Package: BgeeDB

Version: 2.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BgeeDB_2.13.0.tar.gz

StartedAt: 2020-01-16 02:04:13 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:15:16 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 662.6 seconds

RetCode: 0

Status:  OK

CheckDir: BgeeDB.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BgeeDB_2.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BgeeDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeDB’ version ‘2.13.0’
* 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 ‘BgeeDB’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
getData         108.731 15.250 116.273
geneList         20.073  1.258  48.326
makeTable         6.634  1.098  10.028
loadTopAnatData   5.862  0.938  51.070
topAnat           5.044  0.522   7.881
formatData        3.909  0.759   7.969
Bgee-class        0.158  0.026   5.398
listBgeeSpecies   0.076  0.027   7.852
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BgeeDB
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BgeeDB’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (BgeeDB)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(BgeeDB)
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

The following object is masked from 'package:IRanges':

    members

Loading required package: tidyr

Attaching package: 'tidyr'

The following object is masked from 'package:S4Vectors':

    expand

The following object is masked from 'package:testthat':

    matches

> 
> Sys.setenv("R_TESTS" = "")
> test_check("BgeeDB")

Querying Bgee to get release information...

Building URL to query species in Bgee release 14_0...

Submitting URL to Bgee webservice... (https://r.bgee.org/bgee14/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.13.0)
trying URL 'https://r.bgee.org/bgee14/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.13.0'
downloaded 1164 bytes


Query to Bgee webservice successful!

API key built: 4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789

Downloading expression data for the experiment GSE43721 ...
trying URL 'ftp://ftp.bgee.org/bgee_v14_0/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_read_counts_TPM_FPKM_GSE43721.tsv.tar.gz'
Content type 'unknown' length 1867621 bytes (1.8 MB)
==================================================

Saved expression data file in /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0 folder. Now untar /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0/Mus_musculus_RNA-Seq_read_counts_TPM_FPKM_GSE43721.tsv.tar.gz file...

Saving all data in .rds file...

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Querying Bgee to get release information...

Building URL to query species in Bgee release 13_2...

Submitting URL to Bgee webservice... (https://r.bgee.org/bgee13/?page=species&display_type=tsv&source=BgeeDB_R_package&source_version=2.13.0)
trying URL 'https://r.bgee.org/bgee13/?page=species&display_type=tsv&source=BgeeDB_R_package&source_version=2.13.0'
downloaded 707 bytes


Query to Bgee webservice successful!

API key built: 4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789

IMPORTANT INFORMATION: Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/

Downloading expression data for the experiment GSE43721 ...
trying URL 'ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_read_counts_RPKM_GSE43721.tsv.zip'
Content type 'unknown' length 919661 bytes (898 KB)
==================================================

Saved expression data file in /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2 folder. Now unzip /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2/Mus_musculus_RNA-Seq_read_counts_RPKM_GSE43721.tsv.zip file...

Saving all data in .rds file...

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_0 was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789
trying URL 'ftp://ftp.bgee.org/bgee_v14_0/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_experiments_libraries.tar.gz'
Content type 'unknown' length 10966 bytes (10 KB)
==================================================

Saved annotation files in /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0 folder.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_0 was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789
trying URL 'ftp://ftp.bgee.org/bgee_v14_0/download/processed_expr_values/affymetrix/Mus_musculus/Mus_musculus_Affymetrix_experiments_chips.tar.gz'
Content type 'unknown' length 513654 bytes (501 KB)
==================================================

Saved annotation files in /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0 folder.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 13_2 was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789

IMPORTANT INFORMATION: Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/
trying URL 'ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_experiments_libraries.zip'
Content type 'unknown' length 9379 bytes
==================================================

Saved annotation files in /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2 folder.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 13_2 was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789

IMPORTANT INFORMATION: Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/
trying URL 'ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/affymetrix/Mus_musculus/Mus_musculus_Affymetrix_experiments_chips.zip'
Content type 'unknown' length 500591 bytes (488 KB)
==================================================

Saved annotation files in /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2 folder.

Querying Bgee to get release information...

Building URL to query species in Bgee release 14...

Submitting URL to Bgee webservice... (https://r.bgee.org/bgee14/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.13.0)
trying URL 'https://r.bgee.org/bgee14/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.13.0'
downloaded 1164 bytes


Query to Bgee webservice successful!

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_0 was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789

Building URLs to retrieve organ relationships from Bgee.........
   URL successfully built (https://r.bgee.org/bgee14/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=10090&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789&source=BgeeDB_R_package&source_version=2.13.0)
   Submitting URL to Bgee webservice (can be long)
trying URL 'https://r.bgee.org/bgee14/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=10090&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789&source=BgeeDB_R_package&source_version=2.13.0'
downloaded 915 KB

   Got results from Bgee webservice. Files are written in "/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0"

Building URLs to retrieve organ names from Bgee.................
   URL successfully built (https://r.bgee.org/bgee14/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=10090&attr_list=ID&attr_list=NAME&api_key=4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789&source=BgeeDB_R_package&source_version=2.13.0)
   Submitting URL to Bgee webservice (can be long)
trying URL 'https://r.bgee.org/bgee14/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=10090&attr_list=ID&attr_list=NAME&api_key=4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789&source=BgeeDB_R_package&source_version=2.13.0'
downloaded 841 KB

   Got results from Bgee webservice. Files are written in "/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0"

Building URLs to retrieve mapping of gene to organs from Bgee...
   URL successfully built (https://r.bgee.org/bgee14/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=10090&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789&source=BgeeDB_R_package&source_version=2.13.0&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000106)
   Submitting URL to Bgee webservice (can be long)
trying URL 'https://r.bgee.org/bgee14/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=10090&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789&source=BgeeDB_R_package&source_version=2.13.0&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000106'
downloaded 681 KB

   Got results from Bgee webservice. Files are written in "/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0"

Parsing the results.............................................

Adding BGEE:0 as unique root of all terms of the ontology.......

Done.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_0 was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789

The experiment is not defined. Hence taking all rna_seq experiments available for Mus_musculus.

Downloading expression data...
trying URL 'ftp://ftp.bgee.org/bgee_v14_0/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_read_counts_TPM_FPKM.tar.gz'
Content type 'unknown' length 75675166 bytes (72.2 MB)
==================================================

Saved expression data file in /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0 folder. Now untar file...

Saving all data in .rds file...

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_0 was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789

NOTE: expression data file in .rds format was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0 for GSE43721. Data will not be redownloaded.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_0 was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 4dd2a4561a42938fbc254f31cc02be98c19647ad1a2eb40d8cbe3ce07083a9ce886bdfd41933ade047b682e5d328a96697d957ecad19b72800a938f5f2b32789

NOTE: an organ relationships file was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0. Data will not be redownloaded.

NOTE: an organ names file was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0. Data will not be redownloaded.

NOTE: a gene to organs mapping file was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0. Data will not be redownloaded.

Parsing the results.............................................

Adding BGEE:0 as unique root of all terms of the ontology.......

Done.

Checking topAnatData object.............

Checking gene list......................

WARNING: Some genes in your gene list have no expression data in Bgee, and will not be included in the analysis. 78 genes in background will be kept.

Building most specific Ontology terms...  (  1  Ontology terms found. )

Building DAG topology...................  (  11  Ontology terms and  12  relations. )

Annotating nodes (Can be long)..........  (  78  genes annotated to the Ontology terms. )
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 30 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
129.907  24.771 201.991 

name	user	system	elapsed
Bgee-class	0.158	0.026	5.398
formatData	3.909	0.759	7.969
geneList	20.073	1.258	48.326
getAnnotation	0.046	0.031	3.523
getData	108.731	15.250	116.273
listBgeeRelease	0.011	0.004	1.350
listBgeeSpecies	0.076	0.027	7.852
loadTopAnatData	5.862	0.938	51.070
makeTable	6.634	1.098	10.028
topAnat	5.044	0.522	7.881