Davide Risso
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/zinbwave |
| Branch: RELEASE_3_6 |
| Last Commit: ace352e |
| Last Changed Date: 2017-10-30 12:41:31 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:30:00 -0400 (Thu, 12 Apr 2018).
| Package 1471/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| zinbwave 1.0.0 Davide Risso
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: zinbwave |
| Version: 1.0.0 |
| Command: rm -rf zinbwave.buildbin-libdir zinbwave.Rcheck && mkdir zinbwave.buildbin-libdir zinbwave.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=zinbwave.buildbin-libdir zinbwave_1.0.0.tar.gz >zinbwave.Rcheck\00install.out 2>&1 && cp zinbwave.Rcheck\00install.out zinbwave-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=zinbwave.buildbin-libdir --install="check:zinbwave-install.out" --force-multiarch --no-vignettes --timings zinbwave_1.0.0.tar.gz |
| StartedAt: 2018-04-12 03:54:47 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 04:19:15 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 1468.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: zinbwave.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf zinbwave.buildbin-libdir zinbwave.Rcheck && mkdir zinbwave.buildbin-libdir zinbwave.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=zinbwave.buildbin-libdir zinbwave_1.0.0.tar.gz >zinbwave.Rcheck\00install.out 2>&1 && cp zinbwave.Rcheck\00install.out zinbwave-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=zinbwave.buildbin-libdir --install="check:zinbwave-install.out" --force-multiarch --no-vignettes --timings zinbwave_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/zinbwave.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.0.0'
* 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 'zinbwave' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/glmWeightedF.Rd:35: missing file link 'glmLRT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/glmWeightedF.Rd:50: missing file link 'glmLRT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/independentFiltering.Rd:19: missing file link 'glmLRT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbFit.Rd:52: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbFit.Rd:74: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbInitialize.Rd:19: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbOptimize.Rd:28: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbOptimizeDispersion.Rd:27: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbwave.Rd:52: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbwave.Rd:89: missing file link 'SummarizedExperiment'
See 'C:/Users/biocbuild/bbs-3.6-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 installed files from 'inst/doc' ... 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 0.81 0.18 217.50
zinbwave 0.42 0.09 105.18
zinbInitialize 0.16 0.07 79.70
zinbOptimize 0.12 0.03 98.25
zinbOptimizeDispersion 0.10 0.01 75.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
zinbFit 0.81 0.16 241.91
zinbwave 0.50 0.09 116.06
zinbOptimizeDispersion 0.11 0.08 80.92
zinbInitialize 0.13 0.00 87.33
zinbOptimize 0.11 0.00 109.25
* 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-3.6-bioc/meat/zinbwave.Rcheck/00check.log'
for details.
zinbwave.Rcheck/00install.out
install for i386
* installing *source* package 'zinbwave' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/glmWeightedF.Rd:35: missing file link 'glmLRT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/glmWeightedF.Rd:50: missing file link 'glmLRT'
imputeZeros html
independentFiltering html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/independentFiltering.Rd:19: missing file link 'glmLRT'
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-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbFit.Rd:52: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbFit.Rd:74: missing file link 'SummarizedExperiment'
zinbInitialize html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbInitialize.Rd:19: missing file link 'bpparam'
zinbModel html
zinbOptimize html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbOptimize.Rd:28: missing file link 'bpparam'
zinbOptimizeDispersion html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbOptimizeDispersion.Rd:27: missing file link 'bpparam'
zinbSim html
zinbwave html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbwave.Rd:52: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcPEMJs/R.INSTALL176858f638d/zinbwave/man/zinbwave.Rd:89: missing file link 'SummarizedExperiment'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'zinbwave' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'zinbwave' as zinbwave_1.0.0.zip
* DONE (zinbwave)
In R CMD INSTALL
In R CMD INSTALL
|
zinbwave.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, 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
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: SingleCellExperiment
>
> test_check("zinbwave")
user system elapsed
0.03 0.00 0.03
user system elapsed
0.03 0.00 0.03
user system elapsed
0.01 0.00 0.01
user system elapsed
0.02 0.00 0.02
== testthat results ===========================================================
OK: 81 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
17.71 0.35 18.06
|
zinbwave.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, 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
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: SingleCellExperiment
>
> test_check("zinbwave")
user system elapsed
0.03 0.00 0.03
user system elapsed
0.03 0.00 0.03
user system elapsed
0.05 0.00 0.05
user system elapsed
0 0 0
== testthat results ===========================================================
OK: 81 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
20.42 0.31 20.71
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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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