tercen / app-library

Tercen app library

Tercen R client

Install teRcen package

install.packages('remotes')

remotes::install_github("tercen/teRcenApi", ref = "0.12.2", args="--no-multiarch")
remotes::install_github("tercen/teRcen", ref = "0.12.6", args="--no-multiarch")
remotes::install_github("tercen/teRcenApi", args="--no-multiarch")
remotes::install_github("tercen/teRcen", args="--no-multiarch")

app-library's Issues

Add a unit test to autoencoder_operator [d9332f0c]

There is no unit test associated with this operator (https://github.com/tercen/autoencoder_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to dascombat_prediction_operator [667f2a50]

There is no unit test associated with this operator (https://github.com/tercen/dascombat_prediction_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to damacy_operator [662aded6]

There is no unit test associated with this operator (https://github.com/tercen/damacy_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: cluster_annotation_operator [fd85790a]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 0.2.0

ServiceError({statusCode: 400, error: unknown, reason: --ERR--

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in library(tidyr) : there is no package called ‘tidyr’
Execution halted
})

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to cluster_label_matching_operator [c2781c51]

There is no unit test associated with this operator (https://github.com/tercen/cluster_label_matching_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to fastq_to_counts_docker_operator [0fd2e96e]

There is no unit test associated with this operator (https://github.com/tercen/fastq_to_counts_docker_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: optics11_operator [6db5b15d]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 0.1.8

ServiceError({statusCode: 400, error: create.operator.renv.lock.missing, reason: Failed to create operator, renv lock file is missing})

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: flowsom_mst_shiny_operator [c975a7ce]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 0.1.3

ServiceError({statusCode: 400, error: create.operator.docker.failed, reason: Failed to pull operator})

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to data_quality_shiny_operator [734524ab]

There is no unit test associated with this operator (https://github.com/tercen/data_quality_shiny_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to cyclone_operator [677a0c89]

There is no unit test associated with this operator (https://github.com/tercen/cyclone_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: flowsom_operator [205fbd97]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 1.3.4

ServiceError({statusCode: -142, error: task.test.operator.bad.nCols, reason: table.nCols != refTable.nCols})

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: TCRMatch_operator [a30f6ea4]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version:0.0.3

ServiceError({statusCode: -142, error: run.operator.exit.code.1, reason: Failed to run operator, exit code = 1
--ERR--
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
sh: 1: tcrmatch: not found
Error: argument of length 0
Backtrace:
     █
  1. ├─`%>%`(...)
  2. ├─ctx$save(.)
  3. │ └─base::inherits(computed.df, "OperatorResult")
  4. ├─ctx$addNamespace(.)
  5. │ └─base::sapply(...)
  6. │   └─base::lapply(X = X, FUN = FUN, ...)
  7. ├─dplyr::mutate(., .ri = 0)
  8. ├─global::run.tcrmatch(.)
  9. │ └─readr::read_delim(...)
 10. │   └─vroom::vroom(...)
 11. │     └─vroom:::vroom_(...)
 12. ├─(function (spec, num_cols, col_names, col_select, name_repair) ...
 13. │ ├─`%in%`(...)
 14. │ └─tidyselect::vars_select(names(spec$cols), !!col_select, .strict = FALSE)
 15. │   └─tidyselect:::eval_select_impl(...)
 16. │     ├─tidyselect:::with_subscript_errors(...)
 17. │     │ ├─base::tryCatch(...)
 18. │     │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
 19. │     │ │   └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 20. │     │ │     └─base:::doTryCatch(return(expr), name, parentenv, handler)
 21. │     │ └─tidyselect:::instrument_base_errors(expr)
 22. │     │   └─base::withCallingHandlers(...)
 23. │     └─tidyselect:::vars_select_eval(...)
 24. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 25. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
 26. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 27. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
 28. │               └─tidyselect:::eval_colon(expr, data_mask, context_mask)
 29. └─base::.handleSimpleError(...)
 30.   └─tidyselect:::h(simpleError(msg, call))
Warning message:
In system2(cmd, args) : error in running command
Execution halted
})

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: hclust_operator [f9c193ed]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 1.1.2

ServiceError({statusCode: -142, error: task.test.operator.bad.value, reason: At column .ci -- val != refVal -- at line 0 -- val = 8 refVal = 0})

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: regression_coefficients_operator [ff701156]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 0.1.0

ServiceError({statusCode: 400, error: task.test.operator.bad.nRelations, reason: simpleRelations.length != outputSchemas.length})

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to clusterlab_operator [3b5c452a]

There is no unit test associated with this operator (https://github.com/tercen/clusterlab_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to depeche_operator [add581fb]

There is no unit test associated with this operator (https://github.com/tercen/depeche_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to conditional_density_shiny_operator [3ceb38f0]

There is no unit test associated with this operator (https://github.com/tercen/conditional_density_shiny_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to coral_shiny_v2_operator [67a12efe]

There is no unit test associated with this operator (https://github.com/tercen/coral_shiny_v2_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to anova1_operator [edaac15c]

There is no unit test associated with this operator (https://github.com/tercen/anova1_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: change_from_baseline_operator [900c2c4e]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 0.1.1

ServiceError({statusCode: -142, error: create.operator.renv.lock.missing, reason: Failed to create operator, renv lock file is missing})

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to alice_operator [dbaea8c7]

There is no unit test associated with this operator (https://github.com/tercen/alice_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: sum_operator [9b20d4a1]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 1.10.0

ServiceError({statusCode: 500, error: Task.client.unknown, reason: Throw of null.})

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to classification_metrics_operator [7b3289be]

There is no unit test associated with this operator (https://github.com/tercen/classification_metrics_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: atsne_operator [5031413e]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 1.3.0

ServiceError({statusCode: 400, error: unknown, reason: FileSystemException: Cannot open file, path = '/var/lib/tercen/data/operator/e9/1b/ee/ee1be91e-e8f3-4b83-9b78-e6dbe259da90/tercen-atsne_operator-ee88f71/tests/table2.csv' (OS Error: No such file or directory, errno = 2)})

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to coral_docker_operator [074e7591]

There is no unit test associated with this operator (https://github.com/tercen/coral_docker_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to PARC_python_operator [869462de]

There is no unit test associated with this operator. If you
would like this operator to be part of the App Library, it must include
continuous integration workflows

Tercen's operator sentinel has automatically created this issue.

Add a unit test to flowmeans_operator [4c16f04f]

There is no unit test associated with this operator (https://github.com/tercen/flowmeans_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: mixed_model_operator [3b70d06a]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 0.2.1

ServiceError({statusCode: 400, error: create.operator.renv.lock.missing, reason: Failed to create operator, renv lock file is missing})

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to coral_shiny_operator [05985ca0]

There is no unit test associated with this operator (https://github.com/tercen/coral_shiny_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: gfr_operator [c04133cb]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 0.1.1

ServiceError({statusCode: 400, error: create.operator.renv.lock.missing, reason: Failed to create operator, renv lock file is missing})

Note: This issue has automatically been created by Tercen's operator sentinel.

Develop testing model for shiny operators

Add a unit test to dascombat_fit_operator [e36e1b58]

There is no unit test associated with this operator (https://github.com/tercen/dascombat_fit_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

FI-TSNE 0.1.4 Fails on FlowJo Workflow.

Workflow
https://stage.tercen.com/TestTeam/w/a33e2c0f05753e1b035d27049abb9871

Tested on Apple Mac - Safari

Error Message

Unexpected error : run.operator.exit.code.1
run.operator.exit.code.1 : Failed to run operator, exit code = 1
--OUT--
=============== t-SNE v1.2.1 ===============
fast_tsne data_path: /tmp/RtmpOYRgGS/fftRtsne_data_97b48ff4f.dat
fast_tsne result_path: /tmp/RtmpOYRgGS/fftRtsne_result_9799d940f.dat
fast_tsne nthreads: 16
Read the following parameters:
n 1542846 by d 8 dataset, theta 0.500000,
perplexity 30.000000, no_dims 2, max_iter 750,
stop_lying_iter 250, mom_switch_iter 250,
momentum 0.500000, final_momentum 0.800000,
learning_rate 128570.500000, max_step_norm 5.000000,
K -1, sigma -30.000000, nbody_algo 2,
knn_algo 1, early_exag_coeff 12.000000,
no_momentum_during_exag 0, n_trees 50, search_k 4500,
start_late_exag_iter -1, late_exag_coeff 1.000000
nterms 3, interval_per_integer 1.000000, min_num_intervals 50, t-dist df 1.000000
Read the 1542846 x 8 data matrix successfully. X[0,0] = 251.000000
Read the initialization successfully.
Will use momentum during exaggeration phase
Computing input similarities...
Using perplexity, so normalizing input data (to prevent numerical problems)
Using perplexity, not the manually set kernel width. K (number of nearest neighbors) and sigma (bandwidth) parameters are going to be ignored.
Using ANNOY for knn search, with parameters: n_trees 50 and search_k 4500
Going to allocate memory. N: 1542846, K: 90, N*K = 138856140
Building Annoy tree...
Done building tree. Beginning nearest neighbor search...
parallel (16 threads):
[> ] 0% 0.164s
[> ] 0% 1.597s
[> ] 0% 3.054s
[> ] 0% 4.583s
[> ] 0% 6.057s
[> ] 0% 7.506s
[> ] 0% 9.012s
[> ] 0% 10.426s
[> ] 0% 11.895s
[> ] 0% 13.359s
[> ] 1% 14.866s
[> ] 1% 16.364s
[> ] 1% 17.835s
[> ] 1% 19.329s
[> ] 1% 20.795s
[> ] 1% 22.2s
[> ] 1% 23.792s
[=> ] 1% 25.278s
[=> ] 1% 26.708s
[=> ] 1% 28.167s
[=> ] 2% 29.639s
[=> ] 2% 31.137s
[=> ] 2% 32.677s
[=> ] 2% 34.197s
[=> ] 2% 35.773s
[=> ] 2% 37.309s
[=> ] 2% 38.845s
[=> ] 2% 40.398s
[=> ] 2% 41.922s
[=> ] 2% 43.461s
[=> ] 3% 44.965s
[=> ] 3% 46.425s
[=> ] 3% 47.894s
[=> ] 3% 49.491s
[==> ] 3% 50.997s
[==> ] 3% 52.531s
[==>

Failed test: faust_operator [d1b1085b]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 0.0.5

ServiceError({statusCode: -142, error: run.operator.exit.code.1, reason: Failed to run operator, exit code = 1
--ERR--
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in apply(quantileDataLow, 2, function(x) { : 
  object 'quantileDataLow' not found
Calls: <Anonymous> ... generateAnnotationThresholds -> .processChannelBounds -> apply
Execution halted
})

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: flowcut_operator [68d544da]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 0.1.3

ServiceError({statusCode: 400, error: run.operator.exit.code.143, reason: Failed to run operator, exit code = 143
--ERR--
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
})

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to barplot_operator [2e54ec21]

There is no unit test associated with this operator (https://github.com/tercen/barplot_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to barplot_shiny_operator [8d7a3fd4]

There is no unit test associated with this operator (https://github.com/tercen/barplot_shiny_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to data_cleaning_operator [273e47eb]

There is no unit test associated with this operator (https://github.com/tercen/data_cleaning_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to gmm_operator [aa60e11a]

There is no unit test associated with this operator (https://github.com/tercen/gmm_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to fastq_to_counts_operator [5b798099]

There is no unit test associated with this operator (https://github.com/tercen/fastq_to_counts_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: cellplot_shiny_operator [61d254af]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 1.0.3

ServiceError({statusCode: 400, error: create.operator.renv.lock.missing, reason: Failed to create operator, renv lock file is missing})

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: max_operator [fdb738c8]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 0.2.0

ServiceError({statusCode: -142, error: create.operator.renv.failed, reason: Failed to create operator})

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to TraCeR_operator [c6579179]

There is no unit test associated with this operator (https://github.com/tercen/TraCeR_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: dose_response_fit_operator [c085250f]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 1.2.0

ServiceError({statusCode: 400, error: task.test.operator.bad.nRelations, reason: simpleRelations.length != outputSchemas.length})

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to flowsom_mst_operator [900275d6]

There is no unit test associated with this operator (https://github.com/tercen/flowsom_mst_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to findMarkers_operator [88ffe1df]

There is no unit test associated with this operator (https://github.com/tercen/findMarkers_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to dascombat_shiny_fit_operator [427b13ba]

There is no unit test associated with this operator (https://github.com/tercen/dascombat_shiny_fit_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to coralp_shiny_operator [abbb108f]

There is no unit test associated with this operator (https://github.com/tercen/coralp_shiny_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.

Failed test: read_cellranger_operator [3114d54a]

The unit test associated with this operator has failed. If you would like this operator to be part of the App Library, the test must be fixed.

Version: 0.1.1

ServiceError({statusCode: 400, error: unknown, reason: type 'int' is not a subtype of type 'String' in type cast})

Note: This issue has automatically been created by Tercen's operator sentinel.

Add a unit test to TraCeR_summarize_operator [38340790]

There is no unit test associated with this operator (https://github.com/tercen/TraCeR_summarize_operator). If you would like this operator to be part of the App Library, it must include continuous integration workflows.

Note: This issue has automatically been created by Tercen's operator sentinel.