Alan Murphy
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/EWCE |
| git_branch: RELEASE_3_13 |
| git_last_commit: 680dd7d |
| git_last_commit_date: 2021-06-17 12:23:07 -0400 (Thu, 17 Jun 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:35 -0400 (Fri, 15 Oct 2021).
|
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. |
| Package 601/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EWCE 1.0.1 (landing page) Alan Murphy
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: EWCE |
| Version: 1.0.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EWCE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EWCE_1.0.1.tar.gz |
| StartedAt: 2021-10-14 18:55:01 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 19:10:06 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 905.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EWCE.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EWCE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EWCE_1.0.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/EWCE.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.0.1’
* 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 31.592 0.754 34.146
ewce_expression_data 23.759 0.425 26.116
controlled_geneset_enrichment 21.699 1.526 24.291
bootstrap_enrichment_test 21.445 0.412 23.194
check_ewce_genelist_inputs 21.296 0.308 22.941
ewce_plot 19.257 0.278 20.755
add_res_to_merging_list 13.562 0.718 15.681
fix_bad_mgi_symbols 13.408 0.249 14.298
filter_genes_without_1to1_homolog 8.499 0.204 9.164
bin_specificity_into_quantiles 8.052 0.166 8.488
generate_celltype_data 7.761 0.194 8.144
bin_columns_into_quantiles 7.435 0.162 7.837
prep_dendro 7.427 0.087 7.769
get_celltype_table 6.855 0.165 7.283
drop_uninformative_genes 6.335 0.370 6.961
* 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
EWCE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/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)
EWCE.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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(): 2021-05-18
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
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see ?ewceData and browseVignettes('ewceData') for documentation
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see ?ewceData and browseVignettes('ewceData') for documentation
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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
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see ?ewceData and browseVignettes('ewceData') for documentation
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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
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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 38615650 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
393.636 10.048 424.829
EWCE.Rcheck/EWCE-Ex.timings
| name | user | system | elapsed | |
| add_res_to_merging_list | 13.562 | 0.718 | 15.681 | |
| bin_columns_into_quantiles | 7.435 | 0.162 | 7.837 | |
| bin_specificity_into_quantiles | 8.052 | 0.166 | 8.488 | |
| bootstrap_enrichment_test | 21.445 | 0.412 | 23.194 | |
| check_ewce_genelist_inputs | 21.296 | 0.308 | 22.941 | |
| controlled_geneset_enrichment | 21.699 | 1.526 | 24.291 | |
| drop_uninformative_genes | 6.335 | 0.370 | 6.961 | |
| ewce_expression_data | 23.759 | 0.425 | 26.116 | |
| ewce_plot | 19.257 | 0.278 | 20.755 | |
| filter_genes_without_1to1_homolog | 8.499 | 0.204 | 9.164 | |
| fix_bad_hgnc_symbols | 2.851 | 0.053 | 3.101 | |
| fix_bad_mgi_symbols | 13.408 | 0.249 | 14.298 | |
| generate_bootstrap_plots | 31.592 | 0.754 | 34.146 | |
| generate_bootstrap_plots_for_transcriptome | 0.001 | 0.000 | 0.000 | |
| generate_celltype_data | 7.761 | 0.194 | 8.144 | |
| generate_controlled_bootstrap_geneset | 0 | 0 | 0 | |
| get_celltype_table | 6.855 | 0.165 | 7.283 | |
| get_summed_proportions | 0 | 0 | 0 | |
| merge_two_expfiles | 0 | 0 | 0 | |
| merged_ewce | 0 | 0 | 0 | |
| prep_dendro | 7.427 | 0.087 | 7.769 | |
| prepare_genesize_control_network | 0 | 0 | 0 | |