##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:orthogene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings orthogene_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/orthogene.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘orthogene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘orthogene’ version ‘1.12.0’
* 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 for sufficient/correct file permissions ... 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    58.025  2.426  74.363
prepare_tree      17.355  0.472  17.839
all_genes          3.749  0.160   9.366
convert_orthologs  1.221  0.066   5.827
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/orthogene.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL orthogene
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘orthogene’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (orthogene)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(orthogene)
> 
> test_check("orthogene")
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
Mapping many:many rows.
1110012L19Rik : converting 1 row(s) --> 2 row(s).
2610034B18Rik : converting 1 row(s) --> 2 row(s).
AA415398 : converting 1 row(s) --> 2 row(s).
Ankhd1 : converting 1 row(s) --> 2 row(s).
Anxa8 : converting 1 row(s) --> 2 row(s).
Apitd1 : converting 1 row(s) --> 2 row(s).
Arhgap8 : converting 1 row(s) --> 2 row(s).
Asb3 : converting 1 row(s) --> 2 row(s).
C4a : converting 1 row(s) --> 2 row(s).
C4b : converting 1 row(s) --> 2 row(s).
Cbs : converting 1 row(s) --> 2 row(s).
Ccz1 : converting 1 row(s) --> 2 row(s).
Ckmt1 : converting 1 row(s) --> 2 row(s).
Coro7 : converting 1 row(s) --> 2 row(s).
Cryaa : converting 1 row(s) --> 2 row(s).
D10Jhu81e : converting 1 row(s) --> 2 row(s).
F8a : converting 1 row(s) --> 3 row(s).
Fam21 : converting 1 row(s) --> 2 row(s).
Fcgr4 : converting 1 row(s) --> 2 row(s).
Gpr89 : converting 1 row(s) --> 2 row(s).
Gstt2 : converting 1 row(s) --> 2 row(s).
H3f3a : converting 1 row(s) --> 2 row(s).
H3f3b : converting 1 row(s) --> 2 row(s).
Hspa1a : converting 1 row(s) --> 2 row(s).
Icosl : converting 1 row(s) --> 2 row(s).
Klhl23 : converting 1 row(s) --> 2 row(s).
Mrpl23 : converting 1 row(s) --> 2 row(s).
Nbl1 : converting 1 row(s) --> 2 row(s).
Nomo1 : converting 1 row(s) --> 3 row(s).
Pmf1 : converting 1 row(s) --> 2 row(s).
Pom121 : converting 1 row(s) --> 2 row(s).
Pramef8 : converting 1 row(s) --> 2 row(s).
Prodh : converting 1 row(s) --> 2 row(s).
Ranbp2 : converting 1 row(s) --> 7 row(s).
Serf1 : converting 1 row(s) --> 2 row(s).
Sgk3 : converting 1 row(s) --> 2 row(s).
Slx1b : converting 1 row(s) --> 2 row(s).
Smn1 : converting 1 row(s) --> 2 row(s).
Spin2d : converting 1 row(s) --> 2 row(s).
Aggregating rows using: monocle3
Converting obj to sparseMatrix.
Matrix aggregated:
  - Input: 15,259 x 7 
  - Output: 13,316 x 7
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: mmusculus
477 / 482 (98.96%) genes mapped.
Aggregating rows using: monocle3
Converting obj to sparseMatrix.
Matrix aggregated:
  - Input: 482 x 7 
  - Output: 92 x 7
Converting to DelayedArray.
Loading required namespace: DelayedArray
Mapping many:many rows.
Converting obj to sparseMatrix.
1110012L19Rik : converting 1 row(s) --> 2 row(s).
2610034B18Rik : converting 1 row(s) --> 2 row(s).
AA415398 : converting 1 row(s) --> 2 row(s).
Ankhd1 : converting 1 row(s) --> 2 row(s).
Anxa8 : converting 1 row(s) --> 2 row(s).
Apitd1 : converting 1 row(s) --> 2 row(s).
Arhgap8 : converting 1 row(s) --> 2 row(s).
Asb3 : converting 1 row(s) --> 2 row(s).
C4a : converting 1 row(s) --> 2 row(s).
C4b : converting 1 row(s) --> 2 row(s).
Cbs : converting 1 row(s) --> 2 row(s).
Ccz1 : converting 1 row(s) --> 2 row(s).
Ckmt1 : converting 1 row(s) --> 2 row(s).
Coro7 : converting 1 row(s) --> 2 row(s).
Cryaa : converting 1 row(s) --> 2 row(s).
D10Jhu81e : converting 1 row(s) --> 2 row(s).
F8a : converting 1 row(s) --> 3 row(s).
Fam21 : converting 1 row(s) --> 2 row(s).
Fcgr4 : converting 1 row(s) --> 2 row(s).
Gpr89 : converting 1 row(s) --> 2 row(s).
Gstt2 : converting 1 row(s) --> 2 row(s).
H3f3a : converting 1 row(s) --> 2 row(s).
H3f3b : converting 1 row(s) --> 2 row(s).
Hspa1a : converting 1 row(s) --> 2 row(s).
Icosl : converting 1 row(s) --> 2 row(s).
Klhl23 : converting 1 row(s) --> 2 row(s).
Mrpl23 : converting 1 row(s) --> 2 row(s).
Nbl1 : converting 1 row(s) --> 2 row(s).
Nomo1 : converting 1 row(s) --> 3 row(s).
Pmf1 : converting 1 row(s) --> 2 row(s).
Pom121 : converting 1 row(s) --> 2 row(s).
Pramef8 : converting 1 row(s) --> 2 row(s).
Prodh : converting 1 row(s) --> 2 row(s).
Ranbp2 : converting 1 row(s) --> 7 row(s).
Serf1 : converting 1 row(s) --> 2 row(s).
Sgk3 : converting 1 row(s) --> 2 row(s).
Slx1b : converting 1 row(s) --> 2 row(s).
Smn1 : converting 1 row(s) --> 2 row(s).
Spin2d : converting 1 row(s) --> 2 row(s).
Aggregating rows using: monocle3
Converting obj to sparseMatrix.
Matrix aggregated:
  - Input: 15,259 x 7 
  - Output: 13,316 x 7
Converting to DelayedArray.
Converting mouse ==> human orthologs using: gprofiler
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: mmusculus
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: hsapiens
Mapping many:many rows.
Converting obj to sparseMatrix.
1600029O15Rik : converting 1 row(s) --> 2 row(s).
1700030C10Rik : converting 1 row(s) --> 2 row(s).
1700086L19Rik : converting 1 row(s) --> 2 row(s).
1810014B01Rik : converting 1 row(s) --> 2 row(s).
2610005L07Rik : converting 1 row(s) --> 2 row(s).
2810025M15Rik : converting 1 row(s) --> 2 row(s).
2810047C21Rik1 : converting 1 row(s) --> 2 row(s).
4930503E24Rik : converting 1 row(s) --> 2 row(s).
4930519F16Rik : converting 1 row(s) --> 2 row(s).
4931440P22Rik : converting 1 row(s) --> 2 row(s).
4933427D14Rik : converting 1 row(s) --> 2 row(s).
6330549D23Rik : converting 1 row(s) --> 2 row(s).
6820431F20Rik : converting 1 row(s) --> 2 row(s).
9030619P08Rik : converting 1 row(s) --> 2 row(s).
A530058N18Rik : converting 1 row(s) --> 2 row(s).
Adat3 : converting 1 row(s) --> 2 row(s).
Ahcy : converting 1 row(s) --> 2 row(s).
Aldoa : converting 1 row(s) --> 2 row(s).
Alms1-ps2 : converting 1 row(s) --> 2 row(s).
Ap4b1 : converting 1 row(s) --> 2 row(s).
Arfip1 : converting 1 row(s) --> 2 row(s).
Arhgap26 : converting 1 row(s) --> 2 row(s).
Arxes1 : converting 1 row(s) --> 2 row(s).
Arxes2 : converting 1 row(s) --> 2 row(s).
Asnsd1 : converting 1 row(s) --> 2 row(s).
Atn1 : converting 1 row(s) --> 2 row(s).
Atp5o : converting 1 row(s) --> 2 row(s).
Bfar : converting 1 row(s) --> 2 row(s).
Btf3l4 : converting 1 row(s) --> 2 row(s).
Calm1 : converting 1 row(s) --> 3 row(s).
Calm2 : converting 1 row(s) --> 3 row(s).
Calm3 : converting 1 row(s) --> 3 row(s).
Cdk2ap1 : converting 1 row(s) --> 2 row(s).
Cplx2 : converting 1 row(s) --> 2 row(s).
Ctnnd1 : converting 1 row(s) --> 2 row(s).
Cycs : converting 1 row(s) --> 2 row(s).
Ddit3 : converting 1 row(s) --> 2 row(s).
Dohh : converting 1 row(s) --> 2 row(s).
Dpep2 : converting 1 row(s) --> 2 row(s).
Dpm1 : converting 1 row(s) --> 2 row(s).
Eno1 : converting 1 row(s) --> 2 row(s).
Erh : converting 1 row(s) --> 2 row(s).
Fam220a : converting 1 row(s) --> 2 row(s).
Fam78a : converting 1 row(s) --> 2 row(s).
Ftl1 : converting 1 row(s) --> 2 row(s).
Gcat : converting 1 row(s) --> 2 row(s).
Gm10548 : converting 1 row(s) --> 2 row(s).
Gm10653 : converting 1 row(s) --> 2 row(s).
Gm12238 : converting 1 row(s) --> 2 row(s).
Gm14326 : converting 1 row(s) --> 2 row(s).
Gm14327 : converting 1 row(s) --> 2 row(s).
Gm15760 : converting 1 row(s) --> 2 row(s).
Gm16523 : converting 1 row(s) --> 2 row(s).
Gm2011 : converting 1 row(s) --> 2 row(s).
Gm20257 : converting 1 row(s) --> 2 row(s).
Gm3086 : converting 1 row(s) --> 2 row(s).
Gm4832 : converting 1 row(s) --> 2 row(s).
Gm4956 : converting 1 row(s) --> 2 row(s).
Gm5089 : converting 1 row(s) --> 2 row(s).
Gm5113 : converting 1 row(s) --> 2 row(s).
Gm5124 : converting 1 row(s) --> 2 row(s).
Gm5468 : converting 1 row(s) --> 2 row(s).
Gm5766 : converting 1 row(s) --> 2 row(s).
Gm5885 : converting 1 row(s) --> 2 row(s).
Gm6498 : converting 1 row(s) --> 2 row(s).
Gm6578 : converting 1 row(s) --> 2 row(s).
Gm6793 : converting 1 row(s) --> 2 row(s).
Gm7903 : converting 1 row(s) --> 2 row(s).
H2-K2 : converting 1 row(s) --> 2 row(s).
Hist1h2ad : converting 1 row(s) --> 9 row(s).
Hist1h2an : converting 1 row(s) --> 9 row(s).
Hmgn2 : converting 1 row(s) --> 2 row(s).
Hspa1b : converting 1 row(s) --> 2 row(s).
Kpna2 : converting 1 row(s) --> 2 row(s).
Lrrc8a : converting 1 row(s) --> 2 row(s).
Map2k7 : converting 1 row(s) --> 2 row(s).
Mfap1a : converting 1 row(s) --> 2 row(s).
Mfap1b : converting 1 row(s) --> 2 row(s).
Myef2 : converting 1 row(s) --> 2 row(s).
Myl12a : converting 1 row(s) --> 2 row(s).
Myl12b : converting 1 row(s) --> 2 row(s).
Ndor1 : converting 1 row(s) --> 3 row(s).
Nnt : converting 1 row(s) --> 2 row(s).
Nrg1 : converting 1 row(s) --> 2 row(s).
Nudt10 : converting 1 row(s) --> 2 row(s).
Nudt11 : converting 1 row(s) --> 2 row(s).
Nudt8 : converting 1 row(s) --> 2 row(s).
Nutf2 : converting 1 row(s) --> 2 row(s).
Pagr1a : converting 1 row(s) --> 2 row(s).
Pam16 : converting 1 row(s) --> 2 row(s).
Pde2a : converting 1 row(s) --> 2 row(s).
Pfkfb2 : converting 1 row(s) --> 2 row(s).
Plp2 : converting 1 row(s) --> 2 row(s).
Pms2 : converting 1 row(s) --> 2 row(s).
Ppih : converting 1 row(s) --> 2 row(s).
Ppp4r1l-ps : converting 1 row(s) --> 2 row(s).
Psme2 : converting 1 row(s) --> 2 row(s).
Psme2b : converting 1 row(s) --> 2 row(s).
Ptp4a1 : converting 1 row(s) --> 2 row(s).
Raver1 : converting 1 row(s) --> 2 row(s).
Rnasek : converting 1 row(s) --> 2 row(s).
Rnaset2a : converting 1 row(s) --> 4 row(s).
Rnf26 : converting 1 row(s) --> 2 row(s).
Rpl10 : converting 1 row(s) --> 2 row(s).
Rpl34-ps1 : converting 1 row(s) --> 2 row(s).
Rpl35 : converting 1 row(s) --> 2 row(s).
Rpl36a : converting 1 row(s) --> 2 row(s).
Rps27 : converting 1 row(s) --> 2 row(s).
Rsc1a1 : converting 1 row(s) --> 2 row(s).
Serpina3h : converting 1 row(s) --> 2 row(s).
Sft2d1 : converting 1 row(s) --> 2 row(s).
Slc25a37 : converting 1 row(s) --> 2 row(s).
Slc2a4rg-ps : converting 1 row(s) --> 2 row(s).
Smok3b : converting 1 row(s) --> 2 row(s).
Snhg4 : converting 1 row(s) --> 2 row(s).
Snora75 : converting 1 row(s) --> 4 row(s).
Snord22 : converting 1 row(s) --> 2 row(s).
Snurf : converting 1 row(s) --> 2 row(s).
Spag6 : converting 1 row(s) --> 2 row(s).
St6galnac2 : converting 1 row(s) --> 2 row(s).
Styx : converting 1 row(s) --> 2 row(s).
Synj2bp : converting 1 row(s) --> 2 row(s).
T2 : converting 1 row(s) --> 2 row(s).
Taf9 : converting 1 row(s) --> 2 row(s).
Tgtp1 : converting 1 row(s) --> 2 row(s).
Timm10b : converting 1 row(s) --> 2 row(s).
Tmsb10 : converting 1 row(s) --> 2 row(s).
Tuba3a : converting 1 row(s) --> 2 row(s).
Txnl4a : converting 1 row(s) --> 2 row(s).
U05342 : converting 1 row(s) --> 2 row(s).
U2af1l4 : converting 1 row(s) --> 2 row(s).
Uba52 : converting 1 row(s) --> 2 row(s).
Vmn2r89 : converting 1 row(s) --> 2 row(s).
Yy2 : converting 1 row(s) --> 2 row(s).
Zbtb9 : converting 1 row(s) --> 2 row(s).
Zfp133-ps : converting 1 row(s) --> 2 row(s).
Zfp783 : converting 1 row(s) --> 2 row(s).
Zfp935 : converting 1 row(s) --> 2 row(s).
Zfp939 : converting 1 row(s) --> 2 row(s).
Zim3 : converting 1 row(s) --> 2 row(s).
Aggregating rows using: stats
Converting obj to sparseMatrix.
Matrix aggregated:
  - Input: 15,259 x 7 
  - Output: 12,617 x 7
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.
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: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: 7955
Gene table with 20,897 rows retrieved.
Returning all 20,897 genes from zebrafish.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: 7227
Gene table with 8,438 rows retrieved.
Returning all 8,438 genes from fly.
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: dmelanogaster
1 organism identified from search: 7227
Preparing babelgene::orthologs_df.
Gene table with 20,237 rows retrieved.
20237
Retrieving all genes using: gprofiler
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: dmelanogaster
1 organism identified from search: dmelanogaster
Gene table with 4,606 rows retrieved.
4606
WARNING: In order to set gene_output='rownames' while drop_nonorths=FALSE, must convert gene_df into a sparse matrix. Setting as_sparse=TRUE.
WARNING: In order to set gene_output='rownames' while non121_strategy='kbs', must convert gene_df into a sparse matrix. Setting as_sparse=TRUE.
Converting to DelayedArray.
Preparing gene_df.
sparseMatrix format detected.
Extracting genes from rownames.
15,259 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.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.
Converting obj to sparseMatrix.

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

Total genes dropped after convert_orthologs :
   2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
   13,243 / 15,259 (87%)
Preparing gene_df.
Dense matrix format detected.
Extracting genes from rownames.
15,259 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.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.

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

Total genes dropped after convert_orthologs :
   2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
   13,243 / 15,259 (87%)
Preparing gene_df.
Dense matrix format detected.
Extracting genes from rownames.
15,259 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.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
WARNING: Will convert gene_df from dense matrix to data.frame when gene_output='columns'.
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
   13,243 / 15,259 (87%)
Preparing gene_df.
data.frame format detected.
Extracting genes from rownames.
15,259 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.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
   13,243 / 15,259 (87%)
Preparing gene_df.
data.frame format detected.
Preparing gene_df.
data.frame format detected.
Extracting genes from rownames.
15,259 genes extracted.
Converting mouse ==> human orthologs using: homologene
Standardising gene names first.
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: mmusculus
Extracting genes from name.
14,096 genes extracted.
14,096 / 15,259 (92.38%) genes mapped.
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 1:1 orthologs.
Filtering gene_df with gene_map
Sorting rownames alphanumerically.
Adding input_gene col to gene_df.
Adding input_gene_standard col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   2,806 / 15,259 (18%)
Total genes remaining after convert_orthologs :
   12,453 / 15,259 (82%)
Preparing gene_df.
data.frame format detected.
+ orthologs previously converted.
Detected that gene_df was previously converted to orthologs.
 Skipping map_orthologs step.
Checking for genes without orthologs in human.
Extracting genes from input_gene.
12,453 genes extracted.
Extracting genes from ortholog_gene.
12,453 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 30 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   52 / 12,453 (0.42%)
Total genes remaining after convert_orthologs :
   12,401 / 12,453 (100%)
Preparing gene_df.
data.frame format detected.
Extracting genes from rownames.
15,259 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.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Returning gene_map as dictionary

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

Total genes dropped after convert_orthologs :
   2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
   13,243 / 15,259 (87%)
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
100 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.
91 genes extracted.
Extracting genes from ortholog_gene.
91 genes extracted.
Checking for genes without 1:1 orthologs.
Filtering gene_df with gene_map
Returning gene_map as dictionary

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

Total genes dropped after convert_orthologs :
   9 / 100 (9%)
Total genes remaining after convert_orthologs :
   91 / 100 (91%)
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
100 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.
91 genes extracted.
Extracting genes from ortholog_gene.
91 genes extracted.
Checking for genes without 1:1 orthologs.
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.

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

Total genes dropped after convert_orthologs :
   9 / 100 (9%)
Total genes remaining after convert_orthologs :
   91 / 100 (91%)
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
100 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.
91 genes extracted.
Extracting genes from ortholog_gene.
91 genes extracted.
Checking for genes without 1:1 orthologs.
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 :
   9 / 100 (9%)
Total genes remaining after convert_orthologs :
   91 / 100 (91%)
Preparing gene_df.
sparseMatrix format detected.
Extracting genes from rownames.
15,259 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.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Filtering gene_df with gene_map
Mapping many:many rows.
1110012L19Rik : converting 1 row(s) --> 2 row(s).
2610034B18Rik : converting 1 row(s) --> 2 row(s).
AA415398 : converting 1 row(s) --> 2 row(s).
Ankhd1 : converting 1 row(s) --> 2 row(s).
Anxa8 : converting 1 row(s) --> 2 row(s).
Apitd1 : converting 1 row(s) --> 2 row(s).
Arhgap8 : converting 1 row(s) --> 2 row(s).
Asb3 : converting 1 row(s) --> 2 row(s).
C4a : converting 1 row(s) --> 2 row(s).
C4b : converting 1 row(s) --> 2 row(s).
Cbs : converting 1 row(s) --> 2 row(s).
Ccz1 : converting 1 row(s) --> 2 row(s).
Ckmt1 : converting 1 row(s) --> 2 row(s).
Coro7 : converting 1 row(s) --> 2 row(s).
Cryaa : converting 1 row(s) --> 2 row(s).
D10Jhu81e : converting 1 row(s) --> 2 row(s).
F8a : converting 1 row(s) --> 3 row(s).
Fam21 : converting 1 row(s) --> 2 row(s).
Fcgr4 : converting 1 row(s) --> 2 row(s).
Gpr89 : converting 1 row(s) --> 2 row(s).
Gstt2 : converting 1 row(s) --> 2 row(s).
H3f3a : converting 1 row(s) --> 2 row(s).
H3f3b : converting 1 row(s) --> 2 row(s).
Hspa1a : converting 1 row(s) --> 2 row(s).
Icosl : converting 1 row(s) --> 2 row(s).
Klhl23 : converting 1 row(s) --> 2 row(s).
Mrpl23 : converting 1 row(s) --> 2 row(s).
Nbl1 : converting 1 row(s) --> 2 row(s).
Nomo1 : converting 1 row(s) --> 3 row(s).
Pmf1 : converting 1 row(s) --> 2 row(s).
Pom121 : converting 1 row(s) --> 2 row(s).
Pramef8 : converting 1 row(s) --> 2 row(s).
Prodh : converting 1 row(s) --> 2 row(s).
Ranbp2 : converting 1 row(s) --> 7 row(s).
Serf1 : converting 1 row(s) --> 2 row(s).
Sgk3 : converting 1 row(s) --> 2 row(s).
Slx1b : converting 1 row(s) --> 2 row(s).
Smn1 : converting 1 row(s) --> 2 row(s).
Spin2d : converting 1 row(s) --> 2 row(s).
Aggregating rows using: monocle3
Converting obj to sparseMatrix.
Matrix aggregated:
  - Input: 13,370 x 7 
  - Output: 13,316 x 7

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

Total genes dropped after convert_orthologs :
   1,943 / 15,259 (13%)
Total genes remaining after convert_orthologs :
   13,316 / 15,259 (87%)
Preparing gene_df.
sparseMatrix format detected.
Extracting genes from rownames.
15,259 genes extracted.
Converting mouse ==> human orthologs using: babelgene
Retrieving all organisms available in babelgene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: Mus musculus
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Mus musculus
1 organism identified from search: 10090
Preparing babelgene::orthologs_df.
Gene table with 29,651 rows retrieved.
Checking for genes without orthologs in human.
Extracting genes from input_gene.
29,651 genes extracted.
Dropping 37 NAs of all kinds from input_gene.
Extracting genes from ortholog_gene.
29,614 genes extracted.
Dropping 146 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 9,286 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 10,297 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.

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

Total genes dropped after convert_orthologs :
   4,000 / 15,259 (26%)
Total genes remaining after convert_orthologs :
   11,259 / 15,259 (74%)
Preparing gene_df.
sparseMatrix format detected.
Extracting genes from rownames.
15,259 genes extracted.
Converting mouse ==> mouse 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: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
input_species already formatted as output species. Returning input data directly.
Preparing gene_df.
DelayedArray format detected.
Extracting genes from rownames.
15,259 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.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.

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

Total genes dropped after convert_orthologs :
   2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
   13,243 / 15,259 (87%)
Generating gene background for mouse x rat ==> human
Gathering ortholog reports.
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.

-- 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.
--
--
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 (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
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.
Gathering ortholog reports.
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.

-- rat
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from rat.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
20,616 genes extracted.
Converting rat ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
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.
16,989 genes extracted.
Extracting genes from ortholog_gene.
16,989 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 122 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 607 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   4,813 / 20,616 (23%)
Total genes remaining after convert_orthologs :
   15,803 / 20,616 (77%)
--

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

15,803 / 20,616 (76.65%) target_species genes remain after ortholog conversion.
15,803 / 19,129 (82.61%) reference_species genes remain after ortholog conversion.
15,450 intersect background genes used.
Generating gene background for mouse x rat ==> rat
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from rat.

-- 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.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> rat 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: rat
Common name mapping found for rat
1 organism identified from search: 10116
Checking for genes without orthologs in rat.
Extracting genes from input_gene.
20,872 genes extracted.
Extracting genes from ortholog_gene.
20,872 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 2,075 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 1,975 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   4,186 / 21,207 (20%)
Total genes remaining after convert_orthologs :
   17,021 / 21,207 (80%)
--

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

17,021 / 21,207 (80.26%) target_species genes remain after ortholog conversion.
17,021 / 20,616 (82.56%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from rat.

-- rat
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from rat.
--

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

20,616 / 20,616 (100%) target_species genes remain after ortholog conversion.
20,616 / 20,616 (100%) reference_species genes remain after ortholog conversion.
17,021 intersect background genes used.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from rat.
Returning 20,616 unique genes from entire rat genome.
Generating gene background for human x rat ==> mouse
Gathering ortholog reports.
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.

-- 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.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
19,129 genes extracted.
Converting human ==> mouse orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Checking for genes without orthologs in mouse.
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 498 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 131 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   2,647 / 19,129 (14%)
Total genes remaining after convert_orthologs :
   16,482 / 19,129 (86%)
--

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

16,482 / 19,129 (86.16%) target_species genes remain after ortholog conversion.
16,482 / 21,207 (77.72%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
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.

-- rat
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from rat.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
20,616 genes extracted.
Converting rat ==> mouse orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Checking for genes without orthologs in mouse.
Extracting genes from input_gene.
20,872 genes extracted.
Extracting genes from ortholog_gene.
20,872 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 1,975 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 2,075 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   3,595 / 20,616 (17%)
Total genes remaining after convert_orthologs :
   17,021 / 20,616 (83%)
--

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

17,021 / 20,616 (82.56%) target_species genes remain after ortholog conversion.
17,021 / 21,207 (80.26%) reference_species genes remain after ortholog conversion.
15,450 intersect background genes used.
Generating gene background for monkey x chimp ==> human
Gathering ortholog reports.
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.

-- 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.
--
--
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 197 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 215 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   1,726 / 16,816 (10%)
Total genes remaining after convert_orthologs :
   15,090 / 16,816 (90%)
--

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

15,077 / 16,816 (89.66%) target_species genes remain after ortholog conversion.
15,077 / 19,129 (78.82%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
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.

-- chimp
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: chimp
Common name mapping found for chimp
1 organism identified from search: 9598
Gene table with 18,730 rows retrieved.
Returning all 18,730 genes from chimp.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
18,730 genes extracted.
Converting chimp ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: chimp
Common name mapping found for chimp
1 organism identified from search: 9598
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.
17,737 genes extracted.
Extracting genes from ortholog_gene.
17,737 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 257 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 151 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   1,506 / 18,703 (8.1%)
Total genes remaining after convert_orthologs :
   17,197 / 18,703 (92%)
--

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

17,185 / 18,703 (91.88%) target_species genes remain after ortholog conversion.
17,185 / 19,129 (89.84%) reference_species genes remain after ortholog conversion.
14,190 intersect background genes used.
===== mouse tests =====
Preparing gene_df.
sparseMatrix format detected.
Extracting genes from rownames.
200 genes extracted.
Testing for gene overlap with: 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.
Testing for gene overlap with: 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.
Testing for gene overlap with: rat
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from rat.
Testing for gene overlap with: 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.
Testing for gene overlap with: zebrafish
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: 7955
Gene table with 20,897 rows retrieved.
Returning all 20,897 genes from zebrafish.
Testing for gene overlap with: fly
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: 7227
Gene table with 8,438 rows retrieved.
Returning all 8,438 genes from fly.
Top match:
  - species: mouse 
  - percent_match: 96%
Loading required namespace: knitr
===== mouse tests2 =====
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
200 genes extracted.
Testing for gene overlap with: 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.
Testing for gene overlap with: 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.
Testing for gene overlap with: rat
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from rat.
Testing for gene overlap with: 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.
Testing for gene overlap with: zebrafish
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: 7955
Gene table with 20,897 rows retrieved.
Returning all 20,897 genes from zebrafish.
Testing for gene overlap with: fly
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: 7227
Gene table with 8,438 rows retrieved.
Returning all 8,438 genes from fly.
Top match:
  - species: mouse 
  - percent_match: 96%
===== human tests =====
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
100 genes extracted.
Testing for gene overlap with: 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.
Testing for gene overlap with: 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.
Testing for gene overlap with: rat
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from rat.
Testing for gene overlap with: 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.
Testing for gene overlap with: zebrafish
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: 7955
Gene table with 20,897 rows retrieved.
Returning all 20,897 genes from zebrafish.
Testing for gene overlap with: fly
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: 7227
Gene table with 8,438 rows retrieved.
Returning all 8,438 genes from fly.
Top match:
  - species: human 
  - percent_match: 98%
===== mouse tests =====
Preparing gene_df.
sparseMatrix format detected.
Extracting genes from rownames.
200 genes extracted.
Testing for gene overlap with: human
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Preparing babelgene::orthologs_df.
Gene table with 20,492 rows retrieved.
Returning all 20,492 genes from human.
Testing for gene overlap with: monkey
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: monkey
Common name mapping found for monkey
1 organism identified from search: 9544
Preparing babelgene::orthologs_df.
Gene table with 20,402 rows retrieved.
Returning all 20,402 genes from monkey.
Testing for gene overlap with: rat
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Preparing babelgene::orthologs_df.
Gene table with 21,427 rows retrieved.
Returning all 21,427 genes from rat.
Testing for gene overlap with: mouse
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Preparing babelgene::orthologs_df.
Gene table with 29,651 rows retrieved.
Returning all 29,651 genes from mouse.
Testing for gene overlap with: zebrafish
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: 7955
Preparing babelgene::orthologs_df.
Gene table with 30,886 rows retrieved.
Returning all 30,886 genes from zebrafish.
Testing for gene overlap with: fly
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: 7227
Preparing babelgene::orthologs_df.
Gene table with 20,237 rows retrieved.
Returning all 20,237 genes from fly.
Top match:
  - species: mouse 
  - percent_match: 89%
===== mouse tests2 =====
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
200 genes extracted.
Testing for gene overlap with: human
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Preparing babelgene::orthologs_df.
Gene table with 20,492 rows retrieved.
Returning all 20,492 genes from human.
Testing for gene overlap with: monkey
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: monkey
Common name mapping found for monkey
1 organism identified from search: 9544
Preparing babelgene::orthologs_df.
Gene table with 20,402 rows retrieved.
Returning all 20,402 genes from monkey.
Testing for gene overlap with: rat
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Preparing babelgene::orthologs_df.
Gene table with 21,427 rows retrieved.
Returning all 21,427 genes from rat.
Testing for gene overlap with: mouse
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Preparing babelgene::orthologs_df.
Gene table with 29,651 rows retrieved.
Returning all 29,651 genes from mouse.
Testing for gene overlap with: zebrafish
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: 7955
Preparing babelgene::orthologs_df.
Gene table with 30,886 rows retrieved.
Returning all 30,886 genes from zebrafish.
Testing for gene overlap with: fly
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: 7227
Preparing babelgene::orthologs_df.
Gene table with 20,237 rows retrieved.
Returning all 20,237 genes from fly.
Top match:
  - species: mouse 
  - percent_match: 89%
===== human tests =====
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
100 genes extracted.
Testing for gene overlap with: human
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Preparing babelgene::orthologs_df.
Gene table with 20,492 rows retrieved.
Returning all 20,492 genes from human.
Testing for gene overlap with: monkey
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: monkey
Common name mapping found for monkey
1 organism identified from search: 9544
Preparing babelgene::orthologs_df.
Gene table with 20,402 rows retrieved.
Returning all 20,402 genes from monkey.
Testing for gene overlap with: rat
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Preparing babelgene::orthologs_df.
Gene table with 21,427 rows retrieved.
Returning all 21,427 genes from rat.
Testing for gene overlap with: mouse
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Preparing babelgene::orthologs_df.
Gene table with 29,651 rows retrieved.
Returning all 29,651 genes from mouse.
Testing for gene overlap with: zebrafish
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: 7955
Preparing babelgene::orthologs_df.
Gene table with 30,886 rows retrieved.
Returning all 30,886 genes from zebrafish.
Testing for gene overlap with: fly
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: 7227
Preparing babelgene::orthologs_df.
Gene table with 20,237 rows retrieved.
Returning all 20,237 genes from fly.
Top match:
  - species: human 
  - percent_match: 100%
Loading local .RDS file.
Loading local .RDA file.
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: hsapiens
Extracting genes from name.
3 genes extracted.
3 / 9 (33.33%) genes mapped.
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: mmusculus
Extracting genes from name.
7 genes extracted.
7 / 9 (77.78%) genes mapped.
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: drerio
Extracting genes from name.
3 genes extracted.
3 / 9 (33.33%) genes mapped.
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: dmelanogaster
Extracting genes from name.
78 genes extracted.
78 / 1,000 (7.8%) genes mapped.
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: Schmidtea mediterranea
2 organisms identified from search.
Selecting first:
   - scmediprjna12585
   - scmediprjna379262
Mapping genes with Planosphere.
Extracting genes from name.
3 genes extracted.
Dropping 1 NAs of all kinds from name.
2 / 3 (66.67%) genes mapped.
Retrieving all organisms available in babelgene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: Mus musculus
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Mus musculus
1 organism identified from search: 10090
Preparing babelgene::orthologs_df.
Gene table with 29,651 rows retrieved.
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all organisms available in babelgene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: Mus musculus
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Mus musculus
1 organism identified from search: 10090
Preparing babelgene::orthologs_df.
Gene table with 29,651 rows retrieved.
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: 7955
Preparing babelgene::orthologs_df.
Gene table with 30,886 rows retrieved.
Returning all 30,886 genes from zebrafish.
Retrieving all organisms available in babelgene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: Danio rerio
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Danio rerio
1 organism identified from search: 7955
Preparing babelgene::orthologs_df.
Gene table with 30,886 rows retrieved.
Retrieving all organisms available in babelgene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: Mus musculus
Retrieving all organisms available in babelgene.
Mapping species name: Gallus gallus
1 organism identified from search: Gallus gallus
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Mapping species name: 9544
1 organism identified from search: Macaca mulatta
Mapping species name: mus musculus
1 organism identified from search: Mus musculus
Mapping species name: fruit fly
Common name mapping found for fruit fly
1 organism identified from search: Drosophila melanogaster
Mapping species name: Celegans
1 organism identified from search: Caenorhabditis elegans
method='grpofiler' not recognized by get_all_orgs. Defaulting to 'gprofiler'.
Using stored `gprofiler_orgs`.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: hsapiens
Mapping species name: 9544
1 organism identified from search: mmulatta
Mapping species name: mus musculus
1 organism identified from search: mmusculus
Mapping species name: fruit fly
Common name mapping found for fruit fly
1 organism identified from search: dmelanogaster
Mapping species name: Celegans
1 organism identified from search: celegans
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Mapping species name: 9544
1 organism identified from search: 9544
Mapping species name: mus musculus
1 organism identified from search: 10090
Mapping species name: fruit fly
Common name mapping found for fruit fly
1 organism identified from search: 7227
Mapping species name: Celegans
1 organism identified from search: 6239
Retrieving all organisms available in homologene.
`geom_smooth()` using formula = 'y ~ x'
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Homo sapiens
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from Homo sapiens.

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

=========== 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.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
16,843 genes extracted.
Converting monkey ==> Homo sapiens 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: Homo sapiens
1 organism identified from search: 9606
Checking for genes without orthologs in Homo sapiens.
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 197 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 215 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   1,726 / 16,816 (10%)
Total genes remaining after convert_orthologs :
   15,090 / 16,816 (90%)
--

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

15,077 / 16,816 (89.66%) target_species genes remain after ortholog conversion.
15,077 / 19,129 (78.82%) 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.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> Homo sapiens 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: Homo sapiens
1 organism identified from search: 9606
Checking for genes without orthologs in Homo sapiens.
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 (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
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
Loading required namespace: TreeTools
Importing tree from: TimeTree2022
Importing cached tree.
Standardising tip labels.
Mapping 3 species from `species`.
Mapping 3 species from tree.
--
0/3 (0%) tips dropped from tree due to inability to standardise names with `map_species`.
--
0/3 (0%) tips dropped from tree according to overlap with selected `species`.
Loading required namespace: rphylopic
Gathering phylopic silhouettes.
+ homo sapiens
+ macaca mulatta
+ mus musculus
Preparing data for 6 clades.
Warning: Each clade in `clades` must contain a vector of at least 1 species. Omitting clade: Invertebrates
3 species remaining after metadata preparation.
Loading required namespace: ggimage
Creating ggtree plot.
Saving plot ==> /tmp/RtmppHJmTo/file146706a87e6c6.ggtree.pdf
Saving plot ==> /tmp/RtmppHJmTo/file146704007ce.ggtree.png
2024-12-21 04:03:39.769 R[83568:80927165] XType: Using static font registry.
Gathering ortholog reports.
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Homo sapiens
1 organism identified from search: 9606
Preparing babelgene::orthologs_df.
Gene table with 20,492 rows retrieved.
Returning all 20,492 genes from Homo sapiens.

-- human
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Homo sapiens
1 organism identified from search: 9606
Preparing babelgene::orthologs_df.
Gene table with 20,492 rows retrieved.
Returning all 20,492 genes from Homo sapiens.
--

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

20,206 / 20,206 (100%) target_species genes remain after ortholog conversion.
20,206 / 20,206 (100%) reference_species genes remain after ortholog conversion.

-- monkey
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: monkey
Common name mapping found for monkey
1 organism identified from search: 9544
Preparing babelgene::orthologs_df.
Gene table with 20,402 rows retrieved.
Returning all 20,402 genes from monkey.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
20,402 genes extracted.
Converting monkey ==> Homo sapiens orthologs using: babelgene
Retrieving all organisms available in babelgene.
Mapping species name: monkey
Common name mapping found for monkey
1 organism identified from search: Macaca mulatta
Retrieving all organisms available in babelgene.
Mapping species name: Homo sapiens
1 organism identified from search: Homo sapiens
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Macaca mulatta
1 organism identified from search: 9544
Preparing babelgene::orthologs_df.
Gene table with 20,402 rows retrieved.
Checking for genes without orthologs in Homo sapiens.
Extracting genes from input_gene.
20,402 genes extracted.
Dropping 561 NAs of all kinds from input_gene.
Extracting genes from ortholog_gene.
19,841 genes extracted.
Dropping 107 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 1,371 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 1,000 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   1,452 / 18,149 (8%)
Total genes remaining after convert_orthologs :
   16,697 / 18,149 (92%)
--

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

16,459 / 18,149 (90.69%) target_species genes remain after ortholog conversion.
16,459 / 20,206 (81.46%) reference_species genes remain after ortholog conversion.

-- mouse
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Preparing babelgene::orthologs_df.
Gene table with 29,651 rows retrieved.
Returning all 29,651 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
29,651 genes extracted.
Converting mouse ==> Homo sapiens orthologs using: babelgene
Retrieving all organisms available in babelgene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: Mus musculus
Retrieving all organisms available in babelgene.
Mapping species name: Homo sapiens
1 organism identified from search: Homo sapiens
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Mus musculus
1 organism identified from search: 10090
Preparing babelgene::orthologs_df.
Gene table with 29,651 rows retrieved.
Checking for genes without orthologs in Homo sapiens.
Extracting genes from input_gene.
29,651 genes extracted.
Dropping 37 NAs of all kinds from input_gene.
Extracting genes from ortholog_gene.
29,614 genes extracted.
Dropping 146 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 9,286 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 10,297 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   4,602 / 20,075 (23%)
Total genes remaining after convert_orthologs :
   15,473 / 20,075 (77%)
--

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

15,314 / 20,075 (76.28%) target_species genes remain after ortholog conversion.
15,314 / 20,206 (75.79%) reference_species genes remain after ortholog conversion.
Importing tree from: TimeTree2022
Importing cached tree.
Standardising tip labels.
Mapping 3 species from `species`.
Mapping 3 species from tree.
--
0/3 (0%) tips dropped from tree due to inability to standardise names with `map_species`.
--
0/3 (0%) tips dropped from tree according to overlap with selected `species`.
Gathering phylopic silhouettes.
+ homo sapiens
+ macaca mulatta
+ mus musculus
Preparing data for 6 clades.
Warning: Each clade in `clades` must contain a vector of at least 1 species. Omitting clade: Invertebrates
3 species remaining after metadata preparation.
Creating ggtree plot.
Saving plot ==> /tmp/RtmppHJmTo/file146701d632e2b.ggtree.pdf
Saving plot ==> /tmp/RtmppHJmTo/file146705a6c181f.ggtree.png
Importing tree from: TimeTree2022
Importing cached tree.
Standardising tip labels.
Mapping 3 species from `species`.
Mapping 3 species from tree.
--
0/3 (0%) tips dropped from tree due to inability to standardise names with `map_species`.
--
0/3 (0%) tips dropped from tree according to overlap with selected `species`.
Gathering ortholog reports.
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.

-- 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.
--
--
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 (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
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.
Gathering ortholog reports.
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.

-- zebrafish
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: 7955
Gene table with 20,897 rows retrieved.
Returning all 20,897 genes from zebrafish.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
20,897 genes extracted.
Converting zebrafish ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: 7955
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.
14,768 genes extracted.
Extracting genes from ortholog_gene.
14,768 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 2,707 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   10,336 / 20,895 (49%)
Total genes remaining after convert_orthologs :
   10,559 / 20,895 (51%)
--

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

10,557 / 20,895 (50.52%) target_species genes remain after ortholog conversion.
10,557 / 19,129 (55.19%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
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.

-- fly
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: 7227
Gene table with 8,438 rows retrieved.
Returning all 8,438 genes from fly.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
8,438 genes extracted.
Converting fly ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: 7227
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.
4,500 genes extracted.
Dropping 1 NAs of all kinds from input_gene.
Extracting genes from ortholog_gene.
4,499 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 19 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 266 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   4,380 / 8,438 (52%)
Total genes remaining after convert_orthologs :
   4,058 / 8,438 (48%)
--

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

4,058 / 8,438 (48.09%) target_species genes remain after ortholog conversion.
4,058 / 19,129 (21.21%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
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.

-- 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.
Gathering ortholog reports.
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Preparing babelgene::orthologs_df.
Gene table with 20,492 rows retrieved.
Returning all 20,492 genes from human.

-- mouse
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Preparing babelgene::orthologs_df.
Gene table with 29,651 rows retrieved.
Returning all 29,651 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
29,651 genes extracted.
Converting mouse ==> human orthologs using: babelgene
Retrieving all organisms available in babelgene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: Mus musculus
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Mus musculus
1 organism identified from search: 10090
Preparing babelgene::orthologs_df.
Gene table with 29,651 rows retrieved.
Checking for genes without orthologs in human.
Extracting genes from input_gene.
29,651 genes extracted.
Dropping 37 NAs of all kinds from input_gene.
Extracting genes from ortholog_gene.
29,614 genes extracted.
Dropping 146 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 9,286 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 10,297 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   4,602 / 20,075 (23%)
Total genes remaining after convert_orthologs :
   15,473 / 20,075 (77%)
--

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

15,314 / 20,075 (76.28%) target_species genes remain after ortholog conversion.
15,314 / 20,206 (75.79%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Preparing babelgene::orthologs_df.
Gene table with 20,492 rows retrieved.
Returning all 20,492 genes from human.

-- zebrafish
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: 7955
Preparing babelgene::orthologs_df.
Gene table with 30,886 rows retrieved.
Returning all 30,886 genes from zebrafish.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
30,886 genes extracted.
Converting zebrafish ==> human orthologs using: babelgene
Retrieving all organisms available in babelgene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: Danio rerio
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Danio rerio
1 organism identified from search: 7955
Preparing babelgene::orthologs_df.
Gene table with 30,886 rows retrieved.
Checking for genes without orthologs in human.
Extracting genes from input_gene.
30,886 genes extracted.
Dropping 10 NAs of all kinds from input_gene.
Extracting genes from ortholog_gene.
30,876 genes extracted.
Dropping 70 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 10,855 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 14,453 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   11,805 / 19,781 (60%)
Total genes remaining after convert_orthologs :
   7,976 / 19,781 (40%)
--

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

7,860 / 19,781 (39.74%) target_species genes remain after ortholog conversion.
7,860 / 20,206 (38.9%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Preparing babelgene::orthologs_df.
Gene table with 20,492 rows retrieved.
Returning all 20,492 genes from human.

-- fly
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: 7227
Preparing babelgene::orthologs_df.
Gene table with 20,237 rows retrieved.
Returning all 20,237 genes from fly.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
20,237 genes extracted.
Converting fly ==> human orthologs using: babelgene
Retrieving all organisms available in babelgene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: Drosophila melanogaster
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Drosophila melanogaster
1 organism identified from search: 7227
Preparing babelgene::orthologs_df.
Gene table with 20,237 rows retrieved.
Checking for genes without orthologs in human.
Extracting genes from input_gene.
20,237 genes extracted.
Dropping 7 NAs of all kinds from input_gene.
Extracting genes from ortholog_gene.
20,230 genes extracted.
Dropping 32 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 11,721 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 9,141 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   5,175 / 8,471 (61%)
Total genes remaining after convert_orthologs :
   3,296 / 8,471 (39%)
--

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

3,276 / 8,471 (38.67%) target_species genes remain after ortholog conversion.
3,276 / 20,206 (16.21%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Preparing babelgene::orthologs_df.
Gene table with 20,492 rows retrieved.
Returning all 20,492 genes from human.

-- human
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Preparing babelgene::orthologs_df.
Gene table with 20,492 rows retrieved.
Returning all 20,492 genes from human.
--

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

20,206 / 20,206 (100%) target_species genes remain after ortholog conversion.
20,206 / 20,206 (100%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
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.

-- 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.
--
--
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 (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
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.

-- 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.
--
--
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 197 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 215 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   1,726 / 16,816 (10%)
Total genes remaining after convert_orthologs :
   15,090 / 16,816 (90%)
--

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

15,077 / 16,816 (89.66%) target_species genes remain after ortholog conversion.
15,077 / 19,129 (78.82%) reference_species genes remain after ortholog conversion.

==== fruit fly ====


------- Benchmarking homologene -------

Benchmarking all_genes()
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: fruit fly
Common name mapping found for fruit fly
1 organism identified from search: 7227
Gene table with 8,438 rows retrieved.
Extracting genes from Gene.Symbol.
8,438 genes extracted.
Dropping 2 NAs of all kinds from Gene.Symbol.
Returning all 8,436 genes from fruit fly.
Benchmarking convert_orthologs()
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
8,436 genes extracted.
Converting fruit fly ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: fruit fly
Common name mapping found for fruit fly
1 organism identified from search: 7227
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.
4,499 genes extracted.
Extracting genes from ortholog_gene.
4,499 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 19 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 266 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   4,378 / 8,436 (52%)
Total genes remaining after convert_orthologs :
   4,058 / 8,436 (48%)

------- Benchmarking gprofiler -------

Benchmarking all_genes()
Retrieving all genes using: gprofiler
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: fruit fly
Common name mapping found for fruit fly
1 organism identified from search: dmelanogaster
Gene table with 4,606 rows retrieved.
Extracting genes from Gene.Symbol.
4,606 genes extracted.
Dropping 1 NAs of all kinds from Gene.Symbol.
Returning all 4,605 genes from fruit fly.
Benchmarking convert_orthologs()
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
4,605 genes extracted.
Converting fruit fly ==> human orthologs using: gprofiler
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: fruit fly
Common name mapping found for fruit fly
1 organism identified from search: dmelanogaster
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: hsapiens
Checking for genes without orthologs in human.
Extracting genes from input_gene.
6,480 genes extracted.
Extracting genes from ortholog_gene.
6,480 genes extracted.
Dropping 3,440 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 1,871 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 768 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   3,958 / 4,605 (86%)
Total genes remaining after convert_orthologs :
   647 / 4,605 (14%)

------- Benchmarking babelgene -------

Benchmarking all_genes()
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: fruit fly
Common name mapping found for fruit fly
1 organism identified from search: 7227
Preparing babelgene::orthologs_df.
Gene table with 20,237 rows retrieved.
Extracting genes from Gene.Symbol.
20,237 genes extracted.
Dropping 7 NAs of all kinds from Gene.Symbol.
Returning all 20,230 genes from fruit fly.
Benchmarking convert_orthologs()
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
20,230 genes extracted.
Converting fruit fly ==> human orthologs using: babelgene
Retrieving all organisms available in babelgene.
Mapping species name: fruit fly
Common name mapping found for fruit fly
1 organism identified from search: Drosophila melanogaster
Retrieving all organisms available in babelgene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: babelgene.
Retrieving all organisms available in babelgene.
Mapping species name: Drosophila melanogaster
1 organism identified from search: 7227
Preparing babelgene::orthologs_df.
Gene table with 20,237 rows retrieved.
Checking for genes without orthologs in human.
Extracting genes from input_gene.
20,237 genes extracted.
Dropping 7 NAs of all kinds from input_gene.
Extracting genes from ortholog_gene.
20,230 genes extracted.
Dropping 32 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 11,721 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 9,141 genes that have multiple ortholog_gene per input_gene (1:many).
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 :
   5,173 / 8,469 (61%)
Total genes remaining after convert_orthologs :
   3,296 / 8,469 (39%)
Finished fruit fly in 0.175 minutes.
Saving benchmarking results ==> /tmp/RtmppHJmTo/file14670c5b0d25.csv
WARNING: Species 'monkeytypo' not found in taxa dict.
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 155 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 155 ]
> 
> proc.time()
   user  system elapsed 
308.951  12.964 323.202