| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-29 16:33:42 -0000 (Sun, 29 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4021 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 418/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| COTAN 1.3.0 (landing page) Galfrè Silvia Giulia
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: COTAN |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings COTAN_1.3.0.tar.gz |
| StartedAt: 2023-01-28 20:39:21 -0000 (Sat, 28 Jan 2023) |
| EndedAt: 2023-01-28 20:43:54 -0000 (Sat, 28 Jan 2023) |
| EllapsedTime: 273.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: COTAN.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings COTAN_1.3.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/COTAN.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘1.3.0’
* 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 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 loading without being on the library search path ... WARNING
Error in library(COTAN, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") :
there is no package called ‘COTAN’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* 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 ...
‘Guided_tutorial.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/COTAN.Rcheck/00check.log’
for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘COTAN’ ... ** using staged installation ** R ** data ** 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)
COTAN.Rcheck/tests/spelling.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
0.210 0.032 0.233
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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
[1] "Start PCA"
[1] "starting hclust"
[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 0.0241643297642016 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
117.546 4.025 119.493