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Getting bibliographic records from OpenAlex
https://docs.ropensci.org/openalexR/
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Debugging error during snowball #128

Closed rkrug closed 1 year ago

rkrug commented 1 year ago

Hi

I have about 200 articles from which I want to use snowball() which works fine, but in the middle:

Getting 28 pages of results with a total of 5566 records...
  OpenAlex downloading [=====================] 100% eta:  0s
Requesting url: https://api.openalex.org/works?filter=cites%3AW2168682319%7CW1966861654%7CW2101090399%7CW1929181818%7CW2105408058%7CW2161541044%7CW1992970788%7CW2161380895%7CW1900185178%7CW2107030911%7CW2006431779%7CW2779493919%7CW2047136622%7CW2018241482%7CW2162386306%7CW2016801803%7CW1998347864%7CW1595313358%7CW2135908407%7CW2085329586%7CW2104081416%7CW235135751%7CW1994755433%7CW2734708863%7CW2145428182%7CW2160696725%7CW2017573553%7CW2617357665%7CW1966057125%7CW2028740196%7CW1608564693%7CW2156373680%7CW2757568822%7CW1901576207%7CW2015914865%7CW2017047480%7CW2279432690%7CW2559907783%7CW2062688165%7CW2120759161%7CW2152547442%7CW2475703819%7CW2101841878%7CW2487574895%7CW2346307417%7CW2321136864%7CW1159364830%7CW1976178704%7CW2668507809%7CW1992819125
Getting 43 pages of results with a total of 8410 records...
  OpenAlex downloading [=====================] 100% eta:  0s
Requesting url: https://api.openalex.org/works?filter=cites%3AW2132133878%7CW2116272411%7CW2147324701%7CW1964905403%7CW2158562479%7CW2106351369%7CW2496196582%7CW1485106432%7CW2163664734%7CW2080589306%7CW2554000176%7CW2005480114%7CW1982115724%7CW2025640596%7CW2007643437%7CW2101770051%7CW1973422738%7CW1982596679%7CW2000741911%7CW2340594102%7CW1974150937%7CW2148879975%7CW1829030053%7CW4256553588%7CW2560732491%7CW2208397176%7CW2127626302%7CW2523325469%7CW2345739406%7CW2099626405%7CW2166465333%7CW2087638546%7CW1970439584%7CW2611319929%7CW1965859094%7CW2034370381%7CW2112239236%7CW2571226805%7CW2028624884%7CW1693516977%7CW2028649465%7CW2067915749%7CW2047995703%7CW2406241095%7CW2163789349%7CW2164576867%7CW2526369002%7CW2188515674%7CW2016538523%7CW3023837187
Getting 26 pages of results with a total of 5113 records...
  OpenAlex downloading [======>--------------]  35% eta: 36sError: lexical error: invalid char in json text.
                                       There was an error processing y
                     (right here) ------^

r$>

Assuming that the last URL mentioned is causing the problem, I tried

x <- jsonlite::fromJSON("https://api.openalex.org/works?filter=cites%3AW2132133878%7CW21
    16272411%7CW2147324701%7CW1964905403%7CW2158562479%7CW2106351369%7CW2496196582%7CW148510
    6432%7CW2163664734%7CW2080589306%7CW2554000176%7CW2005480114%7CW1982115724%7CW2025640596
    %7CW2007643437%7CW2101770051%7CW1973422738%7CW1982596679%7CW2000741911%7CW2340594102%7CW
    1974150937%7CW2148879975%7CW1829030053%7CW4256553588%7CW2560732491%7CW2208397176%7CW2127
    626302%7CW2523325469%7CW2345739406%7CW2099626405%7CW2166465333%7CW2087638546%7CW19704395
    84%7CW2611319929%7CW1965859094%7CW2034370381%7CW2112239236%7CW2571226805%7CW2028624884%7
    CW1693516977%7CW2028649465%7CW2067915749%7CW2047995703%7CW2406241095%7CW2163789349%7CW21
    64576867%7CW2526369002%7CW2188515674%7CW2016538523%7CW3023837187")

and it worked with no problems.

Any suggestions how I can debug this?

Thanks.

yjunechoe commented 1 year ago

It's more so that one of the papers contained within that JSON has connections to a paper that's failing to parse. So to replicate that last request, you can run:

x <- URLdecode("%3AW2132133878%7CW21
    16272411%7CW2147324701%7CW1964905403%7CW2158562479%7CW2106351369%7CW2496196582%7CW148510
    6432%7CW2163664734%7CW2080589306%7CW2554000176%7CW2005480114%7CW1982115724%7CW2025640596
    %7CW2007643437%7CW2101770051%7CW1973422738%7CW1982596679%7CW2000741911%7CW2340594102%7CW
    1974150937%7CW2148879975%7CW1829030053%7CW4256553588%7CW2560732491%7CW2208397176%7CW2127
    626302%7CW2523325469%7CW2345739406%7CW2099626405%7CW2166465333%7CW2087638546%7CW19704395
    84%7CW2611319929%7CW1965859094%7CW2034370381%7CW2112239236%7CW2571226805%7CW2028624884%7
    CW1693516977%7CW2028649465%7CW2067915749%7CW2047995703%7CW2406241095%7CW2163789349%7CW21
    64576867%7CW2526369002%7CW2188515674%7CW2016538523%7CW3023837187")

library(stringr)
out <- str_extract_all(str_remove_all(x, "\\s"), "W\\d+")[[1]] |> 
  oa_snowball(verbose = TRUE)

However I actually can't reproduce that error. I can fetch all 5113 (citing) records and the 1876 (cited_by) records (which you would've gotten to if it didn't error early).

Could it be a network connection? It happens sometimes (happened to me just a few hours ago too). Can you try just running the snippet of code above and see if you get this back?

out
#> $nodes
#> # A tibble: 7,005 × 31
#>    id          display_name     author ab    publication_date so    so_id host_organization issn_l url   pdf_url license version
#>    <chr>       <chr>            <list> <chr> <chr>            <chr> <chr> <chr>             <chr>  <chr> <chr>   <chr>   <chr>  
#>  1 W2132133878 Shrub Invasions… <df>   "▪ A… 2000-11-01       Annu… http… Annual Reviews    0066-… http… <NA>    <NA>    <NA>   
#>  2 W2116272411 Organic chemica… <df>   "Sig… 2014-06-16       Proc… http… <NA>              <NA>   http… <NA>    <NA>    publis…
#>  3 W2147324701 CONTESTED TERRA… <df>   "▪ A… 2004-11-21       Annu… http… Annual Reviews    1543-… http… <NA>    <NA>    publis…
#>  4 W1964905403 Decentralizatio… <df>   "Thi… 2008-11-01       Annu… http… Annual Reviews    1543-… http… <NA>    pd      publis…
#>  5 W2158562479 Energy access i… <df>   "Thi… 2010-05-01       Ener… http… Elsevier BV       0301-… http… <NA>    <NA>    <NA>   
#>  6 W2106351369 <NA>             <df>   ""    2003-01-01       Huma… http… Springer Science… 0300-… http… <NA>    <NA>    <NA>   
#>  7 W2496196582 The Potential R… <df>   "Exp… 2016-07-26       Fron… http… Frontiers Media   1664-… http… <NA>    cc-by   publis…
#>  8 W1485106432 Policy Options … <df>   "We … 2014-08-14       Cons… http… Wiley             1755-… http… <NA>    <NA>    <NA>   
#>  9 W2163664734 Testing the use… <df>   "Sum… 2008-08-01       Jour… http… Wiley-Blackwell   0021-… http… <NA>    <NA>    <NA>   
#> 10 W2080589306 Land degradatio… <df>   "Rec… 2007-01-01       Land… http… Wiley-Blackwell   1085-… http… <NA>    <NA>    <NA>   
#> # ℹ 6,995 more rows
#> # ℹ 18 more variables: first_page <chr>, last_page <chr>, volume <chr>, issue <chr>, is_oa <lgl>, cited_by_count <int>,
#> #   counts_by_year <list>, publication_year <int>, cited_by_api_url <chr>, ids <list>, doi <chr>, type <chr>,
#> #   referenced_works <list>, related_works <list>, is_paratext <lgl>, is_retracted <lgl>, concepts <list>, oa_input <lgl>
#> 
#> $edges
#> # A tibble: 7,068 × 2
#>    from        to         
#>    <chr>       <chr>      
#>  1 W2168682319 W2080589306
#>  2 W2097686432 W2000741911
#>  3 W2160537686 W2132133878
#>  4 W2336998050 W2158562479
#>  5 W2116950002 W2147324701
#>  6 W2147169550 W2132133878
#>  7 W2147716564 W2132133878
#>  8 W2157062135 W2132133878
#>  9 W2130737082 W2116272411
#> 10 W2007900882 W2132133878
#> # ℹ 7,058 more rows
rkrug commented 1 year ago

OK. Worked for me as well. I am, while trying this, re-running the snowball with per_page = 50 - might help as well.

Thanks.

yjunechoe commented 1 year ago

Great! Thanks for the tip!

rkrug commented 1 year ago

Hm. Same error with:

Getting 23 pages of results with a total of 4475 records...
  OpenAlex downloading [=====================] 100% eta:  0s
Requesting url: https://api.openalex.org/works?filter=cites%3AW2589424942%7CW2594233224%7CW2109428973%7CW2108887391%7CW2118353368%7CW2265892259%7CW2115119268%7CW2071911076%7CW1942798807%7CW2027109090%7CW2097039354%7CW2051207904%7CW2016044675%7CW2549733934%7CW2127806428%7CW2088887692%7CW3016484654%7CW2118476021%7CW2068064564%7CW2015353307%7CW2033502030%7CW2045404798%7CW2077285015%7CW2588584062%7CW1929584539%7CW2078907443%7CW2766942546%7CW2789191954%7CW2507663396%7CW2004014131%7CW2011151752%7CW1994021028%7CW2411108857%7CW2165933828%7CW4235181723%7CW2553303766%7CW2766957840%7CW1978887695%7CW2512305553%7CW1975749733%7CW2559981416%7CW2560959851%7CW2604706251%7CW1963540873%7CW2070099228%7CW2024320912%7CW3088921768%7CW2093809036%7CW2161073656%7CW4212887679
Getting 21 pages of results with a total of 4116 records...
  OpenAlex downloading [=======>-------------]  38% eta: 22sError: lexical error: invalid char in json text.
                                       There was an error processing y
                     (right here) ------^

And it works with the code you provided.

yjunechoe commented 1 year ago

It again works for me with the same code, so unfortunately I can't diagnose the error. I'm not really sure what's going on but I think it's bouncing you somewhere with some information that we don't know the structure of, so you just get a vague parsing error.

I'll make sure to keep an eye out for that error for when it happens to me again. For now, would you like this output to be sent to you somehow?

x <- URLdecode("https://api.openalex.org/works?filter=cites%3AW2589424942%7CW2594233224%7CW2109428973%7CW2108887391%7CW2118353368%7CW2265892259%7CW2115119268%7CW2071911076%7CW1942798807%7CW2027109090%7CW2097039354%7CW2051207904%7CW2016044675%7CW2549733934%7CW2127806428%7CW2088887692%7CW3016484654%7CW2118476021%7CW2068064564%7CW2015353307%7CW2033502030%7CW2045404798%7CW2077285015%7CW2588584062%7CW1929584539%7CW2078907443%7CW2766942546%7CW2789191954%7CW2507663396%7CW2004014131%7CW2011151752%7CW1994021028%7CW2411108857%7CW2165933828%7CW4235181723%7CW2553303766%7CW2766957840%7CW1978887695%7CW2512305553%7CW1975749733%7CW2559981416%7CW2560959851%7CW2604706251%7CW1963540873%7CW2070099228%7CW2024320912%7CW3088921768%7CW2093809036%7CW2161073656%7CW4212887679")
library(stringr)
out <- str_extract_all(str_remove_all(x, "\\s"), "W\\d+")[[1]] |> 
  oa_snowball(verbose = TRUE)
# Requesting url: https://api.openalex.org/works?filter=openalex_id%3AW2589424942%7CW2594233224%7CW2109428973%7CW2108887391%7CW2118353368%7CW2265892259%7CW2115119268%7CW2071911076%7CW1942798807%7CW2027109090%7CW2097039354%7CW2051207904%7CW2016044675%7CW2549733934%7CW2127806428%7CW2088887692%7CW3016484654%7CW2118476021%7CW2068064564%7CW2015353307%7CW2033502030%7CW2045404798%7CW2077285015%7CW2588584062%7CW1929584539%7CW2078907443%7CW2766942546%7CW2789191954%7CW2507663396%7CW2004014131%7CW2011151752%7CW1994021028%7CW2411108857%7CW2165933828%7CW4235181723%7CW2553303766%7CW2766957840%7CW1978887695%7CW2512305553%7CW1975749733%7CW2559981416%7CW2560959851%7CW2604706251%7CW1963540873%7CW2070099228%7CW2024320912%7CW3088921768%7CW2093809036%7CW2161073656%7CW4212887679
# Getting 1 page of results with a total of 50 records...
# converting [===============================] 100% eta:  0s
# Collecting all documents citing the target papers...
# Requesting url: https://api.openalex.org/works?filter=cites%3AW2589424942%7CW2594233224%7CW2109428973%7CW2108887391%7CW2118353368%7CW2265892259%7CW2115119268%7CW2071911076%7CW1942798807%7CW2027109090%7CW2097039354%7CW2051207904%7CW2016044675%7CW2549733934%7CW2127806428%7CW2088887692%7CW3016484654%7CW2118476021%7CW2068064564%7CW2015353307%7CW2033502030%7CW2045404798%7CW2077285015%7CW2588584062%7CW1929584539%7CW2078907443%7CW2766942546%7CW2789191954%7CW2507663396%7CW2004014131%7CW2011151752%7CW1994021028%7CW2411108857%7CW2165933828%7CW4235181723%7CW2553303766%7CW2766957840%7CW1978887695%7CW2512305553%7CW1975749733%7CW2559981416%7CW2560959851%7CW2604706251%7CW1963540873%7CW2070099228%7CW2024320912%7CW3088921768%7CW2093809036%7CW2161073656%7CW4212887679
# Getting 21 pages of results with a total of 4116 records...
# OpenAlex downloading [=====================] 100% eta:  0s
# converting [===============================] 100% eta:  0s
# Collecting all documents cited by the target papers...
# Requesting url: https://api.openalex.org/works?filter=cited_by%3AW2589424942%7CW2594233224%7CW2109428973%7CW2108887391%7CW2118353368%7CW2265892259%7CW2115119268%7CW2071911076%7CW1942798807%7CW2027109090%7CW2097039354%7CW2051207904%7CW2016044675%7CW2549733934%7CW2127806428%7CW2088887692%7CW3016484654%7CW2118476021%7CW2068064564%7CW2015353307%7CW2033502030%7CW2045404798%7CW2077285015%7CW2588584062%7CW1929584539%7CW2078907443%7CW2766942546%7CW2789191954%7CW2507663396%7CW2004014131%7CW2011151752%7CW1994021028%7CW2411108857%7CW2165933828%7CW4235181723%7CW2553303766%7CW2766957840%7CW1978887695%7CW2512305553%7CW1975749733%7CW2559981416%7CW2560959851%7CW2604706251%7CW1963540873%7CW2070099228%7CW2024320912%7CW3088921768%7CW2093809036%7CW2161073656%7CW4212887679
# Getting 6 pages of results with a total of 1199 records...
# OpenAlex downloading [=====================] 100% eta:  0s
# converting [===============================] 100% eta:  0s

out
#> $nodes
#> # A tibble: 5,349 × 31
#>    id          display_name     author ab    publication_date so    so_id host_organization issn_l url   pdf_url license version
#>    <chr>       <chr>            <list> <chr> <chr>            <chr> <chr> <chr>             <chr>  <chr> <chr>   <chr>   <chr>  
#>  1 W2589424942 Valuing nature’… <df>   "Nat… 2017-06-01       Curr… http… Elsevier BV       1877-… http… <NA>    cc-by-… publis…
#>  2 W2594233224 Persistent effe… <df>   "Pas… 2017-03-03       Scie… http… American Associa… 0036-… http… <NA>    <NA>    <NA>   
#>  3 W2109428973 Home gardens: n… <df>   ""    2010-09-17       Biod… http… Springer Science… 0960-… http… <NA>    <NA>    <NA>   
#>  4 W2108887391 Fisheries asses… <df>   "Fis… 1999-10-01       Cana… http… Canadian Science… 0706-… http… <NA>    <NA>    <NA>   
#>  5 W2118353368 Arsenic contami… <df>   "In … 2010-03-01       Envi… http… Elsevier BV       0269-… http… <NA>    <NA>    <NA>   
#>  6 W2265892259 Ecosystem servi… <df>   "In … 2016-08-01       Envi… http… Elsevier BV       1462-… http… <NA>    <NA>    <NA>   
#>  7 W2115119268 Ecological Comp… <df>   "Man… 2010-07-01       BioS… http… American Institu… 0006-… http… <NA>    <NA>    <NA>   
#>  8 W2071911076 Short-term soil… <df>   "The… 2006-12-01       Soil… http… Elsevier BV       0167-… http… <NA>    <NA>    <NA>   
#>  9 W1942798807 No-take Marine … <df>   ""    2006-08-01       AMBI… http… Royal Swedish Ac… 0044-… http… <NA>    <NA>    <NA>   
#> 10 W2027109090 Lessons from In… <df>   ""    2008-10-23       Envi… http… Springer Science… 0364-… http… <NA>    <NA>    <NA>   
#> # ℹ 5,339 more rows
#> # ℹ 18 more variables: first_page <chr>, last_page <chr>, volume <chr>, issue <chr>, is_oa <lgl>, cited_by_count <int>,
#> #   counts_by_year <list>, publication_year <int>, cited_by_api_url <chr>, ids <list>, doi <chr>, type <chr>,
#> #   referenced_works <list>, related_works <list>, is_paratext <lgl>, is_retracted <lgl>, concepts <list>, oa_input <lgl>
#> 
#> $edges
#> # A tibble: 5,455 × 2
#>    from        to         
#>    <chr>       <chr>      
#>  1 W2756791498 W2589424942
#>  2 W2782917446 W2589424942
#>  3 W2105691566 W2115119268
#>  4 W1973981085 W2115119268
#>  5 W2057646086 W2097039354
#>  6 W2122925767 W2016044675
#>  7 W1982116679 W2118353368
#>  8 W2788008213 W2589424942
#>  9 W2159632829 W2108887391
#> 10 W2343199820 W2071911076
#> # ℹ 5,445 more rows
rkrug commented 1 year ago

As I said - this code runs for me too. I am at the moment limiting the works I use - the error is still there when limiting it to the first 1000. Will post an example if it does not go away.

yjunechoe commented 1 year ago

Oh oops sorry I misread! Actually do you mind sharing the full context that's causing oa_snowball() to error?

Any way for us to reproduce the invalid char in json text. would help a lot!

rkrug commented 1 year ago

Will do so. I am narrowing it down at the moment.

trangdata commented 1 year ago

Hi @rkrug, I have seen this "Error: lexical error: invalid char in json text." before in #117 and #122. Could you make sure that you install the current version of openalexR from GitHub and try again? 

install.packages("remotes")
remotes::install_github("ropensci/openalexR")
rkrug commented 1 year ago

OK - reinstalled from GitHub newest version and re-running it.

rkrug commented 1 year ago

OK - I still got the error. Can I somebody on your side send the works ids so that you can check on your side? I would not like to post it here as it should be treated as semi confidential...

trangdata commented 1 year ago

OK - I still got the error. Can I somebody on your side send the works ids so that you can check on your side? I would not like to post it here as it should be treated as semi confidential...

Received. I'll take a look.

rkrug commented 1 year ago

Send it to @trangdata . Here is my session info:

r$> devtools::session_info()
─ Session info ────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.1 (2023-06-16)
 os       macOS Ventura 13.4.1
 system   aarch64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Zurich
 date     2023-07-19
 pandoc   3.1.5 @ /opt/homebrew/bin/pandoc

─ Packages ────────────────────────────────────────────────────────────────────────
 package      * version date (UTC) lib source
 cachem         1.0.7   2023-02-24 [1] CRAN (R 4.3.0)
 callr          3.7.3   2022-11-02 [1] CRAN (R 4.3.0)
 cli            3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
 colorspace     2.1-0   2023-01-23 [1] CRAN (R 4.3.0)
 crayon         1.5.2   2022-09-29 [1] CRAN (R 4.3.0)
 devtools       2.4.5   2022-10-11 [1] CRAN (R 4.3.0)
 digest         0.6.31  2022-12-11 [1] CRAN (R 4.3.0)
 dplyr        * 1.1.2   2023-04-20 [1] CRAN (R 4.3.0)
 ellipsis       0.3.2   2021-04-29 [1] CRAN (R 4.3.0)
 fansi          1.0.4   2023-01-22 [1] CRAN (R 4.3.0)
 farver         2.1.1   2022-07-06 [1] CRAN (R 4.3.0)
 fastmap        1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
 fs             1.6.1   2023-02-06 [1] CRAN (R 4.3.0)
 generics       0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
 ggforce        0.4.1   2022-10-04 [1] CRAN (R 4.3.0)
 ggplot2      * 3.4.2   2023-04-03 [1] CRAN (R 4.3.0)
 ggraph       * 2.1.0   2022-10-09 [1] CRAN (R 4.3.0)
 ggrepel        0.9.3   2023-02-03 [1] CRAN (R 4.3.0)
 glue           1.6.2   2022-02-24 [1] CRAN (R 4.3.0)
 graphlayouts   1.0.0   2023-05-01 [1] CRAN (R 4.3.0)
 gridExtra      2.3     2017-09-09 [1] CRAN (R 4.3.0)
 gtable         0.3.3   2023-03-21 [1] CRAN (R 4.3.0)
 htmltools      0.5.5   2023-03-23 [1] CRAN (R 4.3.0)
 htmlwidgets    1.6.2   2023-03-17 [1] CRAN (R 4.3.0)
 httpuv         1.6.9   2023-02-14 [1] CRAN (R 4.3.0)
 igraph         1.4.2   2023-04-07 [1] CRAN (R 4.3.0)
 jsonlite       1.8.7   2023-06-29 [1] CRAN (R 4.3.0)
 knitr        * 1.42    2023-01-25 [1] CRAN (R 4.3.0)
 later          1.3.0   2021-08-18 [1] CRAN (R 4.3.0)
 lifecycle      1.0.3   2022-10-07 [1] CRAN (R 4.3.0)
 magrittr       2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
 MASS           7.3-59  2023-04-21 [1] CRAN (R 4.3.0)
 memoise        2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
 mime           0.12    2021-09-28 [1] CRAN (R 4.3.0)
 miniUI         0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
 munsell        0.5.0   2018-06-12 [1] CRAN (R 4.3.0)
 openalexR    * 1.1.2.9 2023-07-19 [1] Github (ropensci/openalexR@66f0743)
 pillar         1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
 pkgbuild       1.4.0   2022-11-27 [1] CRAN (R 4.3.0)
 pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
 pkgload        1.3.2   2022-11-16 [1] CRAN (R 4.3.0)
 polyclip       1.10-4  2022-10-20 [1] CRAN (R 4.3.0)
 prettyunits    1.1.1   2020-01-24 [1] CRAN (R 4.3.0)
 processx       3.8.1   2023-04-18 [1] CRAN (R 4.3.0)
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 promises       1.2.0.1 2021-02-11 [1] CRAN (R 4.3.0)
 ps             1.7.5   2023-04-18 [1] CRAN (R 4.3.0)
 purrr          1.0.1   2023-01-10 [1] CRAN (R 4.3.0)
 R6             2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
 Rcpp           1.0.10  2023-01-22 [1] CRAN (R 4.3.0)
 remotes        2.4.2   2021-11-30 [1] CRAN (R 4.3.0)
 rlang          1.1.1   2023-04-28 [1] CRAN (R 4.3.0)
 scales         1.2.1   2022-08-20 [1] CRAN (R 4.3.0)
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 stringi        1.7.12  2023-01-11 [1] CRAN (R 4.3.0)
 stringr        1.5.0   2022-12-02 [1] CRAN (R 4.3.0)
 tibble         3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
 tidygraph    * 1.2.3   2023-02-01 [1] CRAN (R 4.3.0)
 tidyr          1.3.0   2023-01-24 [1] CRAN (R 4.3.0)
 tidyselect     1.2.0   2022-10-10 [1] CRAN (R 4.3.0)
 tweenr         2.0.2   2022-09-06 [1] CRAN (R 4.3.0)
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 usethis        2.1.6   2022-05-25 [1] CRAN (R 4.3.0)
 utf8           1.2.3   2023-01-31 [1] CRAN (R 4.3.0)
 vctrs          0.6.3   2023-06-14 [1] CRAN (R 4.3.0)
 viridis        0.6.2   2021-10-13 [1] CRAN (R 4.3.0)
 viridisLite    0.4.1   2022-08-22 [1] CRAN (R 4.3.0)
 withr          2.5.0   2022-03-03 [1] CRAN (R 4.3.0)
 xfun           0.39    2023-04-20 [1] CRAN (R 4.3.0)
 xtable         1.8-4   2019-04-21 [1] CRAN (R 4.3.0)

 [1] /Users/rainerkrug/R/library/aarch64-apple-darwin20/4.3
 [2] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

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rkrug commented 1 year ago

I did it in batches, and it worked. So I assume, it was a memory issue.