Back to Multiple platform build/check report for BioC 3.14
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-12-01 17:18:17 -0500 (Wed, 01 Dec 2021).

CHECK results for EWCE on machv2

To the developers/maintainers of the EWCE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EWCE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 610/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EWCE 1.2.0  (landing page)
Alan Murphy
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/EWCE
git_branch: RELEASE_3_14
git_last_commit: 1ec3e6d
git_last_commit_date: 2021-10-26 13:08:44 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: EWCE
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EWCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EWCE_1.2.0.tar.gz
StartedAt: 2021-11-30 16:23:38 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 16:40:23 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 1004.6 seconds
RetCode: 0
Status:   OK  
CheckDir: EWCE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EWCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EWCE_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/EWCE.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EWCE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EWCE’ version ‘1.2.0’
* 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 ‘EWCE’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
generate_bootstrap_plots          35.654  0.835  38.147
ewce_expression_data              27.465  0.567  29.631
controlled_geneset_enrichment     25.454  2.082  28.505
check_ewce_genelist_inputs        23.063  0.382  24.672
bootstrap_enrichment_test         22.111  0.393  23.729
ewce_plot                         21.583  0.340  23.075
add_res_to_merging_list           15.189  0.900  17.699
fix_bad_mgi_symbols               15.363  0.310  16.356
filter_genes_without_1to1_homolog 10.859  0.217  11.494
prep_dendro                        8.790  0.124   9.168
bin_specificity_into_quantiles     8.408  0.191   8.858
generate_celltype_data             8.206  0.348   8.729
get_celltype_table                 8.120  0.156   8.545
drop_uninformative_genes           7.775  0.436   8.684
bin_columns_into_quantiles         7.842  0.130   8.207
* 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


Installation output

EWCE.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘EWCE’ ...
** using staged installation
** R
** 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 (EWCE)

Tests output

EWCE.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(EWCE)
Loading required package: RNOmni
> 
> test_check("EWCE")
snapshotDate(): 2021-10-19
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Apoe, Inpp5d, Cd2ap, Nme8, Cass4, Mef2c, Zcwpw1, Bin1, Clu, Celf1, Abca7, Slc24a4, Ptk2b, Picalm, Fermt2, Sorl1
astrocytes_ependymal
0.1

endothelial-mural
0.7

interneurons
1

microglia
0
Fold enrichment: 1.48064767621354
Standard deviations from mean: 3.13462817750597

oligodendrocytes
0.6

pyramidal CA1
0.3

pyramidal SS
0.4

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Tbc1d2b, Cxcr4, Nrip2, Sox12, Selplg
astrocytes_ependymal
1

endothelial-mural
0
Fold enrichment: 1.60961976289823
Standard deviations from mean: 2.17852955614251

interneurons
0.8

microglia
0
Fold enrichment: 2.52561636602415
Standard deviations from mean: 3.28089741006316

oligodendrocytes
1

pyramidal CA1
0.9

pyramidal SS
0.9

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Cirbp, Camk1g, Nat10, Sema3a, Sssca1
astrocytes_ependymal
0.9

endothelial-mural
0.8

interneurons
0
Fold enrichment: 1.46726057430471
Standard deviations from mean: 1.79628195179353

microglia
0.8

oligodendrocytes
1

pyramidal CA1
0.1

pyramidal SS
0
Fold enrichment: 1.74532935167623
Standard deviations from mean: 3.18816102564295

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
CONTROLLED BOOTSTRAPPING NETWORK GENERATED
Abca7, Apoe, Bin1, Cass4, Cd2ap, Celf1, Clu, Fermt2, Inpp5d, Mef2c, Nme8, Picalm, Ptk2b, Slc24a4, Sorl1, Zcwpw1
astrocytes_ependymal
0.07

endothelial-mural
0.74

interneurons
1

microglia
0.02
Fold enrichment: 1.66844158222748
Standard deviations from mean: 2.27154805377459

oligodendrocytes
0.71

pyramidal CA1
0.58

pyramidal SS
0.63

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Prpf38b, Ppp2r5c, Dnajc1, Cbx5, Tbc1d2b, Col6a1, Ncan, Myh14, Cxcr4, Gpr161, Col5a3, Repin1, Ddc, Sall3, Zc3h14, Efcab2, Frzb, Adam33, Tmcc2, Nrip2, Sox12, Wwc1, Itga7, Selplg, Itgb5, Polr3g
astrocytes_ependymal
0.2

endothelial-mural
0
Fold enrichment: 1.35433709426435
Standard deviations from mean: 5.29340612207046

interneurons
1

microglia
0.2

oligodendrocytes
0.8

pyramidal CA1
1

pyramidal SS
1

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Aifm1, Psmd11, Tubb5, Kif9, Ank, Col12a1, Rsrc1, Parp2, Phtf1, Cirbp, Camk1g, Zcchc17, Thumpd3, Nat10, Prkab1, Asap1, Sema3a, Nek3, Ndufa10, Rbm3, Kctd5, Eif5, Nol6, Prss23, Susd4, Sssca1
astrocytes_ependymal
1

endothelial-mural
0.8

interneurons
0.2

microglia
0.4

oligodendrocytes
0.4

pyramidal CA1
0.6

pyramidal SS
0
Fold enrichment: 1.2475597536342
Standard deviations from mean: 3.49792945157607

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Vgll4, Ddx17, Nhsl1, Zc3h10, Sema5a, Add3, Litaf, Strap, Irf5
astrocytes_ependymal
0.2

endothelial-mural
0.2

interneurons
0.9

microglia
0.2

oligodendrocytes
0.2

pyramidal CA1
0.8

pyramidal SS
0.8

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Pdpk1, Sh2b2, Fam184b, Ppig, Egr4, Prpf40a, Plxna2, Ttc17
astrocytes_ependymal
0.7

endothelial-mural
0.7

interneurons
0.6

microglia
0
Fold enrichment: 1.49804244406422
Standard deviations from mean: 1.75098074520754

oligodendrocytes
0.9

pyramidal CA1
0.2

pyramidal SS
0.2

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Wdr31, Prmt2, Arpp19, Gab1, Mid1ip1, Rnf220, Ddx49, Fam171a1, Thap11, Myo10, Mcm7
astrocytes_ependymal
0.5

endothelial-mural
0.6

interneurons
0.8

microglia
0.7

oligodendrocytes
0
Fold enrichment: 1.54867695548019
Standard deviations from mean: 1.91970528493072

pyramidal CA1
0.5

pyramidal SS
0.4

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Rab36, Mab21l2, Pno1, Nup214, Dnajc18, Lgals8, Ahsa2, Rpl27a, Pop1, Fbln1
astrocytes_ependymal
0.6

endothelial-mural
0.1

interneurons
0.8

microglia
0.8

oligodendrocytes
0.3

pyramidal CA1
0.4

pyramidal SS
0.4

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
trying URL 'http://www.informatics.jax.org/downloads/reports/MRK_List2.rpt'
Content type 'unknown' length 38629932 bytes (36.8 MB)
==================================================
downloaded 36.8 MB

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Warning: Input 'exp' stored as characters. Converting to numeric. Check that it looks correct.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
10 of 10 are not proper HGNC symbols
Possible corruption of gene names by excel: Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
10 of 10 are not proper HGNC symbols
Possible corruption of gene names by excel: Mar-01
Maps last updated on: Thu Oct 24 12:31:05 2019
Maps last updated on: Thu Oct 24 12:31:05 2019
9 of 10 gene symbols corrected
1 of 10 gene symbols cannot be mapped
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Tm4sf12
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are: 
Tspan12
1 rows should have been corrected by checking synonms
0 rows STILL do not have proper MGI symbols

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
0 rows do not have proper MGI symbols

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
669 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
308 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are: 
Hjurp
185 rows should have been corrected by checking synonms
126 rows STILL do not have proper MGI symbols
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
308 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are: 
Hjurp
185 rows should have been corrected by checking synonms
126 rows STILL do not have proper MGI symbols
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
440.360  10.892 475.570 

Example timings

EWCE.Rcheck/EWCE-Ex.timings

nameusersystemelapsed
add_res_to_merging_list15.189 0.90017.699
bin_columns_into_quantiles7.8420.1308.207
bin_specificity_into_quantiles8.4080.1918.858
bootstrap_enrichment_test22.111 0.39323.729
check_ewce_genelist_inputs23.063 0.38224.672
controlled_geneset_enrichment25.454 2.08228.505
drop_uninformative_genes7.7750.4368.684
ewce_expression_data27.465 0.56729.631
ewce_plot21.583 0.34023.075
filter_genes_without_1to1_homolog10.859 0.21711.494
fix_bad_hgnc_symbols3.0470.0693.288
fix_bad_mgi_symbols15.363 0.31016.356
generate_bootstrap_plots35.654 0.83538.147
generate_bootstrap_plots_for_transcriptome0.0000.0000.001
generate_celltype_data8.2060.3488.729
generate_controlled_bootstrap_geneset000
get_celltype_table8.1200.1568.545
get_summed_proportions0.0000.0010.000
merge_two_expfiles0.0000.0010.000
merged_ewce0.0000.0000.001
prep_dendro8.7900.1249.168
prepare_genesize_control_network000