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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:orthogene.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings orthogene_1.1.2.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/orthogene.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'orthogene/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'orthogene' version '1.1.2'
* 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 R 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 ... OK
* 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 ... OK
* 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 ... ERROR
Running examples in 'orthogene-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_orthotree
> ### Title: Create a phylogenetic tree of shared orthologs
> ### Aliases: plot_orthotree
> 
> ### ** Examples
> 
> orthotree <- orthogene::plot_orthotree(species = c("human","monkey","mouse"))
Gathering ortholog reports.

-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--

=========== REPORT SUMMARY ===========

19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.

-- monkey
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: monkey
Common name mapping found for monkey
1 organism identified from search: 9544
Gene table with 16,843 rows retrieved.
Returning all 16,843 genes from monkey.
--
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
16,843 genes extracted.
Converting monkey ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: monkey
Common name mapping found for monkey
1 organism identified from search: 9544
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
15,675 genes extracted.
Extracting genes from ortholog_gene.
15,675 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 203 genes that have multiple input_gene per ortholog_gene.
Dropping 221 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

=========== REPORT SUMMARY ===========

Total genes dropped after convert_orthologs :
   1,730 / 16,816 (10%)
Total genes remaining after convert_orthologs :
   15,086 / 16,816 (90%)
--

=========== REPORT SUMMARY ===========

15,075 / 16,816 (89.65%) target_species genes remain after ortholog conversion.
15,075 / 19,129 (78.81%) reference_species genes remain after ortholog conversion.

-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

=========== REPORT SUMMARY ===========

Total genes dropped after convert_orthologs :
   4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
   16,482 / 21,207 (78%)
--

=========== REPORT SUMMARY ===========

16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Loading required namespace: phytools
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Adding ortholog_gene col to gene_df.
  
  =========== REPORT SUMMARY ===========
  
  Total genes dropped after convert_orthologs :
     4,725 / 21,207 (22%)
  Total genes remaining after convert_orthologs :
     16,482 / 21,207 (78%)
  --
  
  =========== REPORT SUMMARY ===========
  
  16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
  16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
  Loading required namespace: phytools
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/orthogene.Rcheck/00check.log'
for details.