* using log directory 'd:/RCompile/CRANincoming/R-devel/comts.Rcheck'
* using R Under development (unstable) (2025-02-12 r87715 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'comts/DESCRIPTION' ... OK
* this is package 'comts' version '0.99.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [15s] NOTE
Maintainer: 'Xiang Zhou <zhouxiang221@mails.ucas.ac.cn>'

New submission

Non-FOSS package license (`use_mit_license()`, `use_gpl3_license()` or friends to pick a
license)

Possibly misspelled words in DESCRIPTION:
  Comts (2:8)
  GAM (8:70)

The Title field starts with the package name.
The Title field should be in title case. Current version is:
  'Comts: A pipeline for estimating the gene abundance in microbial community.'
In title case that is:
  'Comts: A Pipeline for Estimating the Gene Abundance in Microbial Community.'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'comts' 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
Malformed Title field: should not end in a period.
Non-standard license specification:
  `use_mit_license()`, `use_gpl3_license()` or friends to pick a
  license
Standardizable: FALSE
* 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 ... WARNING
Found the following files with non-ASCII characters:
  R/diamond_community.R
  R/hyd.diamond_community.R
  R/ribo_rpkm.R
  R/ter.diamond_community.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function 'tools::showNonASCIIfile' can help in finding non-ASCII
characters in files.
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  'ggplot2' 'ggplt2'
'library' or 'require' calls to packages already attached by Depends:
  'data.table' 'dplyr' 'magrittr' 'tidyr'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'ggplot2' 'ggplt2'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'data.table' 'dplyr' 'magrittr' 'tidyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
diamond_community: no visible global function definition for
  'read.table'
diamond_community: no visible global function definition for
  'install.packages'
diamond_community: no visible global function definition for 'fread'
diamond_community: no visible global function definition for '%>%'
diamond_community: no visible global function definition for
  'group_by_all'
diamond_community: no visible global function definition for 'count'
diamond_community: no visible global function definition for
  'left_join'
diamond_community: no visible global function definition for 'filter'
diamond_community: no visible binding for global variable 'tmp1'
diamond_community: no visible binding for global variable 'tmp2'
diamond_community: no visible global function definition for 'group_by'
diamond_community: no visible binding for global variable 'gene'
diamond_community: no visible global function definition for 'mutate'
diamond_community: no visible binding for global variable 'tmp_RPKM'
diamond_community: no visible binding for global variable 'bitscore'
diamond_community: no visible binding for global variable 'qcovhsp'
diamond_community: no visible binding for global variable 'sseq_id'
diamond_community: no visible binding for global variable 'RPKM'
diamond_community: no visible global function definition for
  'write.table'
diamond_community: no visible binding for global variable 'sample_name'
diamond_community: no visible global function definition for
  'pivot_wider'
diamond_community: no visible global function definition for
  'pivot_longer'
diamond_community: no visible global function definition for 'ggplot'
diamond_community: no visible global function definition for 'aes'
diamond_community: no visible global function definition for
  'geom_tile'
diamond_community: no visible binding for global variable 'val'
diamond_community: no visible global function definition for
  'scale_fill_gradientn'
diamond_community: no visible global function definition for 'theme'
diamond_community: no visible global function definition for
  'element_blank'
diamond_community: no visible global function definition for
  'element_text'
diamond_community: no visible global function definition for
  'element_line'
diamond_community: no visible global function definition for 'ggsave'
hyd.diamond_community: no visible global function definition for
  'read.table'
hyd.diamond_community: no visible global function definition for
  'install.packages'
hyd.diamond_community: no visible global function definition for
  'fread'
hyd.diamond_community: no visible global function definition for '%>%'
hyd.diamond_community: no visible global function definition for
  'group_by_all'
hyd.diamond_community: no visible global function definition for
  'count'
hyd.diamond_community: no visible global function definition for
  'left_join'
hyd.diamond_community: no visible global function definition for
  'filter'
hyd.diamond_community: no visible binding for global variable 'id'
hyd.diamond_community: no visible binding for global variable 'pident'
hyd.diamond_community: no visible binding for global variable 'qcovhsp'
hyd.diamond_community: no visible global function definition for
  'group_by'
hyd.diamond_community: no visible binding for global variable 'gene'
hyd.diamond_community: no visible global function definition for
  'mutate'
hyd.diamond_community: no visible binding for global variable
  'tmp_RPKM'
hyd.diamond_community: no visible binding for global variable
  'bitscore'
hyd.diamond_community: no visible binding for global variable 'sseq_id'
hyd.diamond_community: no visible binding for global variable 'RPKM'
hyd.diamond_community: no visible global function definition for
  'write.table'
hyd.diamond_community: no visible binding for global variable
  'sample_name'
hyd.diamond_community: no visible global function definition for
  'pivot_wider'
hyd.diamond_community: no visible global function definition for
  'pivot_longer'
hyd.diamond_community: no visible global function definition for
  'ggplot'
hyd.diamond_community: no visible global function definition for 'aes'
hyd.diamond_community: no visible global function definition for
  'geom_tile'
hyd.diamond_community: no visible binding for global variable 'val'
hyd.diamond_community: no visible global function definition for
  'scale_fill_gradientn'
hyd.diamond_community: no visible global function definition for
  'theme'
hyd.diamond_community: no visible global function definition for
  'element_blank'
hyd.diamond_community: no visible global function definition for
  'element_text'
hyd.diamond_community: no visible global function definition for
  'element_line'
hyd.diamond_community: no visible global function definition for
  'ggsave'
ribo_rpkm: no visible global function definition for 'install.packages'
ribo_rpkm: no visible global function definition for 'read.table'
ribo_rpkm: no visible global function definition for 'filter'
ribo_rpkm: no visible binding for global variable 'qcovhsp'
ribo_rpkm: no visible binding for global variable 'bitscore'
ribo_rpkm: no visible global function definition for '%>%'
ribo_rpkm: no visible global function definition for 'group_by_all'
ribo_rpkm: no visible global function definition for 'count'
ribo_rpkm: no visible global function definition for 'group_by'
ribo_rpkm: no visible binding for global variable 'sseq_id'
ribo_rpkm: no visible global function definition for 'mutate'
ribo_rpkm: no visible binding for global variable 'RPKM'
ribo_rpkm: no visible global function definition for 'write.table'
ribo_rpkm: no visible binding for global variable 'T_RPKM'
ribo_rpkm2com: no visible global function definition for 'read.table'
ribo_rpkm2com: no visible global function definition for
  'install.packages'
ribo_rpkm2com: no visible global function definition for '%>%'
ribo_rpkm2com: no visible global function definition for 'group_by'
ribo_rpkm2com: no visible binding for global variable 'sample_name'
ribo_rpkm2com: no visible global function definition for 'mutate'
ribo_rpkm2com: no visible binding for global variable 'T_RPKM'
ribo_rpkm2com: no visible global function definition for 'write.table'
ter.diamond_community: no visible global function definition for
  'read.table'
ter.diamond_community: no visible global function definition for
  'install.packages'
ter.diamond_community: no visible global function definition for
  'fread'
ter.diamond_community: no visible global function definition for '%>%'
ter.diamond_community: no visible global function definition for
  'group_by_all'
ter.diamond_community: no visible global function definition for
  'count'
ter.diamond_community: no visible global function definition for
  'filter'
ter.diamond_community: no visible binding for global variable 'gene'
ter.diamond_community: no visible binding for global variable 'pident'
ter.diamond_community: no visible binding for global variable 'qcovhsp'
ter.diamond_community: no visible global function definition for
  'group_by'
ter.diamond_community: no visible global function definition for
  'mutate'
ter.diamond_community: no visible binding for global variable
  'tmp_RPKM'
ter.diamond_community: no visible binding for global variable
  'bitscore'
ter.diamond_community: no visible binding for global variable 'sseq_id'
ter.diamond_community: no visible binding for global variable 'RPKM'
ter.diamond_community: no visible global function definition for
  'write.table'
ter.diamond_community: no visible binding for global variable
  'sample_name'
ter.diamond_community: no visible global function definition for
  'pivot_wider'
ter.diamond_community: no visible global function definition for
  'pivot_longer'
ter.diamond_community: no visible global function definition for
  'ggplot'
ter.diamond_community: no visible global function definition for 'aes'
ter.diamond_community: no visible global function definition for
  'geom_tile'
ter.diamond_community: no visible binding for global variable 'val'
ter.diamond_community: no visible global function definition for
  'scale_fill_gradientn'
ter.diamond_community: no visible global function definition for
  'theme'
ter.diamond_community: no visible global function definition for
  'element_blank'
ter.diamond_community: no visible global function definition for
  'element_text'
ter.diamond_community: no visible global function definition for
  'element_line'
ter.diamond_community: no visible global function definition for
  'ggsave'
Undefined global functions or variables:
  %>% RPKM T_RPKM aes bitscore count element_blank element_line
  element_text filter fread gene geom_tile ggplot ggsave group_by
  group_by_all id install.packages left_join mutate pident pivot_longer
  pivot_wider qcovhsp read.table sample_name scale_fill_gradientn
  sseq_id theme tmp1 tmp2 tmp_RPKM val write.table
Consider adding
  importFrom("stats", "filter")
  importFrom("utils", "install.packages", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'diamond_community.Rd':
  \examples lines wider than 100 characters:
     diamond_community(input_reads = "your/reads/data/sample_1.fastq",result = "sample_1",threads = 40,diamond_db = "your/database/ter_hydB- ... [TRUNCATED]

Rd file 'hyd.diamond_community.Rd':
  \examples lines wider than 100 characters:
     diamond_community(input_reads = "your/reads/data/sample_1.fastq",result = "sample_1",threads = 40,diamond_db = "your/database/hyddb.all ... [TRUNCATED]

Rd file 'ribo_rpkm.Rd':
  \examples lines wider than 100 characters:
     ribo_rpkm(input_reads = "your/reads/data/sample_1.fastq",result = "sample_1",threads = 40,UCSG_db = "your/database/Ribo_14.dmnd",skip_f ... [TRUNCATED]

Rd file 'ribo_rpkm2com.Rd':
  \examples lines wider than 100 characters:
     function(input_geneset = "your/data/geneset.RPKM.txt",input_ribo_rpkm = "your/database/Ribo.RPKM.txt",output = "geneset.GAM.txt")

Rd file 'ter.diamond_community.Rd':
  \examples lines wider than 100 characters:
     diamond_community(input_reads = "your/reads/data/sample_1.fastq",result = "sample_1",threads = 40,diamond_db = "your/database/ter_hydB- ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'comts-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diamond_community
> ### Title: To calculate the gene abundance in microbial community (GAM,%).
> ### Aliases: diamond_community
> 
> ### ** Examples
> 
> diamond_community(input_reads = "your/reads/data/sample_1.fastq",result = "sample_1",threads = 40,diamond_db = "your/database/ter_hydB-aprA.dmnd",UCSG_db = "your/database/Ribo_14.dmnd",min_length = 90,filter_condition = "default")
your/database/Ribo_14.dmnd: cannot open `your/database/Ribo_14.dmnd' (No such file or directory)
>:                          cannot open `>' (No such file or directory)
tmp.txt:                    cannot open `tmp.txt' (No such file or directory)
/usr/bin/sed: can't read tmp.txt: No such file or directory
/usr/bin/sed: can't read tmp.txt: No such file or directory
Warning in file(file, "rt") :
  cannot open file 'tmp.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: diamond_community -> read.table -> file
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(comts)
  Loading required package: tidyr
  
  Attaching package: 'tidyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following object is masked from 'package:tidyr':
  
      extract
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  Loading required package: data.table
  
  Attaching package: 'data.table'
  
  The following objects are masked from 'package:dplyr':
  
      between, first, last
  
  > 
  > test_check("comts")
  Error in `test_dir()`:
  ! No test files found
  Backtrace:
      ▆
   1. └─testthat::test_check("comts")
   2.   └─testthat::test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
   3.     └─rlang::abort("No test files found")
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [26s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 ERRORs, 2 WARNINGs, 4 NOTEs