Dharmesh D. Bhuva
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/dcanr |
| git_branch: RELEASE_3_18 |
| git_last_commit: 01a78db |
| git_last_commit_date: 2023-10-24 11:13:22 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:35 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 | ||||
| Package 502/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dcanr 1.18.0 (landing page) Dharmesh D. Bhuva
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: dcanr |
| Version: 1.18.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:dcanr.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings dcanr_1.18.0.tar.gz |
| StartedAt: 2023-11-02 09:47:43 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 09:48:57 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 73.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dcanr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:dcanr.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings dcanr_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/dcanr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dcanr/DESCRIPTION’ ... OK
* this is package ‘dcanr’ version ‘1.18.0’
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/dcanr.Rcheck/00check.log’
for details.
dcanr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL dcanr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
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.
> 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: 0.0160000000000018
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: 0.0100000000000016
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: 0.0100000000000016
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: 0.00999999999999801
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: 0.00999999999999801
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0100000000000016
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: 0.0120000000000005
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0109999999999992
[ FAIL 0 | WARN 313 | SKIP 0 | PASS 172 ]
[ FAIL 0 | WARN 313 | SKIP 0 | PASS 172 ]
>
> proc.time()
user system elapsed
24.580 1.571 27.388
dcanr.Rcheck/dcanr-Ex.timings
| name | user | system | elapsed | |
| cor.pairs | 0.002 | 0.000 | 0.002 | |
| dcAdjust | 0.002 | 0.002 | 0.003 | |
| dcEvaluate | 2.202 | 0.076 | 2.297 | |
| dcMethods | 0.001 | 0.000 | 0.000 | |
| dcNetwork | 0.111 | 0.000 | 0.116 | |
| dcPipeline | 1.632 | 0.000 | 1.635 | |
| dcScore | 0.002 | 0.000 | 0.002 | |
| dcTest | 1.863 | 0.020 | 1.888 | |
| dcZscore | 0.093 | 0.002 | 0.095 | |
| getSimData | 0.106 | 0.004 | 0.110 | |
| mi.ap | 0.185 | 0.000 | 0.185 | |
| perfMethods | 0 | 0 | 0 | |
| performanceMeasure | 0.000 | 0.000 | 0.001 | |
| plotSimNetwork | 0.187 | 0.004 | 0.191 | |