Keegan Korthauer
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/scDD |
| Branch: RELEASE_3_11 |
| Last Commit: df4ad90 |
| Last Changed Date: 2020-04-27 15:04:13 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:45 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE scDD PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1589/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scDD 1.12.0 Keegan Korthauer
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: scDD |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scDD.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings scDD_1.12.0.tar.gz |
| StartedAt: 2020-10-17 07:58:57 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 08:13:57 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 900.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scDD.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scDD.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings scDD_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/scDD.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scDD/DESCRIPTION' ... OK
* this is package 'scDD' version '1.12.0'
* 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 whether package 'scDD' 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 ... NOTE
Namespaces in Imports field not imported from:
'grDevices' 'graphics' 'stats'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcMV: no visible global function definition for 'var'
classifyDD: no visible global function definition for 'quantile'
classifyDD: no visible global function definition for 'rt'
classifyDD: no visible global function definition for 'lm'
classifyDD: no visible global function definition for 't.test'
feDP: no visible global function definition for 'runif'
feDP: no visible global function definition for 'lm'
feDP: no visible global function definition for 't.test'
feDP: no visible global function definition for 'fisher.test'
feDP: no visible global function definition for 'p.adjust'
findFC : createFindFC: no visible global function definition for
'quantile'
findFC : createFindFC : f: no visible global function definition for
'runif'
findFC: no visible global function definition for 'par'
findFC: no visible global function definition for 'points'
mclustRestricted: no visible global function definition for 'runif'
permMclustCov: no visible global function definition for 'model.matrix'
permMclustCov: no visible global function definition for 'lm'
permMclustCov : getPerm: no visible global function definition for
'residuals'
permMclustGene: no visible global function definition for
'model.matrix'
permMclustGene: no visible global function definition for 'lm'
permMclustGene: no visible global function definition for 'residuals'
scDD: no visible global function definition for 'p.adjust'
scDD : fishersCombinedPval: no visible global function definition for
'pchisq'
sideHist : ggplotColours: no visible global function definition for
'hcl'
sideHist: no visible global function definition for 'hist'
sideHist: no visible global function definition for 'axis'
sideHist: no visible global function definition for 'rect'
sideHist: no visible global function definition for 'lines'
sideHist: no visible global function definition for 'density'
simuDB: no visible global function definition for 'rnbinom'
simuDE: no visible global function definition for 'rnbinom'
simuDE: no visible global function definition for 'var'
simuDM: no visible global function definition for 'rnbinom'
simuDP: no visible global function definition for 'rbinom'
simuDP: no visible global function definition for 'rnbinom'
simulateSet: no visible global function definition for 'pdf'
simulateSet: no visible global function definition for 'dev.off'
simulateSet: no visible global function definition for 'runif'
singleCellSimu: no visible global function definition for 'var'
singleCellSimu: no visible global function definition for 'lm'
testKS : onegene: no visible global function definition for 'ks.test'
testKS: no visible global function definition for 'p.adjust'
testZeroes : onegene: no visible global function definition for
'binomial'
validation : <anonymous>: no visible global function definition for
'var'
validation: no visible binding for global variable 'var'
validation: no visible global function definition for 'par'
validation: no visible global function definition for 'abline'
validation: no visible global function definition for 'points'
Undefined global functions or variables:
abline axis binomial density dev.off fisher.test hcl hist ks.test
lines lm model.matrix p.adjust par pchisq pdf points quantile rbinom
rect residuals rnbinom rt runif t.test var
Consider adding
importFrom("grDevices", "dev.off", "hcl", "pdf")
importFrom("graphics", "abline", "axis", "hist", "lines", "par",
"points", "rect")
importFrom("stats", "binomial", "density", "fisher.test", "ks.test",
"lm", "model.matrix", "p.adjust", "pchisq", "quantile",
"rbinom", "residuals", "rnbinom", "rt", "runif", "t.test",
"var")
to your NAMESPACE file.
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
results 9.60 0.43 46.21
scDD 9.42 0.14 101.37
simulateSet 2.65 0.12 112.77
testKS 0.97 0.05 17.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
scDD 11.72 0.19 111.48
results 11.08 0.17 47.98
simulateSet 3.21 0.16 117.34
testKS 0.94 0.04 19.55
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/scDD.Rcheck/00check.log'
for details.
scDD.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/scDD_1.12.0.tar.gz && rm -rf scDD.buildbin-libdir && mkdir scDD.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scDD.buildbin-libdir scDD_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL scDD_1.12.0.zip && rm scDD_1.12.0.tar.gz scDD_1.12.0.zip
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% 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 520k 100 520k 0 0 8147k 0 --:--:-- --:--:-- --:--:-- 9126k
install for i386
* installing *source* package 'scDD' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'scDD'
finding HTML links ... done
calcMV html
calcRP html
classifyDD html
feDP html
findFC html
findIndex html
findOutliers html
getPosteriorParams html
jointPosterior html
lu html
luOutlier html
mclustRestricted html
permMclust html
permMclustCov html
permMclustGene html
permZero html
preprocess html
results html
scDD html
scDatEx html
scDatExList html
scDatExSim html
sideHist html
sideViolin html
simuDB html
simuDE html
simuDM html
simuDP html
simulateSet html
singleCellSimu html
testKS html
testZeroes html
validation html
** 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
install for x64
* installing *source* package 'scDD' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scDD' as scDD_1.12.0.zip
* DONE (scDD)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'scDD' successfully unpacked and MD5 sums checked
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scDD.Rcheck/examples_i386/scDD-Ex.timings
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scDD.Rcheck/examples_x64/scDD-Ex.timings
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