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massimoaria / bibliometrix

An R-tool for comprehensive science mapping analysis. A package for quantitative research in scientometrics and bibliometrics.
https://www.bibliometrix.org
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Error in importing data from PubMed #108

Closed tzengji closed 4 years ago

tzengji commented 4 years ago

(https://cran.r-project.org/web/packages/bibliometrix/vignettes/Data-Importing-and-Converting.html)

In executing the code (bibliometrix 3.0.0), an error occurred:

file <- "https://www.bibliometrix.org/datasets/pubmed_txt.txt" M <- convert2df(file, dbsource = "pubmed", format = "pubmed")

Error: Names must be unique.

Run rlang::last_error() to see where the error occurred.

TKS for the new version. Best regards Tzeng-Ji Chen

massimoaria commented 4 years ago

Sorry, but I am not able to replicate your issue. If I run the code, all works well on my PC

file <- "https://www.bibliometrix.org/datasets/pubmed_txt.txt"
M <- convert2df(file, dbsource = "pubmed", format = "pubmed")

Converting your pubmed collection into a bibliographic dataframe

Done!

Generating affiliation field tag AU_UN from C1:  Done!

Try to update bibliometrix from github

tzengji commented 4 years ago

Dear Sir

Thank you for the prompt reply.

Your solution is right.

I have removed the bibliometrix package from CRAN and re-installed it from GitHub. It works perfect now.

I think the problem is due to the old version of vctrs package.

devtools::install_github("massimoaria/bibliometrix") Downloading GitHub repo massimoaria/bibliometrix@master These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: vctrs (0.2.4 -> 0.3.0) [CRAN] 5: scales (1.1.0 -> 1.1.1) [CRAN] 6: tidyselect (1.0.0 -> 1.1.0) [CRAN] 7: tidygraph (1.1.2 -> 1.2.0) [CRAN]

The similar problem occurred elsewhere at other R packages.

https://github.com/IndrajeetPatil/ggstatsplot/issues/396 https://github.com/IndrajeetPatil/groupedstats/issues/24

Thanks again.

Tzeng-Ji Chen

yuyllove commented 4 years ago

A similar error occurs in localCitations function My R version is 4.0.1, and the Rstudio version is 1.3.959. I updated all packages. I updated the bibliometrix package using the code 'devtools::install_github("massimoaria/bibliometrix")' .

My code is as follow: easypackages::packages('bibliometrix','rio') wosfiles <-'F:/data/b7944_1-500.txt' Bw <- convert2df(file = wosfiles, dbsource = 'wos', format = 'plaintext') lcs <- localCitations(Bw)

The results are as follow: -----start----- WOS DB: Searching local citations (LCS) by reference items (SR) and DOIs...

Analyzing 309867 reference items... error: x must be a vector, not a data.frame/bibliometrixDB object. Run rlang::last_error() to see where the error occurred. ------end------

Run 'rlang::error()'. The results are as follow: -----start----- <error/vctrs_error_scalar_type> x must be a vector, not a data.frame/bibliometrixDB object. Backtrace:

  1. bibliometrix::localCitations(Bw1)
  2. bibliometrix::histNetwork(...)
  3. bibliometrix:::wos(...)
    1. dplyr::select(...)
    2. tidyselect::eval_select(expr(c(...)), .data)
    3. tidyselect:::eval_select_impl(...)
    4. vctrs::vec_assert(x)
    5. vctrs:::stop_scalar_type(x, arg)
    6. vctrs:::stop_vctrs(msg, "vctrs_error_scalar_type", actual = x) Run rlang::last_trace() to see the full context. ------end------

My version of vctrs package is 0.3.1(it is the newest version).

I tried several methods to explore this issue:

  1. I run 'example(localCitations)', it worked.
  2. And if I run these codes: 'rio::export(Bw1,file = 'F:/data/bw1.xlsx') m1 <- import('F:/data/bw1.xlsx') lcs <- localCitations(m1)', it also worked.
  3. I also tried to do this in the R 3.6.3 version, it also worked.

I don't known why it does not work in the R 4.0.1 version?

Thanks for your excellent work best, Yunlong Yu

My data: b7944_1-500.txt

massimoaria commented 4 years ago

Unfortunately, I am not able to identify the issue.

Using my MacBook 10.15 with Rstudio 1.3.959, R 4.0.1, and all R packages updated, your script works fine. Here my results:

wosfiles <-'b7944_1-500.txt' Bw <- convert2df(file = wosfiles, dbsource = 'wos', format = 'plaintext')

Converting your wos collection into a bibliographic dataframe

Done!

Generating affiliation field tag AU_UN from C1: Done!

lcs <- localCitations(Bw)

WOS DB: Searching local citations (LCS) by reference items (SR) and DOIs...

Analyzing 10666 reference items...

Found 174 documents with no empty Local Citations (LCS)

I think the issue depends on a bug of the rlang package included in the R 4.0 version.

yuyllove commented 4 years ago

Thanks. 发自我的华为手机-------- 原始邮件 --------发件人： Massimo Aria notifications@github.com日期： 2020年6月12日周五 15:14收件人： massimoaria/bibliometrix bibliometrix@noreply.github.com抄送： yuyllove yuyllove@yeah.net, Comment comment@noreply.github.com主 题： Re: [massimoaria/bibliometrix] Error in importing data from PubMed (#108) Unfortunately, I am not able to identify the issue. Using my MacBook 10.15 with Rstudio 1.3.959 and R 4.0.1, the functions work fine.

wosfiles <-'b7944_1-500.txt' Bw <- convert2df(file = wosfiles, dbsource = 'wos', format = 'plaintext')

Converting your wos collection into a bibliographic dataframe Done! Generating affiliation field tag AU_UN from C1: Done!

lcs <- localCitations(Bw)

WOS DB: Searching local citations (LCS) by reference items (SR) and DOIs... Analyzing 10666 reference items... Found 174 documents with no empty Local Citations (LCS)

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massimoaria commented 4 years ago

I discovered that the issue is due to a bug of dplyr and R 4.0. I have just added a commit that solves it.