##############################################################################
##############################################################################
###
### 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_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/orthogene.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘orthogene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘orthogene’ version ‘1.0.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
all_genes              6.732  0.439  17.185
report_orthologs       5.268  0.264  18.886
aggregate_mapped_genes 3.921  0.137   8.249
convert_orthologs      1.776  0.113  19.534
map_orthologs          1.561  0.098   6.140
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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: 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
nrow(gene_map) > nrow(gene_df)
Checking for genes without 1:1 orthologs.
Dropping 2,971 genes that have multiple ortholog_gene per input_gene.
Extracting genes from input_gene.
12,811 genes extracted.
Extracting genes from ortholog_gene.
12,811 genes extracted.
Aggregating rows using: monocle3
Matrix aggregated:
  - Input: 12,811 x 7 
  - Output: 12,811 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
482 / 482 (100%) genes mapped.
Aggregating rows using: monocle3
Matrix aggregated:
  - Input: 482 x 7 
  - Output: 92 x 7
Loading required namespace: DelayedArray
Converting to DelayedArray.
nrow(gene_map) > nrow(gene_df)
Checking for genes without 1:1 orthologs.
Dropping 2,971 genes that have multiple ortholog_gene per input_gene.
Extracting genes from input_gene.
12,811 genes extracted.
Extracting genes from ortholog_gene.
12,811 genes extracted.
Aggregating rows using: monocle3
Matrix aggregated:
  - Input: 12,811 x 7 
  - Output: 12,811 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: gprofiler
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: dmelanogaster
1 organism identified from search: dmelanogaster
Gene table with 4,493 rows retrieved.
4493
WARNING: In order to set gene_output='rownames' must set drop_nonorths=TRUE.
 Setting drop_nonorths=TRUE.
WARNING: In order to set gene_output='rownames' must ensure unqiue rownmaes by setting non121_strategy to:
   'drop_both_species' or 'keep_popular' 
 or an aggregation function:
    'sum','mean','median','min','max' .
 Setting non121_strategy='drop_both_species'.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   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.
14,199 genes extracted.
15,259 / 14,199 (93.05%) 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
Adding input_gene col to gene_df.
Adding input_gene_standard col to gene_df.
Adding ortholog_gene col to gene_df.
Sorting rownames alphanumerically.

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

Total genes dropped after convert_orthologs :
   2,690 / 15,259 (18%)
Total genes remaining after convert_orthologs :
   12,569 / 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.
12,569 genes extracted.
Extracting genes from ortholog_gene.
12,569 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 30 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   52 / 12,569 (0.41%)
Total genes remaining after convert_orthologs :
   12,517 / 12,569 (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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
nrow(gene_map) > nrow(gene_df)
Checking for genes without 1:1 orthologs.
Extracting genes from input_gene.
13,320 genes extracted.
Extracting genes from input_gene.
13,320 genes extracted.
gene_map has the same number of rows as gene_df, 
                 and thus there is nothing to aggregate.
 Returning gene_df with gene names from gene_map instead
Aggregating rows using: monocle3
Matrix aggregated:
  - Input: 13,320 x 7 
  - Output: 13,320 x 7
Converting obj to sparseMatrix.

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

Total genes dropped after convert_orthologs :
   1,939 / 15,259 (13%)
Total genes remaining after convert_orthologs :
   13,320 / 15,259 (87%)
Preparing gene_df.
sparseMatrix format detected.
Extracting genes from rownames.
15,259 genes extracted.
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
Checking for genes without orthologs in human.
Extracting genes from input_gene.
15,999 genes extracted.
Extracting genes from ortholog_gene.
15,999 genes extracted.
Dropping 2,634 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 438 genes that have multiple input_gene per ortholog_gene.
Dropping 339 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.

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

Total genes dropped after convert_orthologs :
   2,896 / 15,259 (19%)
Total genes remaining after convert_orthologs :
   12,363 / 15,259 (81%)
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 29,786 rows retrieved.
Checking for genes without orthologs in human.
Extracting genes from input_gene.
29,786 genes extracted.
Dropping 55 NAs of all kinds from input_gene.
Extracting genes from ortholog_gene.
29,731 genes extracted.
Dropping 247 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 9,406 genes that have multiple input_gene per ortholog_gene.
Dropping 10,441 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.

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

Total genes dropped after convert_orthologs :
   4,028 / 15,259 (26%)
Total genes remaining after convert_orthologs :
   11,231 / 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
Checking for genes without orthologs in mouse.
Extracting genes from input_gene.
15,335 genes extracted.
Extracting genes from ortholog_gene.
15,335 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 1,342 genes that have multiple input_gene per ortholog_gene.
Dropping 807 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.
Converting obj to sparseMatrix.

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

Total genes dropped after convert_orthologs :
   1,545 / 15,259 (10%)
Total genes remaining after convert_orthologs :
   13,714 / 15,259 (90%)
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: Mus musculus
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Mus musculus
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from Mus musculus.
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.
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting Mus musculus ==> Homo sapiens orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: Mus musculus
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

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

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

16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: Rattus norvegicus
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Rattus norvegicus
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from Rattus norvegicus.
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.
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
20,616 genes extracted.
Converting Rattus norvegicus ==> Homo sapiens orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: Rattus norvegicus
1 organism identified from search: 10116
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.
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.
Dropping 607 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   4,813 / 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
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: Mus musculus
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: Rattus norvegicus
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Mus musculus
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from Mus musculus.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Rattus norvegicus
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from Rattus norvegicus.
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting Mus musculus ==> Rattus norvegicus orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: Mus musculus
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: Rattus norvegicus
1 organism identified from search: 10116
Checking for genes without orthologs in Rattus norvegicus.
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.
Dropping 1,975 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   4,186 / 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.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: Rattus norvegicus
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: Rattus norvegicus
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Rattus norvegicus
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from Rattus norvegicus.

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

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

Total genes dropped after convert_orthologs :
   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.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: Rattus norvegicus
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: Mus musculus
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Rattus norvegicus
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from Rattus norvegicus.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Mus musculus
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from Mus musculus.
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
20,616 genes extracted.
Converting Rattus norvegicus ==> Mus musculus orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: Rattus norvegicus
1 organism identified from search: 10116
Retrieving all organisms available in homologene.
Mapping species name: Mus musculus
1 organism identified from search: 10090
Checking for genes without orthologs in Mus musculus.
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.
Dropping 2,075 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   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
Retrieving all organisms available in homologene.
Mapping species name: monkey
Common name mapping found for monkey
1 organism identified from search: Macaca mulatta
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Macaca mulatta
1 organism identified from search: 9544
Gene table with 16,843 rows retrieved.
Returning all 16,843 genes from Macaca mulatta.
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.
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
16,843 genes extracted.
Converting Macaca mulatta ==> Homo sapiens orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: Macaca mulatta
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 203 genes that have multiple input_gene per ortholog_gene.
Dropping 221 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

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

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

15,075 / 16,816 (89.65%) target_species genes remain after ortholog conversion.
15,075 / 19,129 (78.81%) reference_species genes remain after ortholog conversion.
Retrieving all organisms available in homologene.
Mapping species name: chimp
Common name mapping found for chimp
1 organism identified from search: Pan troglodytes
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Pan troglodytes
1 organism identified from search: 9598
Gene table with 18,730 rows retrieved.
Returning all 18,730 genes from Pan troglodytes.
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.
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
18,730 genes extracted.
Converting Pan troglodytes ==> Homo sapiens orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: Pan troglodytes
1 organism identified from search: 9598
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.
17,737 genes extracted.
Extracting genes from ortholog_gene.
17,737 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 281 genes that have multiple input_gene per ortholog_gene.
Dropping 175 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   1,511 / 18,703 (8.1%)
Total genes remaining after convert_orthologs :
   17,192 / 18,703 (92%)

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

17,183 / 18,703 (91.87%) target_species genes remain after ortholog conversion.
17,183 / 19,129 (89.83%) reference_species genes remain after ortholog conversion.
14,187 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%
===== 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%
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.
9 / 3 (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.
9 / 7 (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.
9 / 3 (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.
71 genes extracted.
1,000 / 71 (7.1%) genes mapped.
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
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 29,786 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 29,786 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
input_species==output_species. Returning input genes.
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
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
Retrieving all organisms available in homologene.
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'
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: Mus musculus
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Mus musculus
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from Mus musculus.
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.
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting Mus musculus ==> Homo sapiens orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: Mus musculus
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

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

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

16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Retrieving all organisms available in homologene.
Mapping species name: zebrafish
Common name mapping found for zebrafish
1 organism identified from search: Danio rerio
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Danio rerio
1 organism identified from search: 7955
Gene table with 20,897 rows retrieved.
Returning all 20,897 genes from Danio rerio.
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.
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
20,897 genes extracted.
Converting Danio rerio ==> Homo sapiens orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: Danio rerio
1 organism identified from search: 7955
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.
14,768 genes extracted.
Extracting genes from ortholog_gene.
14,768 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 47 genes that have multiple input_gene per ortholog_gene.
Dropping 2,708 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   10,338 / 20,895 (49%)
Total genes remaining after convert_orthologs :
   10,557 / 20,895 (51%)

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

10,556 / 20,895 (50.52%) target_species genes remain after ortholog conversion.
10,556 / 19,129 (55.18%) reference_species genes remain after ortholog conversion.
Retrieving all organisms available in homologene.
Mapping species name: fly
Common name mapping found for fly
1 organism identified from search: Drosophila melanogaster
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: Homo sapiens
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: Drosophila melanogaster
1 organism identified from search: 7227
Gene table with 8,438 rows retrieved.
Returning all 8,438 genes from Drosophila melanogaster.
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.
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
8,438 genes extracted.
Converting Drosophila melanogaster ==> Homo sapiens orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: Drosophila melanogaster
1 organism identified from search: 7227
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.
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.
Dropping 266 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   4,380 / 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.
Retrieving all organisms available in homologene.
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
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.

==== dmelanogaster ====

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

Benchmarking all_genes()
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: dmelanogaster
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 dmelanogaster.
Benchmarking convert_orthologs()
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
8,436 genes extracted.
Converting dmelanogaster ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: dmelanogaster
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.
Dropping 266 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   4,378 / 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: dmelanogaster
1 organism identified from search: dmelanogaster
Gene table with 4,493 rows retrieved.
Extracting genes from Gene.Symbol.
4,493 genes extracted.
Dropping 1 NAs of all kinds from Gene.Symbol.
Returning all 4,492 genes from dmelanogaster.
Benchmarking convert_orthologs()
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
4,492 genes extracted.
Converting dmelanogaster ==> human orthologs using: gprofiler
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: dmelanogaster
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.
6,476 genes extracted.
Extracting genes from ortholog_gene.
6,476 genes extracted.
Dropping 3,406 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 1,922 genes that have multiple input_gene per ortholog_gene.
Dropping 743 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.

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

Total genes dropped after convert_orthologs :
   3,849 / 4,492 (86%)
Total genes remaining after convert_orthologs :
   643 / 4,492 (14%)
Finisheddmelanogasterin0.121minutes.
Saving benchmarking results ==> /tmp/RtmpEzXcLa/file873e75d16e34.csv
WARNING: Species 'monkeytypo' not found in taxa dict.
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 104 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 104 ]
> 
> proc.time()
   user  system elapsed 
 89.272   3.050 145.671