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Plumber 1.1 fails when using `BiocGenerics` #807

Closed blairj09 closed 3 years ago

blairj09 commented 3 years ago

System details

Output of sessioninfo::session_info()():

─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.1.0 (2021-05-18)
 os       macOS Big Sur 11.3.1        
 system   x86_64, darwin17.0          
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/Denver              
 date     2021-05-25                  

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────
 ! package      * version date       lib source        
   BiocGenerics * 0.38.0  2021-05-19 [1] Bioconductor  
 P BiocManager    1.30.15 2021-05-11 [?] CRAN (R 4.1.0)
 P cli            2.5.0   2021-04-26 [?] CRAN (R 4.1.0)
 P ellipsis       0.3.2   2021-04-29 [?] CRAN (R 4.1.0)
 P httpuv         1.6.1   2021-05-07 [?] CRAN (R 4.1.0)
 P jsonlite       1.7.2   2020-12-09 [?] CRAN (R 4.1.0)
 P later          1.2.0   2021-04-23 [?] CRAN (R 4.1.0)
 P lifecycle      1.0.0   2021-02-15 [?] CRAN (R 4.1.0)
 P magrittr       2.0.1   2020-11-17 [?] CRAN (R 4.1.0)
 P plumber      * 1.1.0   2021-03-24 [?] CRAN (R 4.1.0)
 P promises       1.2.0.1 2021-02-11 [?] CRAN (R 4.1.0)
 P R6             2.5.0   2020-10-28 [?] CRAN (R 4.1.0)
 P Rcpp           1.0.6   2021-01-15 [?] CRAN (R 4.1.0)
   renv           0.13.2  2021-03-30 [1] CRAN (R 4.1.0)
 P rlang          0.4.11  2021-04-30 [?] CRAN (R 4.1.0)
 P sessioninfo    1.1.1   2018-11-05 [?] CRAN (R 4.1.0)
 P stringi        1.6.2   2021-05-17 [?] CRAN (R 4.1.0)
 P swagger        3.33.1  2020-10-02 [?] CRAN (R 4.1.0)
 P webutils       1.1     2020-04-28 [?] CRAN (R 4.1.0)
 P withr          2.4.2   2021-04-18 [?] CRAN (R 4.1.0)

[1] /Users/jamesblair/Documents/RStudio/bugs/plumber-bioconductor/renv/library/R-4.1/x86_64-apple-darwin17.0
[2] /private/var/folders/d_/_k539mwd3xsg0chwvt782vzm0000gn/T/RtmpcDTrL7/renv-system-library

 P ── Loaded and on-disk path mismatch.

Reprex

Install BiocGenerics: `BiocManager::install("BiocGenerics")

library(BiocGenerics)
library(plumber)

#* @apiTitle Plumber Example API

#* Echo back the input
#* @param msg The message to echo
#* @get /echo
function(msg = "") {
    list(msg = paste0("The message is: '", msg, "'"))
}

When running the file defined above, the following error is returned:

Error in nchar(ctype) : 
  cannot coerce type 'closure' to vector of type 'character'

This may very well be a side effect from the following message returned when BiocGenerics is loaded:

Attaching package: ‘BiocGenerics’

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
    parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated,
    eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min

It's been indicated that this wasn't an issue with Plumber 1.0, but I have not been able to confirm that firsthand.

meztez commented 3 years ago

Welps, It works on Windows 10 when using the Run API button from within RStudio (with RStudio Preview edition)... weird.

Also tested on Debian and had no issue.

I do not have access to a mac to replicate the problem. I'm sorry.

schloerke commented 3 years ago

I could not reproduce an error on macOS 4.0.2. (Worked for me.)

Terminal output ``` > R ❯❯ BiocManager::install("BiocGenerics") Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22) Installing package(s) 'BiocGenerics' trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/BiocGenerics_0.34.0.tgz' Content type 'application/x-gzip' length 645159 bytes (630 KB) ================================================== downloaded 630 KB The downloaded binary packages are in /var/folders/0k/bxg5lhr92sq74mb1d446ql540000gp/T//Rtmpol756e/downloaded_packages Old packages: 'analogsea', 'AnnotationHub', 'antaresViz', 'ape', 'arules', 'av', 'bayesplot', 'betareg', 'biclust', 'BiocFileCache', 'BiocManager', 'biomaRt', 'BioNetStat', 'bitops', 'blogdown', 'bookdown', 'boot', 'bridgesampling', 'brio', 'brms', 'broom', 'broom.helpers', 'C50', 'cachem', 'caret', 'caTools', 'circlize', 'class', 'cli', 'clue', 'cluster', 'clusterProfiler', 'clustMixType', 'coin', 'colorspace', 'ComplexHeatmap', 'compositions', 'config', 'corrplot', 'cowplot', 'crul', 'Cubist', 'DBI', 'dbplyr', 'DelayedArray', 'DelayedMatrixStats', 'deldir', 'dendextend', 'DEoptimR', 'Deriv', 'devtools', 'dfidx', 'diptest', 'doBy', 'dotCall64', 'downlit', 'dplyr', 'DT', 'e1071', 'edgeR', 'effectsize', 'emmeans', 'epiR', 'esquisse', 'exactRankTests', 'ExperimentHub', 'expm', 'fansi', 'fields', 'fixest', 'foghorn', 'forecast', 'formatR', 'formattable', 'freetypeharfbuzz', 'furrr', 'future.apply', 'future.callr', 'GA', 'gamlss', 'gamlss.data', 'gamlss.dist', 'gargle', 'geepack', 'GenomeInfoDb', 'GenomicFeatures', 'geojsonio', 'gert', 'GGally', 'ggplotify', 'ggraph', 'ggrepel', 'ggridges', 'ggsignif', 'ggthemes', 'gh', 'git2r', 'glmnet', 'glmnetUtils', 'gmm', 'gmp', 'GO.db', 'GOSemSim', 'gstat', 'gt', 'gtsummary', 'haven', 'HDF5Array', 'heatmaply', 'hms', 'htmlTable', 'httpuv', 'huxtable', 'inline', 'interactiveDisplayBase', 'inum', 'ipred', 'IRdisplay', 'joineRML', 'jqr', 'keras', 'KernSmooth', 'ks', 'labelled', 'Lahman', 'lattice', 'lava', 'lavaan', 'leaflet.minicharts', 'lfe', 'libcoin', 'limma', 'lme4', 'loon', 'loon.ggplot', 'lubridate', 'lwgeom', 'maftools', 'magick', 'maptools', 'margins', 'MASS', 'mathjaxr', 'Matrix', 'MatrixModels', 'matrixStats', 'maxLik', 'mclogit', 'memoise', 'mgcv', 'mlbench', 'modeltests', 'mondate', 'muhaz', 'multcomp', 'naniar', 'nnet', 'nycflights13', 'odbc', 'officer', 'openssl', 'org.Hs.eg.db', 'packrat', 'paletteer', 'palr', 'pals', 'parallelly', 'parsedate', 'partitions', 'party', 'partykit', 'pbkrtest', 'PBSmapping', 'pcaPP', 'pdftools', 'pegas', 'performance', 'phangorn', 'pillar', 'pixmap', 'pkgcache', 'pkgcond', 'pkgdepends', 'pkgKitten', 'plm', 'plotrix', 'plumberDeploy', 'pool', 'prettydoc', 'prismatic', 'pROC', 'processx', 'prompt', 'psych', 'psychTools', 'quantreg', 'R.cache', 'radiant.model', 'rapidoc', 'raster', 'rbibutils', 'RcppArmadillo', 'RcppDate', 'RcppParallel', 'RCurl', 'Rdpack', 'reactR', 'recipes', 'redoc', 'renv', 'repr', 'reprex', 'RestRserve', 'reticulate', 'rgdal', 'rgl', 'rhdf5', 'Rhdf5lib', 'rio', 'riverplot', 'rJava', 'RMariaDB', 'RMySQL', 'RPostgres', 'rsample', 'rsconnect', 'RSiena', 'RSQLite', 'rstan', 'rstatix', 'rsvg', 'rticles', 'rtracklayer', 'rversions', 'rvest', 'sandwich', 'scatterpie', 'segmented', 'seqinr', 'servr', 'sf', 'shape', 'shinyloadtest', 'shinythemes', 'shinyvalidate', 'shinyWidgets', 'slider', 'spacetime', 'spam', 'SparseM', 'spatial', 'spatialreg', 'spatstat', 'spatstat.data', 'spatstat.utils', 'spdep', 'speedglm', 'SQUAREM', 'ssh', 'StanHeaders', 'stars', 'statmod', 'stringi', 'styler', 'SummarizedExperiment', 'survC1', 'survival', 'survminer', 'svglite', 'swfscMisc', 'systemfonts', 'TCGAbiolinks', 'tensorflow', 'testit', 'textshaping', 'tfruns', 'thematic', 'tibble', 'tidyselect', 'tidyverse', 'tinytest', 'tinytex', 'TMB', 'tufte', 'tweedie', 'tweenr', 'units', 'urlchecker', 'usethis', 'V8', 'venn', 'vip', 'viridis', 'viridisLite', 'websocket', 'writexl', 'xfun', 'xgboost', 'XML', 'xmlparsedata', 'zoo' Update all/some/none? [a/s/n]: a also installing the dependencies ‘geometries’, ‘jsonify’, ‘rapidjsonr’, ‘sfheaders’, ‘misc3d’, ‘spatstat.sparse’, ‘gridtext’, ‘ids’, ‘curry’, ‘proxy’, ‘datamods’, ‘geojsonsf’, ‘plot3D’, ‘ggmulti’, ‘norm’, ‘spatstat.geom’, ‘spatstat.core’, ‘spatstat.linnet’, ‘ggtext’, ‘kknn’, ‘dtplyr’, ‘googledrive’, ‘googlesheets4’ There are binary versions available but the source versions are later: binary source needs_compilation plot3D 1.3 1.4 FALSE biclust 2.0.2 2.0.3 TRUE DEoptimR 1.0-8 1.0-9 FALSE e1071 1.7-6 1.7-7 TRUE effectsize 0.4.4-1 0.4.5 FALSE fansi 0.4.2 0.5.0 TRUE formatR 1.9 1.10 FALSE ks 1.12.0 1.13.0 TRUE performance 0.7.1 0.7.2 FALSE pkgcache 1.2.1 1.2.2 FALSE RcppArmadillo 0.10.4.0.0 0.10.5.0.0 TRUE RcppDate 0.0.2 0.0.3 FALSE rsconnect 0.8.17 0.8.18 FALSE rstan 2.21.1 2.21.2 TRUE rversions 2.0.2 2.1.0 FALSE shape 1.4.5 1.4.6 FALSE spdep 1.1-7 1.1-8 TRUE swfscMisc 1.4.3 1.5 FALSE Binaries will be installed trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/geometries_0.2.0.tgz' Content type 'application/x-gzip' length 1245078 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/jsonify_1.2.1.tgz' Content type 'application/x-gzip' length 1556439 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/rapidjsonr_1.2.0.tgz' Content type 'application/x-gzip' length 130409 bytes (127 KB) ================================================== downloaded 127 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/sfheaders_0.4.0.tgz' Content type 'application/x-gzip' length 2126231 bytes (2.0 MB) ================================================== downloaded 2.0 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/misc3d_0.9-0.tgz' Content type 'application/x-gzip' length 237482 bytes (231 KB) ================================================== downloaded 231 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/spatstat.sparse_2.0-0.tgz' Content type 'application/x-gzip' length 214535 bytes (209 KB) ================================================== downloaded 209 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/gridtext_0.1.4.tgz' Content type 'application/x-gzip' length 944192 bytes (922 KB) ================================================== downloaded 922 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/ids_1.0.1.tgz' Content type 'application/x-gzip' length 120090 bytes (117 KB) ================================================== downloaded 117 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/curry_0.1.1.tgz' Content type 'application/x-gzip' length 21724 bytes (21 KB) ================================================== downloaded 21 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/proxy_0.4-25.tgz' Content type 'application/x-gzip' length 232197 bytes (226 KB) ================================================== downloaded 226 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/datamods_1.1.4.tgz' Content type 'application/x-gzip' length 500072 bytes (488 KB) ================================================== downloaded 488 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/geojsonsf_2.0.1.tgz' Content type 'application/x-gzip' length 2702284 bytes (2.6 MB) ================================================== downloaded 2.6 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/ggmulti_1.0.2.tgz' Content type 'application/x-gzip' length 1535270 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/norm_1.0-9.5.tgz' Content type 'application/x-gzip' length 103931 bytes (101 KB) ================================================== downloaded 101 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/spatstat.geom_2.1-0.tgz' Content type 'application/x-gzip' length 3881934 bytes (3.7 MB) ================================================== downloaded 3.7 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/spatstat.core_2.1-2.tgz' Content type 'application/x-gzip' length 6711939 bytes (6.4 MB) ================================================== downloaded 6.4 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/spatstat.linnet_2.1-1.tgz' Content type 'application/x-gzip' length 1276708 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/ggtext_0.1.1.tgz' Content type 'application/x-gzip' length 1253756 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/kknn_1.3.1.tgz' Content type 'application/x-gzip' length 319103 bytes (311 KB) ================================================== downloaded 311 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/dtplyr_1.1.0.tgz' Content type 'application/x-gzip' length 239909 bytes (234 KB) ================================================== downloaded 234 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/googledrive_1.0.1.tgz' Content type 'application/x-gzip' length 1766935 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/googlesheets4_0.3.0.tgz' Content type 'application/x-gzip' length 472180 bytes (461 KB) ================================================== downloaded 461 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/analogsea_0.9.4.tgz' Content type 'application/x-gzip' length 341243 bytes (333 KB) ================================================== downloaded 333 KB trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/AnnotationHub_2.20.2.tgz' Content type 'application/x-gzip' length 1504663 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/antaresViz_0.15.4.tgz' Content type 'application/x-gzip' length 3055221 bytes (2.9 MB) ================================================== downloaded 2.9 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/ape_5.5.tgz' Content type 'application/x-gzip' length 3601707 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/arules_1.6-8.tgz' Content type 'application/x-gzip' length 2611902 bytes (2.5 MB) ================================================== downloaded 2.5 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/av_0.6.0.tgz' Content type 'application/x-gzip' length 11718642 bytes (11.2 MB) ================================================== downloaded 11.2 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/bayesplot_1.8.0.tgz' Content type 'application/x-gzip' length 4923335 bytes (4.7 MB) ================================================== downloaded 4.7 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/betareg_3.1-4.tgz' Content type 'application/x-gzip' length 926526 bytes (904 KB) ================================================== downloaded 904 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/biclust_2.0.2.tgz' Content type 'application/x-gzip' length 1321877 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/BiocFileCache_1.12.1.tgz' Content type 'application/x-gzip' length 513589 bytes (501 KB) ================================================== downloaded 501 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/BiocManager_1.30.15.tgz' Content type 'application/x-gzip' length 322718 bytes (315 KB) ================================================== downloaded 315 KB trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/biomaRt_2.44.4.tgz' Content type 'application/x-gzip' length 950292 bytes (928 KB) ================================================== downloaded 928 KB trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/BioNetStat_1.8.4.tgz' Content type 'application/x-gzip' length 3141683 bytes (3.0 MB) ================================================== downloaded 3.0 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/bitops_1.0-7.tgz' Content type 'application/x-gzip' length 29061 bytes (28 KB) ================================================== downloaded 28 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/blogdown_1.3.tgz' Content type 'application/x-gzip' length 274311 bytes (267 KB) ================================================== downloaded 267 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/bookdown_0.22.tgz' Content type 'application/x-gzip' length 1078877 bytes (1.0 MB) ================================================== downloaded 1.0 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/boot_1.3-28.tgz' Content type 'application/x-gzip' length 628477 bytes (613 KB) ================================================== downloaded 613 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/bridgesampling_1.1-2.tgz' Content type 'application/x-gzip' length 1723146 bytes (1.6 MB) ================================================== downloaded 1.6 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/brio_1.1.2.tgz' Content type 'application/x-gzip' length 37284 bytes (36 KB) ================================================== downloaded 36 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/brms_2.15.0.tgz' Content type 'application/x-gzip' length 5615948 bytes (5.4 MB) ================================================== downloaded 5.4 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/broom_0.7.6.tgz' Content type 'application/x-gzip' length 1777025 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/broom.helpers_1.3.0.tgz' Content type 'application/x-gzip' length 346841 bytes (338 KB) ================================================== downloaded 338 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/C50_0.1.4.tgz' Content type 'application/x-gzip' length 482215 bytes (470 KB) ================================================== downloaded 470 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/cachem_1.0.5.tgz' Content type 'application/x-gzip' length 65744 bytes (64 KB) ================================================== downloaded 64 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/caret_6.0-88.tgz' Content type 'application/x-gzip' length 6288820 bytes (6.0 MB) ================================================== downloaded 6.0 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/caTools_1.18.2.tgz' Content type 'application/x-gzip' length 243209 bytes (237 KB) ================================================== downloaded 237 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/circlize_0.4.12.tgz' Content type 'application/x-gzip' length 3285245 bytes (3.1 MB) ================================================== downloaded 3.1 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/class_7.3-19.tgz' Content type 'application/x-gzip' length 96057 bytes (93 KB) ================================================== downloaded 93 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/cli_2.5.0.tgz' Content type 'application/x-gzip' length 531400 bytes (518 KB) ================================================== downloaded 518 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/clue_0.3-59.tgz' Content type 'application/x-gzip' length 1146524 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/cluster_2.1.2.tgz' Content type 'application/x-gzip' length 605101 bytes (590 KB) ================================================== downloaded 590 KB trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/clusterProfiler_3.16.1.tgz' Content type 'application/x-gzip' length 658894 bytes (643 KB) ================================================== downloaded 643 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/clustMixType_0.2-11.tgz' Content type 'application/x-gzip' length 170664 bytes (166 KB) ================================================== downloaded 166 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/coin_1.4-1.tgz' Content type 'application/x-gzip' length 1470780 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/colorspace_2.0-1.tgz' Content type 'application/x-gzip' length 2608831 bytes (2.5 MB) ================================================== downloaded 2.5 MB trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/ComplexHeatmap_2.4.3.tgz' Content type 'application/x-gzip' length 2669889 bytes (2.5 MB) ================================================== downloaded 2.5 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/compositions_2.0-1.tgz' Content type 'application/x-gzip' length 1986403 bytes (1.9 MB) ================================================== downloaded 1.9 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/config_0.3.1.tgz' Content type 'application/x-gzip' length 79254 bytes (77 KB) ================================================== downloaded 77 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/corrplot_0.88.tgz' Content type 'application/x-gzip' length 3879412 bytes (3.7 MB) ================================================== downloaded 3.7 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/cowplot_1.1.1.tgz' Content type 'application/x-gzip' length 1373669 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/crul_1.1.0.tgz' Content type 'application/x-gzip' length 629935 bytes (615 KB) ================================================== downloaded 615 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/Cubist_0.2.40.tgz' Content type 'application/x-gzip' length 986840 bytes (963 KB) ================================================== downloaded 963 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/DBI_1.1.1.tgz' Content type 'application/x-gzip' length 670916 bytes (655 KB) ================================================== downloaded 655 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/dbplyr_2.1.1.tgz' Content type 'application/x-gzip' length 799462 bytes (780 KB) ================================================== downloaded 780 KB trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/DelayedArray_0.14.1.tgz' Content type 'application/x-gzip' length 2254881 bytes (2.2 MB) ================================================== downloaded 2.2 MB trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/DelayedMatrixStats_1.10.1.tgz' Content type 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'https://cloud.r-project.org/bin/macosx/contrib/4.0/usethis_2.0.1.tgz' Content type 'application/x-gzip' length 707071 bytes (690 KB) ================================================== downloaded 690 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/V8_3.4.2.tgz' Content type 'application/x-gzip' length 7578642 bytes (7.2 MB) ================================================== downloaded 7.2 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/venn_1.10.tgz' Content type 'application/x-gzip' length 296584 bytes (289 KB) ================================================== downloaded 289 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/vip_0.3.2.tgz' Content type 'application/x-gzip' length 2777788 bytes (2.6 MB) ================================================== downloaded 2.6 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/viridis_0.6.1.tgz' Content type 'application/x-gzip' length 3022034 bytes (2.9 MB) ================================================== downloaded 2.9 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/viridisLite_0.4.0.tgz' Content type 'application/x-gzip' length 1296423 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/websocket_1.4.0.tgz' Content type 'application/x-gzip' length 5605928 bytes (5.3 MB) ================================================== downloaded 5.3 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/writexl_1.4.0.tgz' Content type 'application/x-gzip' length 457651 bytes (446 KB) ================================================== downloaded 446 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/xfun_0.23.tgz' Content type 'application/x-gzip' length 338371 bytes (330 KB) ================================================== downloaded 330 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/xgboost_1.4.1.1.tgz' Content type 'application/x-gzip' length 10036617 bytes (9.6 MB) ================================================== downloaded 9.6 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/XML_3.99-0.6.tgz' Content type 'application/x-gzip' length 3747121 bytes (3.6 MB) ================================================== downloaded 3.6 MB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/xmlparsedata_1.0.5.tgz' Content type 'application/x-gzip' length 18389 bytes (17 KB) ================================================== downloaded 17 KB trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/zoo_1.8-9.tgz' Content type 'application/x-gzip' length 1026442 bytes (1002 KB) ================================================== downloaded 1002 KB The downloaded binary packages are in /var/folders/0k/bxg5lhr92sq74mb1d446ql540000gp/T//Rtmpol756e/downloaded_packages installing the source packages ‘plot3D’, ‘DEoptimR’, ‘effectsize’, ‘formatR’, ‘GO.db’, ‘org.Hs.eg.db’, ‘performance’, ‘pkgcache’, ‘RcppDate’, ‘rsconnect’, ‘rversions’, ‘shape’, ‘shinyvalidate’, ‘swfscMisc’ trying URL 'https://cloud.r-project.org/src/contrib/plot3D_1.4.tar.gz' Content type 'application/x-gzip' length 2616461 bytes (2.5 MB) ================================================== downloaded 2.5 MB trying URL 'https://cloud.r-project.org/src/contrib/DEoptimR_1.0-9.tar.gz' Content type 'application/x-gzip' length 36148 bytes (35 KB) ================================================== downloaded 35 KB trying URL 'https://cloud.r-project.org/src/contrib/effectsize_0.4.5.tar.gz' Content type 'application/x-gzip' length 831887 bytes (812 KB) ================================================== downloaded 812 KB trying URL 'https://cloud.r-project.org/src/contrib/formatR_1.10.tar.gz' Content type 'application/x-gzip' length 94221 bytes (92 KB) ================================================== downloaded 92 KB trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GO.db_3.11.4.tar.gz' Content type 'application/x-gzip' length 31975305 bytes (30.5 MB) ================================================== downloaded 30.5 MB trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/org.Hs.eg.db_3.11.4.tar.gz' Content type 'application/x-gzip' length 79959831 bytes (76.3 MB) ================================================== downloaded 76.3 MB trying URL 'https://cloud.r-project.org/src/contrib/performance_0.7.2.tar.gz' Content type 'application/x-gzip' length 1817653 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://cloud.r-project.org/src/contrib/pkgcache_1.2.2.tar.gz' Content type 'application/x-gzip' length 164094 bytes (160 KB) ================================================== downloaded 160 KB trying URL 'https://cloud.r-project.org/src/contrib/RcppDate_0.0.3.tar.gz' Content type 'application/x-gzip' length 89092 bytes (87 KB) ================================================== downloaded 87 KB trying URL 'https://cloud.r-project.org/src/contrib/rsconnect_0.8.18.tar.gz' Content type 'application/x-gzip' length 388883 bytes (379 KB) ================================================== downloaded 379 KB trying URL 'https://cloud.r-project.org/src/contrib/rversions_2.1.0.tar.gz' Content type 'application/x-gzip' length 41716 bytes (40 KB) ================================================== downloaded 40 KB trying URL 'https://cloud.r-project.org/src/contrib/shape_1.4.6.tar.gz' Content type 'application/x-gzip' length 677262 bytes (661 KB) ================================================== downloaded 661 KB trying URL 'https://cloud.r-project.org/src/contrib/shinyvalidate_0.1.0.tar.gz' Content type 'application/x-gzip' length 228690 bytes (223 KB) ================================================== downloaded 223 KB trying URL 'https://cloud.r-project.org/src/contrib/swfscMisc_1.5.tar.gz' Content type 'application/x-gzip' length 37001 bytes (36 KB) ================================================== downloaded 36 KB * installing *source* package ‘plot3D’ ... ** package ‘plot3D’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘plot3D.rnw’ ‘volcano.rnw’ ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (plot3D) * installing *source* package ‘DEoptimR’ ... ** package ‘DEoptimR’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DEoptimR) * installing *source* package ‘effectsize’ ... ** package ‘effectsize’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (effectsize) * installing *source* package ‘formatR’ ... ** package ‘formatR’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (formatR) * installing *source* package ‘GO.db’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GO.db) * installing *source* package ‘org.Hs.eg.db’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (org.Hs.eg.db) * installing *source* package ‘performance’ ... ** package ‘performance’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (performance) * installing *source* package ‘pkgcache’ ... ** package ‘pkgcache’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pkgcache) * installing *source* package ‘RcppDate’ ... ** package ‘RcppDate’ successfully unpacked and MD5 sums checked ** using staged installation ** inst ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RcppDate) * installing *source* package ‘rsconnect’ ... ** package ‘rsconnect’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rsconnect) * installing *source* package ‘rversions’ ... ** package ‘rversions’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rversions) * installing *source* package ‘shape’ ... ** package ‘shape’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘shape.Rnw’ using ‘latin1’ ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (shape) * installing *source* package ‘shinyvalidate’ ... ** package ‘shinyvalidate’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (shinyvalidate) * installing *source* package ‘swfscMisc’ ... ** package ‘swfscMisc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (swfscMisc) The downloaded source packages are in ‘/private/var/folders/0k/bxg5lhr92sq74mb1d446ql540000gp/T/Rtmpol756e/downloaded_packages’ ✔ 271.8 MiB (131s) ❯❯ remotes::install_cran("plumber") Skipping install of 'plumber' from a cran remote, the SHA1 (1.1.0) has not changed since last install. Use `force = TRUE` to force installation ✔ 279.1 MiB ❯❯ ✖ 279.1 MiB ❯❯ q() > R ✔ 73.3 MiB ❯❯ library(plumber) ✔ 89.4 MiB ❯❯ plumb("biogenerics.R") %>% pr_run(port = 8080) Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Running plumber API at http://127.0.0.1:8080 Running swagger Docs at http://127.0.0.1:8080/__docs__/ ^C ✔ 89.4 MiB ❯❯ sessioninfo::session_info() ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.0.2 (2020-06-22) os macOS 10.16 system x86_64, darwin17.0 ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/New_York date 2021-05-26 ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── package * version date lib source BiocGenerics * 0.34.0 2020-04-27 [1] Bioconductor cli 2.5.0 2021-04-26 [1] CRAN (R 4.0.2) clisymbols 1.2.0 2017-05-21 [1] CRAN (R 4.0.0) colorout 1.2-2 2020-05-06 [1] Github (jalvesaq/colorout@726d681) crayon 1.4.1 2021-02-08 [1] standard (@1.4.1) desc 1.3.0 2021-03-05 [1] standard (@1.3.0) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.0.2) git2r 0.28.0 2021-01-10 [1] CRAN (R 4.0.2) httpuv 1.6.1 2021-05-07 [1] CRAN (R 4.0.2) jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.2) later 1.2.0 2021-04-23 [1] CRAN (R 4.0.2) lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.2) magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.2) memuse 4.1-0 2020-02-17 [1] CRAN (R 4.0.0) pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.0.2) plumber * 1.1.0 2021-03-24 [1] CRAN (R 4.0.2) promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.0.2) prompt 1.0.1 2021-03-12 [1] CRAN (R 4.0.2) R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2) Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.0.2) rlang 0.4.11.9000 2021-05-19 [1] Github (r-lib/rlang@7021ebe) rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.2) rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.2) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0) stringi 1.6.2 2021-05-17 [1] CRAN (R 4.0.2) swagger 3.33.1 2020-10-02 [1] CRAN (R 4.0.2) testthat 3.0.2 2021-02-14 [1] standard (@3.0.2) webutils 1.1 2020-04-28 [1] CRAN (R 4.0.0) withr 2.4.2 2021-04-18 [1] standard (@2.4.2) [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library ✔ 131.5 MiB ❯❯ ```
schloerke commented 3 years ago

The error is prolly coming from line 70: https://github.com/rstudio/plumber/blob/3d0c4ae8b62a62b5bb6b363a83e8f52889c72a2e/R/openapi-spec.R#L62-L76

I'm wondering if they have a function for their type value. Trying to reproduce...

schloerke commented 3 years ago

There was a PR that fixed how type was retrieved (https://github.com/rstudio/plumber/pull/789).

@blairj09 I bet if they install the master branch remotes::install_github("rstudio/plumber"), then their problem will go away.

blairj09 commented 3 years ago

Doh - should've checked against master. It seems this resolves the problem 😁 Thanks!

sdgd165 commented 1 year ago

一键安装win

sdgd165 commented 1 year ago

苹果笔记本最高是多少

sdgd165 commented 1 year ago

mac一键链接网络

sdgd165 commented 1 year ago

mac一键链接网络

sdgd165 commented 1 year ago

一键破解wlan加密