* using log directory ‘/srv/hornik/tmp/CRAN_pretest/XYlabmiR.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.1 (1)
    Debian flang-new version 19.1.1 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘XYlabmiR/DESCRIPTION’ ... OK
* this is package ‘XYlabmiR’ version ‘0.0.0.9000’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Xuyang Yi <627251009@qq.com>’

New submission

Version contains large components (0.0.0.9000)

Possibly misspelled words in DESCRIPTION:
  mRNA (2:14)
  miRNA (2:8, 10:53)

The Title field should be in title case. Current version is:
  ‘miRNA-mRNA-protein analysis’
In title case that is:
  ‘miRNA-mRNA-Protein Analysis’

Size of tarball: 87424018 bytes
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘XYlabmiR’ can be installed ... [11s/11s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/15s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [49s/157s] ERROR
Running examples in ‘XYlabmiR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculate_node_importance
> ### Title: Title
> ### Aliases: calculate_node_importance
> 
> ### ** Examples
> 
> library(data.table)  # 用于读取数据
> library(igraph)      # 用于网络分析

Attaching package: ‘igraph’

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

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

> library(biomaRt)     # 用于基因ID转换
> library(ggraph)
Loading required package: ggplot2
> library(R.utils)
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.26.0 (2024-01-24 05:12:50 UTC) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following object is masked from ‘package:R.methodsS3’:

    throw

The following object is masked from ‘package:igraph’:

    hierarchy

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

    getClasses, getMethods

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

    attach, detach, load, save

R.utils v2.12.3 (2023-11-18 01:00:02 UTC) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

    timestamp

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

    cat, commandArgs, getOption, isOpen, nullfile, parse, use, warnings

> # 读取 protein_file 和 mirna_file
> protein_file <- system.file("extdata", "9606.protein.links.v12.0.txt.gz", package = "XYlabmiR")
> 
> # 假设 gene_list 是一个已有的基因列表
> gene_list <- c("EGFR", "EPCAM", "VIM")
> 
> calculate_node_importance(gene_list, protein_file, use_full_data = TRUE)
Ensembl site unresponsive, trying asia mirror
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached: [asia.ensembl.org:443] Operation timed out after 60002 milliseconds with 0 bytes received
Backtrace:
     ▆
  1. └─XYlabmiR::calculate_node_importance(...)
  2.   └─biomaRt::useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
  3.     └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
  4.       └─biomaRt:::.getAttributes(mart, verbose = verbose)
  5.         └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes")
  6.           └─biomaRt:::bmRequest(...)
  7.             └─httr2::req_perform(request)
  8.               └─base::tryCatch(...)
  9.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.                     └─value[[3L]](cond)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
calculate_final_weights 27.875   2.71  60.822
* checking PDF version of manual ... [4s/3s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
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! LaTeX Error: Unicode character 网 (U+7F51)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 络 (U+7EDC)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 分 (U+5206)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 析 (U+6790)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 用 (U+7528)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 于 (U+4E8E)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 基 (U+57FA)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 因 (U+56E0)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 转 (U+8F6C)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 换 (U+6362)
               not set up for use with LaTeX.

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! LaTeX Error: Unicode character 读 (U+8BFB)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 取 (U+53D6)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 和 (U+548C)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 假 (U+5047)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 设 (U+8BBE)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 是 (U+662F)
               not set up for use with LaTeX.

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! LaTeX Error: Unicode character 一 (U+4E00)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 个 (U+4E2A)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 已 (U+5DF2)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 有 (U+6709)
               not set up for use with LaTeX.

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! LaTeX Error: Unicode character 的 (U+7684)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 基 (U+57FA)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 因 (U+56E0)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 列 (U+5217)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
! LaTeX Error: Unicode character 表 (U+8868)
               not set up for use with LaTeX.

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Type  H <return>  for immediate help.
* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘XYlabmiR-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 2 NOTEs