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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:orthogene.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings orthogene_1.13.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/orthogene.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 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
* using option '--no-vignettes'
* checking for file 'orthogene/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'orthogene' version '1.13.0'
* package encoding: UTF-8
* 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 whether package 'orthogene' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... 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 ... 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) aggregate_mapped_genes.Rd:37-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate_mapped_genes.Rd:41-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate_mapped_genes.Rd:45-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_gene_df_type.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_gene_df_type.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_gene_df_type.Rd:18: Lost braces
    18 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.}
       |           ^
checkRd: (-1) check_gene_df_type.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_gene_df_type.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_gene_df_type.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_gene_df_type.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:38: Lost braces
    38 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.}
       |           ^
checkRd: (-1) convert_orthologs.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:101-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:105-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:114-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:118-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:156-159: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:160-163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert_orthologs.Rd:164-167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_background.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_background.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_background.Rd:66-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_background.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_background.Rd:72-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_background.Rd:76-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_silhouettes.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_silhouettes.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_silhouettes.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_silhouettes.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gprofiler_namespace.Rd:20: Lost braces
    20 | Available namespaces used by link[gprofiler2]{gconvert}.
       |                                              ^
checkRd: (-1) infer_species.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) infer_species.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) infer_species.Rd:26: Lost braces
    26 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.}
       |           ^
checkRd: (-1) infer_species.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) infer_species.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) infer_species.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) infer_species.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) infer_species.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) infer_species.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) infer_species.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) map_orthologs.Rd:57-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) map_orthologs.Rd:61-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) map_orthologs.Rd:65-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) map_orthologs_custom.Rd:21-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) map_orthologs_custom.Rd:25-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) map_orthologs_custom.Rd:29-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) orthogene-package.Rd:10-11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) orthogene-package.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:62-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:65-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:68-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:72-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:75-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:83-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:87-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:90-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:93-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:96-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:100-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_orthotree.Rd:135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_orthotree.Rd:136: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_orthotree.Rd:137-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_orthotree.Rd:139-140: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_orthotree.Rd:141: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_orthotree.Rd:142: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_orthotree.Rd:143: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_orthotree.Rd:144: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prepare_tree.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_tree.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_tree.Rd:34-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_tree.Rd:38-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_tree.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:60-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:67-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:73-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:77-82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:112: Lost braces
   112 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.}
       |           ^
checkRd: (-1) report_orthologs.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:127-128: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:135-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:138-139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:140-141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:180-183: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:184-187: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:188-191: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report_orthologs.Rd:204: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) report_orthologs.Rd:205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) set_gprofiler.Rd:18: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'run_benchmark.Rd':
  'benchmark_homologene' 'benchmark_gprofiler' 'benchmark_babelgene'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plot_orthotree 55.22   2.89   60.63
prepare_tree   20.34   0.51   21.78
all_genes       4.34   0.22    9.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/orthogene.Rcheck/00check.log'
for details.