| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:23 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 dcanr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dcanr.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 492/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dcanr 1.15.0 (landing page) Dharmesh D. Bhuva
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: dcanr |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:dcanr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings dcanr_1.15.0.tar.gz |
| StartedAt: 2023-04-11 19:43:17 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 19:44:49 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 92.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dcanr.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:dcanr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings dcanr_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/dcanr.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘dcanr/DESCRIPTION’ ... OK
* this is package ‘dcanr’ version ‘1.15.0’
* 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 ‘dcanr’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
It is recommended to use ‘given’ instead of ‘middle’.
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 ... 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
ftgi.score: no visible binding for global variable ‘i’
ftgi.score: no visible binding for global variable ‘j’
Undefined global functions or variables:
i j
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 ...
‘dcanr_evaluation_vignette.Rmd’ using ‘UTF-8’... OK
‘dcanr_vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/dcanr.Rcheck/00check.log’
for details.
dcanr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL dcanr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘dcanr’ ... ** using staged installation Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘dcScore’ with signature ‘"Matrix","ANY","ANY"’: no definition for class “Matrix” in method for ‘dcScore’ with signature ‘"ExpressionSet","ANY","ANY"’: no definition for class “ExpressionSet” in method for ‘dcScore’ with signature ‘"SummarizedExperiment","ANY","ANY"’: no definition for class “SummarizedExperiment” in method for ‘dcScore’ with signature ‘"DGEList","ANY","ANY"’: no definition for class “DGEList” ** 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 (dcanr)
dcanr.Rcheck/tests/testthat.Rout
R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 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.
> library(testthat)
> library(dcanr)
>
> test_check("dcanr")
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00600000000000023
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00700000000000145
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00600000000000023
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00500000000000078
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00600000000000023
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00600000000000023
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00600000000000023
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00599999999999845
[ FAIL 0 | WARN 313 | SKIP 0 | PASS 172 ]
[ FAIL 0 | WARN 313 | SKIP 0 | PASS 172 ]
>
> proc.time()
user system elapsed
15.087 0.695 15.774
dcanr.Rcheck/dcanr-Ex.timings
| name | user | system | elapsed | |
| cor.pairs | 0.002 | 0.000 | 0.002 | |
| dcAdjust | 0.004 | 0.000 | 0.003 | |
| dcEvaluate | 1.635 | 0.115 | 1.751 | |
| dcMethods | 0 | 0 | 0 | |
| dcNetwork | 0.086 | 0.000 | 0.087 | |
| dcPipeline | 1.067 | 0.016 | 1.084 | |
| dcScore | 0.002 | 0.000 | 0.002 | |
| dcTest | 1.233 | 0.008 | 1.241 | |
| dcZscore | 0.058 | 0.000 | 0.058 | |
| getSimData | 0.093 | 0.000 | 0.093 | |
| mi.ap | 0.121 | 0.000 | 0.121 | |
| perfMethods | 0 | 0 | 0 | |
| performanceMeasure | 0 | 0 | 0 | |
| plotSimNetwork | 0.146 | 0.011 | 0.158 | |