* using log directory 'd:/RCompile/CRANincoming/R-devel/linkage.Rcheck'
* using R Under development (unstable) (2024-05-30 r86651 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'linkage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'linkage' version '1.2.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [43s] ERROR
Maintainer: 'Siwen Xu<siwxu@gdpu.edu.cn>'

New submission

Conflicting package names (submitted: linkage, existing: Linkage [https://CRAN.R-project.org])

Possibly misspelled words in DESCRIPTION:
  ATAC (3:45, 13:176)
  CREs (13:161, 13:292, 13:325, 13:477)
  omics (13:355)

Unknown, possibly misspelled, fields in DESCRIPTION:
  'Remotes'

Package has a FOSS license but eventually depends on the following
package which restricts use:
  CNEr

Suggests or Enhances not in mainstream repositories:
  LinkageData

The Title field should be in title case. Current version is:
'An R shiny web server for linking of ATAC-seq to gene expression data'
In title case that is:
'An R Shiny Web Server for Linking of ATAC-Seq to Gene Expression Data'

The Description field should not start with the package name,
  'This package' or similar.

Size of tarball: 14517370 bytes
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'LinkageData'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'linkage' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Maintainer field differs from that derived from Authors@R
  Maintainer: 'Siwen Xu<siwxu@gdpu.edu.cn>'
  Authors@R:  'Zenghui Liu <2470587020@qq.com>'

* 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 ... [16s] OK
* checking whether the package can be loaded with stated dependencies ... [13s] OK
* checking whether the package can be unloaded cleanly ... [15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s] OK
* checking whether the namespace can be unloaded cleanly ... [17s] OK
* checking loading without being on the library search path ... [17s] OK
* checking whether startup messages can be suppressed ... [15s] 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 ... [67s] NOTE
AnnoUpsetPlot: no visible binding for global variable 'annotation'
AnnoUpsetPlot: no visible binding for global variable 'GenreMember'
BuildGRNs: no visible global function definition for 'data'
BuildGRNs: no visible binding for global variable 'Mus.PFMatrixList'
BuildGRNs: no visible binding for global variable 'Mus.pwm_library_dt'
BuildGRNs: no visible global function definition for 'cor.test'
BuildGRNs: no visible global function definition for 'p.adjust'
BuildGRNs: no visible global function definition for 'new'
CombinePlots : <anonymous>: no visible global function definition for
  'NoLegend'
CorrPlot: no visible binding for global variable 'peak'
CreateLinkageObject: no visible global function definition for 'data'
CreateLinkageObject: no visible binding for global variable
  'Homo.position'
CreateLinkageObject: no visible binding for global variable
  'Mus.position'
CreateLinkageObject: no visible global function definition for
  'everything'
CreateLinkageObject: no visible global function definition for 'new'
EnrichWordCloud: no visible global function definition for 'read.table'
FilterGRNs: no visible global function definition for 'new'
GOEnrichment: no visible global function definition for 'data'
GOEnrichment: no visible binding for global variable 'Homo.position'
GOEnrichment: no visible binding for global variable 'Mus.position'
KEGGEnrichment: no visible global function definition for 'data'
KEGGEnrichment: no visible binding for global variable 'Homo.position'
KEGGEnrichment: no visible binding for global variable 'Mus.position'
Linkage.UIO: no visible binding for global variable 'name'
MotifEnrichment: no visible global function definition for 'data'
MotifEnrichment: no visible binding for global variable
  'Mus.PFMatrixList'
MotifEnrichment: no visible binding for global variable
  'Mus.pwm_library_dt'
PeakAnnotation: no visible global function definition for 'new'
RegulatoryPeak: no visible global function definition for 'cor.test'
RegulatoryPeak: no visible global function definition for 'p.adjust'
RegulatoryPeak: no visible global function definition for 'new'
TrackPlot: no visible binding for global variable 'gene'
TrackPlot: no visible binding for global variable 'group'
VisualGRNs: no visible global function definition for 'na.omit'
VisualGRNs: no visible binding for global variable 'gene'
VisualGRNs: no visible binding for global variable 'TF'
VisualGRNs: no visible binding for global variable 'id'
VisualGRNs: no visible global function definition for 'everything'
VisualGRNs: no visible binding for global variable 'a'
show,LinkageObject: no visible binding for global variable
  'LinkageObject'
Undefined global functions or variables:
  GenreMember Homo.position LinkageObject Mus.PFMatrixList Mus.position
  Mus.pwm_library_dt NoLegend TF a annotation cor.test data everything
  gene group id na.omit name new p.adjust peak read.table
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "cor.test", "na.omit", "p.adjust")
  importFrom("utils", "data", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found the following calls to data() loading into the global environment:
File 'linkage/R/CreateLinkageObject.R':
  data("Homo.position")
  data("Mus.position")
File 'linkage/R/GO.KEGG.Enrichment.R':
  data("Homo.position")
  data("Mus.position")
  data("Homo.position")
  data("Mus.position")
File 'linkage/R/MotifAnalysis.R':
  data("PFMatrixList")
  data("pwm_library_dt")
  data("Mus.PFMatrixList")
  data("Mus.pwm_library_dt")
  data("PFMatrixList")
  data("pwm_library_dt")
  data("Mus.PFMatrixList")
  data("Mus.pwm_library_dt")
See section 'Good practice' in '?data'.

Found if() conditions comparing class() to string:
File 'linkage/R/RegulatoryPeaks.R': if (class(LinkageObject) != "LinkageObject") ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [13s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [63s] ERROR
Running examples in 'linkage-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BuildGRNs
> ### Title: MotifAnalysis.
> ### Aliases: BuildGRNs
> 
> ### ** Examples
> 
> library(linkage)
> library(LinkageData)
Error in library(LinkageData) : there is no package called 'LinkageData'
Execution halted
Examples with CPU (user + system) or elapsed time > 10s
               user system elapsed
AnnoUpsetPlot 41.71   2.14    45.6
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: 'devtools'
'library' or 'require' call not declared from: 'devtools'
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [19s] ERROR
Error(s) in re-building vignettes:
--- re-building 'Enrichment.Rmd' using rmarkdown

Quitting from lines 42-60 [unnamed-chunk-2] (Enrichment.Rmd)
Error: processing vignette 'Enrichment.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building 'Enrichment.Rmd'

--- re-building 'GRN-tutorial.Rmd' using rmarkdown

Quitting from lines 41-71 [unnamed-chunk-2] (GRN-tutorial.Rmd)
Error: processing vignette 'GRN-tutorial.Rmd' failed with diagnostics:
there is no package called 'LinkageData'
--- failed re-building 'GRN-tutorial.Rmd'

--- re-building 'Install.Rmd' using rmarkdown
--- finished re-building 'Install.Rmd'

--- re-building 'Linkage.Rmd' using rmarkdown
--- finished re-building 'Linkage.Rmd'

--- re-building 'TCGA-BRCA-guided-tutorial.Rmd' using rmarkdown

Quitting from lines 47-59 [unnamed-chunk-2] (TCGA-BRCA-guided-tutorial.Rmd)
Error: processing vignette 'TCGA-BRCA-guided-tutorial.Rmd' failed with diagnostics:
there is no package called 'LinkageData'
--- failed re-building 'TCGA-BRCA-guided-tutorial.Rmd'

SUMMARY: processing the following files failed:
  'Enrichment.Rmd' 'GRN-tutorial.Rmd' 'TCGA-BRCA-guided-tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... OK
* DONE
Status: 3 ERRORs, 4 NOTEs