0.14 blob_1.2.4 [34] org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 KEGGREST_1.34.0 [37] RCurl_1.98-1.12 cachem_1.0.8 crayon_1.5.2 $pathway_id_fp [1] "/corral4/main/objects/5/9/3/dataset_593fdcdc-4fc6-4276-8d89-81df5b70022a.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/8/9/a/dataset_89abdb4a-fdb4-4019-9c72-4f9ec4a38a0c.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." [1] "Note: 497 of 17559 unique input IDs unmapped." dme00010.pathview.png dme00010.png dme00010.xml dme00480.pathview.png dme00480.png dme00480.xml ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": false, "nb": "multiple", "tabular": {"values": [{"id": 113091074, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": false, "idtype": "ensembl", "tabular": {"values": [{"id": 113091076, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` true ` | | match\_data | ` true ` | | out | ` {"kegg_native": {"__current_case__": 0, "map_null": true, "out": "TRUE", "same_layer": true}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview (Test #4)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Loading required namespace: org.Dm.eg.db 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00010, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/050/973/50973029/working Info: Writing image file dme00010.pathview.pdf 'select()' returned 1:many mapping between keys and columns Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for dme00480, 1/1 pathways.. Info: Working in directory /corral4/main/jobs/050/973/50973029/working Info: Writing image file dme00480.pathview.pdf Warning messages: 1: In .local(from, to, graph) : edges replaced: '139|61', '139|62', '118|117' 2: In .local(from, to, graph) : edges replaced: '66|53' ``` **Standard Output:** * ```console R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.21.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] compiler_4.1.3 GenomeInfoDb_1.30.1 XVector_0.34.0 [4] bitops_1.0-7 tools_4.1.3 zlibbioc_1.40.0 [7] bit_4.0.5 RSQLite_2.3.1 memoise_2.0.1 [10] pkgconfig_2.0.3 png_0.1-8 rlang_1.1.1 [13] KEGGgraph_1.54.0 graph_1.72.0 DBI_1.1.3 [16] cli_3.6.1 Rgraphviz_2.38.0 fastmap_1.1.1 [19] GenomeInfoDbData_1.2.7 httr_1.4.6 Biostrings_2.62.0 [22] S4Vectors_0.32.4 vctrs_0.6.2 IRanges_2.28.0 [25] stats4_4.1.3 bit64_4.0.5 grid_4.1.3 [28] getopt_1.20.3 Biobase_2.54.0 R6_2.5.1 [31] AnnotationDbi_1.56.2 XML_3.99-0.14 blob_1.2.4 [34] org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 KEGGREST_1.34.0 [37] RCurl_1.98-1.12 cachem_1.0.8 crayon_1.5.2 $pathway_id_fp [1] "/corral4/main/objects/5/9/3/dataset_593fdcdc-4fc6-4276-8d89-81df5b70022a.dat" $pathway_id_header [1] FALSE $species [1] "dme" $gene_data [1] "/corral4/main/objects/8/9/a/dataset_89abdb4a-fdb4-4019-9c72-4f9ec4a38a0c.dat" $gd_header [1] FALSE $gene_idtype [1] "ensembl" $cpd_header [1] FALSE $cpd_idtype [1] "kegg" $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] FALSE $same_layer [1] FALSE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] "bottomright" $help [1] FALSE [1] "Note: 497 of 17559 unique input IDs unmapped." [1] "Note: 497 of 17559 unique input IDs unmapped." dme00010.pathview.pdf dme00010.xml dme00480.pathview.pdf dme00480.xml ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | pathway | ` {"__current_case__": 1, "header": false, "nb": "multiple", "tabular": {"values": [{"id": 113091074, "src": "hda"}]}} ` | | species | ` "dme" ` | | gene\_data | ` {"__current_case__": 0, "gd": "true", "header": false, "idtype": "ensembl", "tabular": {"values": [{"id": 113091076, "src": "hda"}]}} ` | | cpd\_data | ` {"__current_case__": 1, "cpd": "false"} ` | | multi\_state | ` true ` | | match\_data | ` true ` | | out | ` {"kegg_native": {"__current_case__": 1, "expand_node": false, "out": "FALSE", "same_layer": false, "sign_pos": "bottomright", "split_group": false}} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |