Galfrè Silvia Giulia
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/COTAN |
| git_branch: master |
| git_last_commit: 27234e7 |
| git_last_commit_date: 2021-12-26 04:55:08 -0400 (Sun, 26 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:16 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the COTAN package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.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 410/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| COTAN 0.99.10 (landing page) Galfrè Silvia Giulia
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: COTAN |
| Version: 0.99.10 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:COTAN.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings COTAN_0.99.10.tar.gz |
| StartedAt: 2022-03-17 18:49:24 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:52:41 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 197.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COTAN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:COTAN.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings COTAN_0.99.10.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/COTAN.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'COTAN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'COTAN' version '0.99.10'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'COTAN' 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 ... NOTE
automatic.COTAN.object.creation,data.frame: no visible binding for
global variable 'means'
automatic.COTAN.object.creation,data.frame: no visible binding for
global variable 'PC1'
automatic.COTAN.object.creation,data.frame: no visible binding for
global variable 'PC2'
automatic.COTAN.object.creation,data.frame: no visible binding for
global variable 'nu'
clean,scCOTAN: no visible binding for global variable 'PC1'
clean,scCOTAN: no visible binding for global variable 'PC2'
fun_linear,scCOTAN : <anonymous>: no visible global function definition
for 'python_PCA'
plot_GDI,scCOTAN: no visible binding for global variable 'sum.raw.norm'
plot_heatmap,ANY: no visible binding for global variable 'time'
plot_heatmap,ANY: no visible binding for global variable 'g2'
Undefined global functions or variables:
PC1 PC2 g2 means nu python_PCA sum.raw.norm time
Consider adding
importFrom("stats", "time")
to your NAMESPACE file.
* 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 line endings in shell scripts ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
automatic.COTAN.object.creation 28.53 3.11 34.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'spelling.R'
Comparing 'spelling.Rout' to 'spelling.Rout.save' ...6c6
< NULL
---
> All Done!
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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/COTAN.Rcheck/00check.log'
for details.
COTAN.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL COTAN
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'COTAN' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'COTAN'
finding HTML links ... done
ERCC.cotan html
ERCCraw html
add.row.to.meta html
automatic.COTAN.object.creation html
clean html
cotan_analysis html
drop.genes.cells html
fun_linear html
get.GDI html
get.a html
get.cell.number html
get.cell.size html
get.coex html
get.constitutive.genes html
get.expected.ct html
get.gene.coexpression.space html
get.genes html
get.lambda html
get.metadata html
get.normdata html
get.nu html
get.observed.ct html
get.pval html
get.rawdata html
initRaw html
plot_GDI html
plot_general.heatmap html
plot_heatmap html
raw.dataset html
scCOTAN-class html
** 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 (COTAN)
Making 'packages.html' ... done
COTAN.Rcheck/tests/spelling.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.14 0.09 0.20
COTAN.Rcheck/tests/spelling.Rout.save
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
All Done!
>
> proc.time()
user system elapsed
0.372 0.039 0.408
COTAN.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> Sys.setenv(R_TESTS="")
> library(testthat)
> library(COTAN)
> test_check("COTAN")
[1] "Initializing S4 object"
[1] "Initializing S4 object"
[1] "Start estimation mu with linear method"
[1] 2000 815
rowname TGTGATGGAGCC AGTCCGAATGAG GTTGTGAGCTAG CTATTGATCAAA GCTTAGATCATA
589 Fabp7 124.178696 122.783009 127.44699 0.000000 112.708375
1354 Ptn 10.166677 41.280494 18.60540 0.000000 13.775468
1834 Tuba1a 21.059545 7.409319 10.23297 30.128165 6.261576
443 Dbi 23.238119 19.052536 12.09351 0.000000 22.541675
107 Apoe 15.250015 14.818639 8.37243 0.000000 41.326404
1119 Nnat 0.000000 4.233897 4.65135 73.168400 6.261576
410 Cst3 26.142883 11.643216 2.79081 0.000000 10.018522
1788 Tmsb4x 17.428589 13.760165 9.30270 2.152012 6.261576
51 Actb 15.250015 11.643216 14.88432 11.836065 15.027783
1649 Sparcl1 0.000000 14.818639 15.81459 0.000000 13.775468
1016 Mt3 22.511927 3.175423 1.86054 0.000000 1.252315
1833 Ttyh1 7.261912 13.760165 8.37243 0.000000 17.532414
917 Malat1 4.357147 23.286433 3.72108 5.380029 8.766207
395 Cpe 1.452382 4.233897 7.44216 1.076006 5.009261
782 Hnrnpa2b1 2.904765 10.584742 7.44216 7.532041 12.523153
GCCGAGTAAGTC TCGCCCTAATCG TTCAGAATACAG CACGCCGTCCCA CCGACGTCTCCG
589 0.000000 128.628433 119.479408 0.000000 126.746326
1354 0.000000 55.868915 25.075925 0.000000 10.689449
1834 57.823526 2.598554 2.950109 36.613679 4.581193
443 0.000000 14.292048 10.325381 1.017047 16.797706
107 0.000000 5.197108 25.075925 0.000000 21.378898
1119 43.104810 9.094940 2.950109 46.784146 9.162385
410 1.051337 2.598554 17.700653 1.017047 10.689449
1788 7.359358 11.693494 17.700653 26.443213 13.743578
51 15.770052 5.197108 8.850326 9.153420 4.581193
1649 0.000000 6.496385 19.175707 0.000000 18.324770
1016 0.000000 0.000000 4.425163 0.000000 3.054128
1833 0.000000 9.094940 5.900218 0.000000 10.689449
917 10.513368 7.795663 2.950109 3.051140 0.000000
395 0.000000 0.000000 5.900218 1.017047 13.743578
782 9.462031 9.094940 7.375272 7.119327 3.054128
CTGATTTGTCGA GCTGGAGCCACT GCATGGAAACCA GTCTCAAGAATT GCGGAGCCTCCT
589 124.730601 114.463566 148.861898 141.926311 0.00000
1354 8.427743 19.077261 54.843857 16.455224 0.00000
1834 10.113292 13.874372 10.446449 20.569031 54.92052
443 23.597681 26.014447 10.446449 32.910449 0.00000
107 6.742195 32.951633 28.727735 6.170709 0.00000
1119 1.685549 0.000000 0.000000 4.113806 51.86938
410 23.597681 17.342965 18.281286 2.056903 1.52557
1788 20.226584 6.937186 0.000000 12.341418 3.05114
51 13.484389 10.405779 5.223225 6.170709 13.73013
1649 15.169938 0.000000 36.562572 0.000000 0.00000
1016 18.541035 22.545854 7.834837 16.455224 0.00000
1833 5.056646 10.405779 10.446449 4.113806 0.00000
917 1.685549 3.468593 7.834837 2.056903 6.10228
395 5.056646 13.874372 15.669674 6.170709 1.52557
782 1.685549 0.000000 5.223225 6.170709 1.52557
AGACTCAGGATT GCCGCGGAAGGT ACCGATGTTCCC
589 125.447444 135.320935 130.799708
1354 53.763190 29.417595 20.927953
1834 4.480266 21.572903 13.079971
443 17.921063 33.339941 36.623918
107 22.401329 49.029324 7.847982
1119 2.240133 0.000000 2.615994
410 8.960532 31.378768 20.927953
1788 8.960532 5.883519 18.311959
51 6.720399 9.805865 18.311959
1649 11.200665 0.000000 18.311959
1016 11.200665 13.728211 5.231988
1833 8.960532 11.767038 2.615994
917 8.960532 7.844692 10.463977
395 6.720399 25.495249 0.000000
782 6.720399 1.961173 13.079971
[1] "cotan analysis"
[1] "On windows the numebr of cores used will be 1! Multicore is not supported."
[1] "mu estimator creation"
[1] "save effective constitutive genes"
[1] "start a minimization"
[1] "Next gene: Trim2 number 1810"
[1] "Final trance!"
[1] "a min: -0.08001708984375 | a max 24.5703125 | negative a %: 2.4"
[1] "coex dataframe creation"
[1] "Generating contingency tables for observed data"
[1] "creation of observed yes/yes contingency table"
[1] "mu estimator creation"
[1] "expected contingency tables creation"
[1] "The distance between estimated n of zeros and observed number of zero is 0.0241643297635298 over 2000"
[1] "Done"
[1] "coex estimation"
[1] "Diagonal coex values substituted with 0"
[1] "0610009D07Rik" "0610010F05Rik" "1110001J03Rik" "1110004F10Rik"
[5] "1110008F13Rik" "1110038B12Rik" "1500011B03Rik" "1500012F01Rik"
[9] "1700020I14Rik" "1700021F05Rik" "1700025G04Rik" "1810022K09Rik"
[13] "1810037I17Rik" "2010107E04Rik" "2010107G23Rik" "2210016L21Rik"
[17] "2310036O22Rik" "2410002F23Rik" "2410006H16Rik" "2410015M20Rik"
[21] "2410066E13Rik" "2610017I09Rik" "2610203C20Rik" "2700029M09Rik"
[25] "2700060E02Rik" "2700094K13Rik" "2810004N23Rik" "2810008D09Rik"
[29] "2810428I15Rik" "2900011O08Rik" "4833420G17Rik" "4833439L19Rik"
[33] "4921524J17Rik" "4930506M07Rik" "4931428F04Rik" "6330403K07Rik"
[37] "9130024F11Rik" "9330159F19Rik" "A030009H04Rik" "Aamp"
[41] "Abcf1" "Abr" "Abracl" "Acat1"
[45] "Acat2" "Acbd5" "Acbd6" "Acin1"
[49] "Aco2" "Acot7" "Actb" "Actl6b"
[53] "Actr10" "Actr1a" "Actr2" "Actr3"
[57] "Adam10" "Add1" "Add2" "Adh5"
[61] "Adprh" "Adss" "Aes" "Aff4"
[65] "Aggf1" "Agrn" "Ahi1" "Ahsa1"
[69] "Ahsa2" "Aimp1" "Akap8" "Akap8l"
[73] "Akap9" "Akirin2" "Akr1a1" "Akt3"
[77] "Aldoa" "Aldoc" "Alg2" "Amer2"
[81] "Anapc11" "Anapc13" "Anapc16" "Anapc5"
[85] "Ank2" "Ank3" "Ankra2" "Ankrd10"
[89] "Ankrd11" "Ankrd12" "Ankrd32" "Anp32a"
[93] "Anp32b" "Anp32e" "Ap1m1" "Ap1s1"
[97] "Ap2m1" "Ap2s1" "Ap3b2" "Apba2"
[1] "Get p-values on a set of genes on columns on a set of genes on rows"
[1] "Using function S"
[1] "function to generate S "
[1] "function to generate GDI dataframe"
[1] "Using S"
[1] "function to generate S "
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
>
> proc.time()
user system elapsed
43.51 4.43 49.82
COTAN.Rcheck/COTAN-Ex.timings
| name | user | system | elapsed | |
| add.row.to.meta | 0.03 | 0.02 | 0.05 | |
| automatic.COTAN.object.creation | 28.53 | 3.11 | 34.01 | |
| clean | 1.13 | 0.23 | 1.16 | |
| cotan_analysis | 1.18 | 0.04 | 1.22 | |
| drop.genes.cells | 0.05 | 0.01 | 0.06 | |
| get.GDI | 0.08 | 0.00 | 0.08 | |
| get.a | 0.06 | 0.00 | 0.07 | |
| get.cell.number | 0.04 | 0.00 | 0.04 | |
| get.cell.size | 0.05 | 0.00 | 0.04 | |
| get.coex | 0.42 | 0.02 | 0.44 | |
| get.constitutive.genes | 0.06 | 0.00 | 0.06 | |
| get.expected.ct | 0.39 | 0.01 | 0.41 | |
| get.gene.coexpression.space | 0.08 | 0.02 | 0.10 | |
| get.genes | 0.03 | 0.01 | 0.04 | |
| get.lambda | 0.03 | 0.02 | 0.04 | |
| get.metadata | 0.05 | 0.00 | 0.05 | |
| get.normdata | 0.11 | 0.00 | 0.11 | |
| get.nu | 0.05 | 0.01 | 0.06 | |
| get.observed.ct | 0.07 | 0.00 | 0.06 | |
| get.pval | 0.06 | 0.00 | 0.06 | |
| get.rawdata | 0.06 | 0.00 | 0.06 | |
| initRaw | 0.19 | 0.16 | 0.35 | |
| plot_GDI | 0.26 | 0.04 | 0.31 | |
| plot_general.heatmap | 0.86 | 0.05 | 0.93 | |
| plot_heatmap | 0.51 | 0.02 | 0.55 | |
| scCOTAN-class | 0.00 | 0.01 | 0.01 | |