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Use 'parallel' package as suggest #42

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florisvdh opened this issue Sep 3, 2020 · 1 comment
Closed

Use 'parallel' package as suggest #42

florisvdh opened this issue Sep 3, 2020 · 1 comment

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@florisvdh
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@florisvdh florisvdh commented Sep 3, 2020

Regarding the 'parallel' examples in the download_zenodo documenation. It appears that the package-import of parallel::mclapply doesn't help to execute first example. The parallel package must be loaded explicitly. Same holds for the parLapply anyway.

Further, note there's an error coming from stopCluster, which isn't imported.

Cf. below reprex. BTW, congrats for having solved most warnings!

library(zen4R)
download_zenodo("10.5281/zenodo.2547036", 
                parallel = TRUE,
                parallel_handler = mclapply,
                mc.cores = 2)
#> Warning in Sys.setlocale("LC_TIME", "us_US"): OS reports request to set locale
#> to "us_US" cannot be honored
#> [zen4R][INFO] ZenodoRecord - Download in parallel mode
#> Error in rec$downloadFiles(path = path, quiet = quiet, ...): object 'mclapply' not found
download_zenodo("10.5281/zenodo.2547036", 
                parallel = TRUE,
                parallel_handler = parLapply,
                cl = makeCluster(2))
#> Warning in Sys.setlocale("LC_TIME", "us_US"): OS reports request to set locale
#> to "us_US" cannot be honored
#> [zen4R][INFO] ZenodoRecord - Download in parallel mode
#> Error in rec$downloadFiles(path = path, quiet = quiet, ...): object 'parLapply' not found
download_zenodo("10.5281/zenodo.2547036", 
                parallel = TRUE,
                parallel_handler = parallel::mclapply,
                mc.cores = 2)
#> Warning in Sys.setlocale("LC_TIME", "us_US"): OS reports request to set locale
#> to "us_US" cannot be honored
#> [zen4R][INFO] ZenodoRecord - Download in parallel mode 
#> [zen4R][INFO] ZenodoRecord - Using non cluster-based (no cluster 'cl' argument specified) 
#> [zen4R][INFO] ZenodoRecord - Will download 2 files from record '4011667' (doi: '10.5281/zenodo.4011667') - total size: 72 KiB 
#> [zen4R][INFO] Files downloaded at '/tmp/Rtmp1ohh87/reprex2dd149277a26'.
#> [zen4R][INFO] ZenodoRecord - Verifying file integrity... 
#> [zen4R][INFO] File 'zen4R-0.4.tar.gz': integrity verified (md5sum: e36420deeaf30ebd25fd74dfdcf6d7cd)
#> [zen4R][INFO] File 'zen4R-0.4.zip': integrity verified (md5sum: 5fa140b3837c315bfc9733813b152fd3)
#> [zen4R][INFO] ZenodoRecord - End of download
download_zenodo("10.5281/zenodo.2547036", 
                parallel = TRUE,
                parallel_handler = parallel::parLapply,
                cl = parallel::makeCluster(2))
#> Warning in Sys.setlocale("LC_TIME", "us_US"): OS reports request to set locale
#> to "us_US" cannot be honored
#> [zen4R][INFO] ZenodoRecord - Download in parallel mode 
#> [zen4R][INFO] ZenodoRecord - Using cluster-based parallel handler (cluster 'cl' argument specified) 
#> [zen4R][INFO] ZenodoRecord - Will download 2 files from record '4011667' (doi: '10.5281/zenodo.4011667') - total size: 72 KiB 
#> Error in stopCluster(cl) : could not find function "stopCluster"
#> [zen4R][INFO] Files downloaded at '/tmp/Rtmp1ohh87/reprex2dd149277a26'.
#> [zen4R][INFO] ZenodoRecord - Verifying file integrity... 
#> [zen4R][INFO] File 'zen4R-0.4.tar.gz': integrity verified (md5sum: e36420deeaf30ebd25fd74dfdcf6d7cd)
#> [zen4R][INFO] File 'zen4R-0.4.zip': integrity verified (md5sum: 5fa140b3837c315bfc9733813b152fd3)
#> [zen4R][INFO] ZenodoRecord - End of download

Created on 2020-09-03 by the reprex package (v0.3.0)

Session info
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.0.2 (2020-06-22)
#>  os       Linux Mint 20               
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language nl_BE:nl                    
#>  collate  nl_BE.UTF-8                 
#>  ctype    nl_BE.UTF-8                 
#>  tz       Europe/Brussels             
#>  date     2020-09-03                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date       lib source        
#>  assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.2)
#>  backports     1.1.8   2020-06-17 [1] CRAN (R 4.0.2)
#>  callr         3.4.3   2020-03-28 [1] CRAN (R 4.0.2)
#>  cli           2.0.2   2020-02-28 [1] CRAN (R 4.0.2)
#>  crayon        1.3.4   2017-09-16 [1] CRAN (R 4.0.2)
#>  curl          4.3     2019-12-02 [1] CRAN (R 4.0.2)
#>  desc          1.2.0   2018-05-01 [1] CRAN (R 4.0.2)
#>  devtools      2.3.1   2020-07-21 [1] CRAN (R 4.0.2)
#>  digest        0.6.25  2020-02-23 [1] CRAN (R 4.0.2)
#>  ellipsis      0.3.1   2020-05-15 [1] CRAN (R 4.0.2)
#>  evaluate      0.14    2019-05-28 [1] CRAN (R 4.0.2)
#>  fansi         0.4.1   2020-01-08 [1] CRAN (R 4.0.2)
#>  fs            1.5.0   2020-07-31 [1] CRAN (R 4.0.2)
#>  glue          1.4.1   2020-05-13 [1] CRAN (R 4.0.2)
#>  highr         0.8     2019-03-20 [1] CRAN (R 4.0.2)
#>  htmltools     0.5.0   2020-06-16 [1] CRAN (R 4.0.2)
#>  httr          1.4.2   2020-07-20 [1] CRAN (R 4.0.2)
#>  jsonlite      1.7.0   2020-06-25 [1] CRAN (R 4.0.2)
#>  keyring       1.1.0   2018-07-16 [1] CRAN (R 4.0.2)
#>  knitr         1.29    2020-06-23 [1] CRAN (R 4.0.2)
#>  magrittr      1.5     2014-11-22 [1] CRAN (R 4.0.2)
#>  memoise       1.1.0   2017-04-21 [1] CRAN (R 4.0.2)
#>  pkgbuild      1.1.0   2020-07-13 [1] CRAN (R 4.0.2)
#>  pkgload       1.1.0   2020-05-29 [1] CRAN (R 4.0.2)
#>  prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.0.2)
#>  processx      3.4.3   2020-07-05 [1] CRAN (R 4.0.2)
#>  ps            1.3.4   2020-08-11 [1] CRAN (R 4.0.2)
#>  R6            2.4.1   2019-11-12 [1] CRAN (R 4.0.2)
#>  remotes       2.2.0   2020-07-21 [1] CRAN (R 4.0.2)
#>  reprex        0.3.0   2019-05-16 [1] CRAN (R 4.0.2)
#>  rlang         0.4.7   2020-07-09 [1] CRAN (R 4.0.2)
#>  rmarkdown     2.3     2020-06-18 [1] CRAN (R 4.0.2)
#>  rprojroot     1.3-2   2018-01-03 [1] CRAN (R 4.0.2)
#>  sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.0.2)
#>  stringi       1.4.6   2020-02-17 [1] CRAN (R 4.0.2)
#>  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.0.2)
#>  testthat      2.3.2   2020-03-02 [1] CRAN (R 4.0.2)
#>  usethis       1.6.1   2020-04-29 [1] CRAN (R 4.0.2)
#>  withr         2.2.0   2020-04-20 [1] CRAN (R 4.0.2)
#>  xfun          0.16    2020-07-24 [1] CRAN (R 4.0.2)
#>  xml2          1.3.2   2020-04-23 [1] CRAN (R 4.0.2)
#>  yaml          2.2.1   2020-02-01 [1] CRAN (R 4.0.2)
#>  zen4R       * 0.4-1   2020-09-03 [1] local         
#> 
#> [1] /home/floris/lib/R/library
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
eblondel added a commit that referenced this issue Sep 3, 2020
Alternative fix to #42
@eblondel eblondel closed this Sep 3, 2020
@eblondel eblondel added this to the 0.4 milestone Sep 3, 2020
@eblondel eblondel changed the title Examples in download_zenodo documentation miss the 'parallel' package Use 'parallel' package as suggest Sep 4, 2020
@eblondel
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@eblondel eblondel commented Sep 7, 2020

Available in CRAN (zen4R 0.4-2)

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