Davide Risso
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/zinbwave |
| Branch: master |
| Last Commit: 53dca9a |
| Last Changed Date: 2019-03-11 11:31:23 -0400 (Mon, 11 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:31:24 -0400 (Tue, 09 Apr 2019).
| Package 1702/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| zinbwave 1.5.2 Davide Risso
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: zinbwave |
| Version: 1.5.2 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:zinbwave.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings zinbwave_1.5.2.tar.gz |
| StartedAt: 2019-04-09 06:42:38 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 07:19:58 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 2240.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: zinbwave.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:zinbwave.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings zinbwave_1.5.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/zinbwave.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'zinbwave/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'zinbwave' version '1.5.2'
* 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 'zinbwave' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/glmWeightedF.Rd:35: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/glmWeightedF.Rd:52: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/independentFiltering.Rd:19: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbFit.Rd:62: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbFit.Rd:90: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbInitialize.Rd:22: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbOptimize.Rd:28: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbOptimizeDispersion.Rd:27: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbsurf.Rd:48: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbsurf.Rd:79: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbwave.Rd:64: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbwave.Rd:117: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/zinbwave.Rcheck/00install.out' for details.
* 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 ... OK
* 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 or elapsed time > 5s
user system elapsed
zinbFit 1.01 0.30 299.32
zinbsurf 0.87 0.17 144.64
zinbOptimize 0.49 0.10 130.23
zinbwave 0.50 0.06 145.68
zinbInitialize 0.21 0.09 95.70
zinbOptimizeDispersion 0.22 0.08 87.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
zinbsurf 0.92 0.17 149.48
zinbFit 0.82 0.26 299.64
zinbwave 0.44 0.11 148.53
zinbOptimize 0.23 0.14 141.68
zinbOptimizeDispersion 0.27 0.08 90.32
zinbInitialize 0.20 0.03 100.22
* 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 WARNING
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/zinbwave.Rcheck/00check.log'
for details.
zinbwave.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/zinbwave_1.5.2.tar.gz && rm -rf zinbwave.buildbin-libdir && mkdir zinbwave.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=zinbwave.buildbin-libdir zinbwave_1.5.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL zinbwave_1.5.2.zip && rm zinbwave_1.5.2.tar.gz zinbwave_1.5.2.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 100k 100 100k 0 0 1606k 0 --:--:-- --:--:-- --:--:-- 1771k
install for i386
* installing *source* package 'zinbwave' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'zinbwave'
finding HTML links ... done
ZinbModel-class html
computeDevianceResiduals html
computeObservationalWeights html
getAlpha_mu html
getAlpha_pi html
getBeta_mu html
getBeta_pi html
getEpsilon_W html
getEpsilon_alpha html
getEpsilon_beta_mu html
getEpsilon_beta_pi html
getEpsilon_gamma_mu html
getEpsilon_gamma_pi html
getEpsilon_zeta html
getGamma_mu html
getGamma_pi html
getLogMu html
getLogitPi html
getMu html
getPhi html
getPi html
getTheta html
getV_mu html
getV_pi html
getW html
getX_mu html
getX_pi html
getZeta html
glmWeightedF html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/glmWeightedF.Rd:35: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/glmWeightedF.Rd:52: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
imputeZeros html
independentFiltering html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/independentFiltering.Rd:19: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
loglik html
nFactors html
nFeatures html
nParams html
nSamples html
orthogonalizeTraceNorm html
penalty html
pvalueAdjustment html
solveRidgeRegression html
toydata html
zinb.loglik html
zinb.loglik.dispersion html
zinb.loglik.dispersion.gradient html
zinb.loglik.matrix html
zinb.loglik.regression html
zinb.loglik.regression.gradient html
zinb.regression.parseModel html
zinbAIC html
zinbBIC html
zinbFit html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbFit.Rd:62: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbFit.Rd:90: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
zinbInitialize html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbInitialize.Rd:22: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
zinbModel html
zinbOptimize html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbOptimize.Rd:28: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
zinbOptimizeDispersion html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbOptimizeDispersion.Rd:27: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
zinbSim html
zinbsurf html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbsurf.Rd:48: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbsurf.Rd:79: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
zinbwave html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbwave.Rd:64: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8oo7QK/R.INSTALLe2062e7887/zinbwave/man/zinbwave.Rd:117: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
** 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 'zinbwave' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'zinbwave' as zinbwave_1.5.2.zip
* DONE (zinbwave)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'zinbwave' successfully unpacked and MD5 sums checked
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zinbwave.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(zinbwave)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: SingleCellExperiment
>
> test_check("zinbwave")
user system elapsed
0.02 0.00 0.02
user system elapsed
0.03 0.00 0.03
user system elapsed
0.01 0.00 0.01
user system elapsed
0 0 0
== testthat results ===========================================================
OK: 159 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
56.84 0.90 57.73
|
zinbwave.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(zinbwave)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: SingleCellExperiment
>
> test_check("zinbwave")
user system elapsed
0.03 0.00 0.03
user system elapsed
0.02 0.00 0.01
user system elapsed
0.03 0.00 0.04
user system elapsed
0.02 0.00 0.01
== testthat results ===========================================================
OK: 159 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
59.26 0.40 59.65
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zinbwave.Rcheck/examples_i386/zinbwave-Ex.timings
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zinbwave.Rcheck/examples_x64/zinbwave-Ex.timings
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