Lukas M. Weber
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/diffcyt |
| Branch: RELEASE_3_10 |
| Last Commit: 24bb88c |
| Last Changed Date: 2020-04-06 18:41:11 -0400 (Mon, 06 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:14:02 -0400 (Wed, 15 Apr 2020).
| Package 454/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| diffcyt 1.6.6 Lukas M. Weber
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: diffcyt |
| Version: 1.6.6 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings diffcyt_1.6.6.tar.gz |
| StartedAt: 2020-04-15 05:38:45 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:43:51 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 306.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: diffcyt.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings diffcyt_1.6.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/diffcyt.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffcyt/DESCRIPTION’ ... OK
* this is package ‘diffcyt’ version ‘1.6.6’
* 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 ‘diffcyt’ 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
calcCounts: no visible binding for global variable ‘cluster_id’
calcCounts: no visible binding for global variable ‘sample_id’
calcMedians: no visible binding for global variable ‘cluster_id’
calcMedians: no visible binding for global variable ‘sample_id’
calcMedians: no visible binding for global variable ‘value’
calcMediansByClusterMarker: no visible binding for global variable
‘cluster_id’
calcMediansByClusterMarker: no visible binding for global variable
‘marker_id’
calcMediansByClusterMarker: no visible binding for global variable
‘value’
calcMediansBySampleMarker: no visible binding for global variable
‘sample_id’
calcMediansBySampleMarker: no visible binding for global variable
‘marker_id’
calcMediansBySampleMarker: no visible binding for global variable
‘value’
Undefined global functions or variables:
cluster_id marker_id sample_id value
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
testDA_GLMM 10.564 0.004 10.614
diffcyt 10.544 0.004 10.616
plotHeatmap 6.376 0.012 6.397
topTable 6.020 0.008 6.115
testDS_LMM 5.504 0.004 5.550
* 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-3.10-bioc/meat/diffcyt.Rcheck/00check.log’
for details.
diffcyt.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL diffcyt ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘diffcyt’ ... ** using staged installation ** R ** 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 (diffcyt)
diffcyt.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(diffcyt)
>
> test_check("diffcyt")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.972 0.556 15.623
diffcyt.Rcheck/diffcyt-Ex.timings
| name | user | system | elapsed | |
| calcCounts | 1.824 | 0.004 | 1.834 | |
| calcMedians | 1.844 | 0.040 | 1.908 | |
| calcMediansByClusterMarker | 1.496 | 0.000 | 1.499 | |
| calcMediansBySampleMarker | 1.216 | 0.000 | 1.218 | |
| createContrast | 0 | 0 | 0 | |
| createDesignMatrix | 0.008 | 0.000 | 0.008 | |
| createFormula | 0.004 | 0.000 | 0.002 | |
| diffcyt | 10.544 | 0.004 | 10.616 | |
| generateClusters | 1.388 | 0.000 | 1.396 | |
| plotHeatmap | 6.376 | 0.012 | 6.397 | |
| prepareData | 0.024 | 0.000 | 0.025 | |
| testDA_GLMM | 10.564 | 0.004 | 10.614 | |
| testDA_edgeR | 2.096 | 0.000 | 2.099 | |
| testDA_voom | 1.940 | 0.000 | 1.948 | |
| testDS_LMM | 5.504 | 0.004 | 5.550 | |
| testDS_limma | 2.964 | 0.004 | 3.025 | |
| topTable | 6.020 | 0.008 | 6.115 | |
| transformData | 0.056 | 0.000 | 0.056 | |