Lukas M. Weber
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/diffcyt |
| Branch: RELEASE_3_8 |
| Last Commit: 8bdfd18 |
| Last Changed Date: 2019-04-04 13:58:46 -0400 (Thu, 04 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:09 -0400 (Sat, 13 Apr 2019).
| Package 408/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| diffcyt 1.2.23 Lukas M. Weber
| malbec1 | Linux (Ubuntu 16.04.6 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: 1.2.23 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings diffcyt_1.2.23.tar.gz |
| StartedAt: 2019-04-13 01:48:26 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:54:28 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 361.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: diffcyt.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings diffcyt_1.2.23.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/diffcyt.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'diffcyt/DESCRIPTION' ... OK
* this is package 'diffcyt' version '1.2.23'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
testDA_GLMM 8.27 0.08 8.44
diffcyt 7.09 0.01 7.11
plotHeatmap 6.24 0.25 6.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
testDA_GLMM 8.84 0.03 8.88
diffcyt 7.47 0.03 7.50
plotHeatmap 6.28 0.08 6.36
topTable 5.93 0.03 5.96
testDS_LMM 5.32 0.00 5.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.8-bioc/meat/diffcyt.Rcheck/00check.log'
for details.
diffcyt.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/diffcyt_1.2.23.tar.gz && rm -rf diffcyt.buildbin-libdir && mkdir diffcyt.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diffcyt.buildbin-libdir diffcyt_1.2.23.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL diffcyt_1.2.23.zip && rm diffcyt_1.2.23.tar.gz diffcyt_1.2.23.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 188k 100 188k 0 0 4173k 0 --:--:-- --:--:-- --:--:-- 4498k
install for i386
* installing *source* package 'diffcyt' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'diffcyt'
finding HTML links ... done
calcCounts html
finding level-2 HTML links ... done
calcMedians html
calcMediansByClusterMarker html
calcMediansBySampleMarker html
createContrast html
createDesignMatrix html
createFormula html
diffcyt html
generateClusters html
plotHeatmap html
prepareData html
testDA_GLMM html
testDA_edgeR html
testDA_voom html
testDS_LMM html
testDS_limma html
topClusters html
topTable html
transformData html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'diffcyt' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'diffcyt' as diffcyt_1.2.23.zip
* DONE (diffcyt)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'diffcyt' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
diffcyt.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 FAILED: 0
>
> proc.time()
user system elapsed
9.37 0.79 10.15
|
diffcyt.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 FAILED: 0
>
> proc.time()
user system elapsed
7.67 0.39 8.04
|
|
diffcyt.Rcheck/examples_i386/diffcyt-Ex.timings
|
diffcyt.Rcheck/examples_x64/diffcyt-Ex.timings
|