Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:08 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for COTAN on nebbiolo1


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? 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 421/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COTAN 1.0.0  (landing page)
Galfrè Silvia Giulia
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/COTAN
git_branch: RELEASE_3_15
git_last_commit: b6a43f1
git_last_commit_date: 2022-04-26 12:20:54 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: COTAN
Version: 1.0.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings COTAN_1.0.0.tar.gz
StartedAt: 2022-10-18 19:13:12 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:16:23 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 191.5 seconds
RetCode: 0
Status:   OK  
CheckDir: COTAN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings COTAN_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/COTAN.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘1.0.0’
* 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 ... 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 for sufficient/correct file permissions ... 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 ... 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 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 31.187  1.974  32.988
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/COTAN.Rcheck/00check.log’
for details.



Installation output

COTAN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL COTAN
###
##############################################################################
##############################################################################


* installing to library ‘/home/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
** 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)

Tests output

COTAN.Rcheck/tests/spelling.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.209   0.031   0.225 

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 version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 CTATTGATCAAA GCCGAGTAAGTC CACGCCGTCCCA TAAATACGTTAT GCGGAGCCTCCT
1119      Nnat    73.168400    43.104810    46.784146    18.684677     51.86938
1834    Tuba1a    30.128165    57.823526    36.613679     8.304301     54.92052
1787    Tmsb10    20.444112    14.718716    11.187513    16.608602     10.67899
917     Malat1     5.380029    10.513368     3.051140    31.141129      6.10228
51        Actb    11.836065    15.770052     9.153420     4.152151     13.73013
1788    Tmsb4x     2.152012     7.359358    26.443213     6.228226      3.05114
1841     Tubb5    11.836065    10.513368    13.221606     0.000000      9.15342
1460     Rpl32     2.152012    13.667379     8.136373    12.456452      6.10228
801   Hsp90ab1     5.380029     6.308021     6.102280    16.608602      6.10228
1837    Tubb2b     5.380029    10.513368     7.119327     2.076075     10.67899
757      H3f3b     7.532041     8.410695     6.102280     4.152151      7.62785
1838     Tubb3     5.380029    11.564705     2.034093     0.000000     13.73013
175     Atpif1     2.152012     6.308021    11.187513     4.152151      7.62785
782  Hnrnpa2b1     7.532041     9.462031     7.119327     4.152151      1.52557
939   Marcksl1     4.304024     6.308021     6.102280     0.000000     12.20456
[1] "cotan analysis"
[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] "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 0.0241643297635311 over 2000"
[1] "Done"
[1] "coex estimation"
[1] "Cleaning RAM"
  [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 16 ]
> 
> proc.time()
   user  system elapsed 
 45.139   5.515  47.130 

Example timings

COTAN.Rcheck/COTAN-Ex.timings

nameusersystemelapsed
add.row.to.meta0.1020.0040.106
automatic.COTAN.object.creation31.187 1.97432.988
clean1.1220.1561.150
cotan_analysis1.2680.0041.271
drop.genes.cells0.0900.0040.095
est.min.parameters0.0850.0040.089
extract.coex0.090.000.09
get.GDI0.1020.0000.103
get.a0.090.000.09
get.cell.number0.0900.0000.089
get.cell.size0.0860.0000.086
get.coex1.8830.0041.887
get.constitutive.genes0.0930.0000.092
get.expected.ct0.5040.0000.505
get.gene.coexpression.space0.0930.0000.093
get.genes0.0860.0000.087
get.lambda0.090.000.09
get.metadata0.090.000.09
get.normdata0.1320.0040.136
get.nu0.0880.0000.088
get.observed.ct0.1040.0000.104
get.pval0.0900.0040.094
get.rawdata0.0930.0000.093
get.subset0.0820.0000.082
initRaw0.3870.0200.407
mat2vec_rfast0.0140.0000.014
plot_GDI0.2300.0280.258
plot_general.heatmap0.8220.0200.842
plot_heatmap0.4980.0080.505
scCOTAN-class0.0210.0000.020
vec2mat_rfast0.0150.0000.015