Lukas M. Weber
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/diffcyt |
| Branch: RELEASE_3_9 |
| Last Commit: cb777f8 |
| Last Changed Date: 2019-09-16 16:16:06 -0400 (Mon, 16 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:13:55 -0400 (Wed, 16 Oct 2019).
| Package 433/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| diffcyt 1.4.4 Lukas M. Weber
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: diffcyt |
| Version: 1.4.4 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings diffcyt_1.4.4.tar.gz |
| StartedAt: 2019-10-16 01:10:42 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:14:58 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 255.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: diffcyt.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings diffcyt_1.4.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/diffcyt.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.4’
* 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
diffcyt 10.953 0.039 11.051
testDA_GLMM 10.609 0.012 10.629
testDS_LMM 6.542 0.000 6.550
topTable 5.370 0.004 5.379
* 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-3.9-bioc/meat/diffcyt.Rcheck/00check.log’
for details.
diffcyt.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL diffcyt ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
9.547 0.374 9.906
diffcyt.Rcheck/diffcyt-Ex.timings
| name | user | system | elapsed | |
| calcCounts | 1.406 | 0.068 | 1.474 | |
| calcMedians | 1.782 | 0.055 | 1.837 | |
| calcMediansByClusterMarker | 1.332 | 0.000 | 1.332 | |
| calcMediansBySampleMarker | 0.97 | 0.00 | 0.97 | |
| createContrast | 0 | 0 | 0 | |
| createDesignMatrix | 0.008 | 0.000 | 0.008 | |
| createFormula | 0.003 | 0.000 | 0.003 | |
| diffcyt | 10.953 | 0.039 | 11.051 | |
| generateClusters | 1.297 | 0.004 | 1.300 | |
| plotHeatmap | 4.893 | 0.012 | 4.906 | |
| prepareData | 0.019 | 0.000 | 0.020 | |
| testDA_GLMM | 10.609 | 0.012 | 10.629 | |
| testDA_edgeR | 1.627 | 0.000 | 1.671 | |
| testDA_voom | 1.715 | 0.004 | 1.719 | |
| testDS_LMM | 6.542 | 0.000 | 6.550 | |
| testDS_limma | 2.619 | 0.000 | 2.620 | |
| topTable | 5.370 | 0.004 | 5.379 | |
| transformData | 0.046 | 0.000 | 0.046 | |