Michael Cole
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/scone |
| Branch: RELEASE_3_6 |
| Last Commit: 49ae3d9 |
| Last Changed Date: 2017-10-30 12:41:24 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:29:11 -0400 (Thu, 12 Apr 2018).
| Package 1260/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scone 1.2.0 Michael Cole
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: scone |
| Version: 1.2.0 |
| Command: rm -rf scone.buildbin-libdir scone.Rcheck && mkdir scone.buildbin-libdir scone.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scone.buildbin-libdir scone_1.2.0.tar.gz >scone.Rcheck\00install.out 2>&1 && cp scone.Rcheck\00install.out scone-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=scone.buildbin-libdir --install="check:scone-install.out" --force-multiarch --no-vignettes --timings scone_1.2.0.tar.gz |
| StartedAt: 2018-04-12 03:00:48 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:13:49 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 780.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scone.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf scone.buildbin-libdir scone.Rcheck && mkdir scone.buildbin-libdir scone.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scone.buildbin-libdir scone_1.2.0.tar.gz >scone.Rcheck\00install.out 2>&1 && cp scone.Rcheck\00install.out scone-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=scone.buildbin-libdir --install="check:scone-install.out" --force-multiarch --no-vignettes --timings scone_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/scone.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 'scone/DESCRIPTION' ... OK * this is package 'scone' version '1.2.0' * 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 'scone' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyazJ2R/R.INSTALL3a24154e463e/scone/man/control_genes.Rd:28: missing file link 'toupper' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyazJ2R/R.INSTALL3a24154e463e/scone/man/control_genes.Rd:29: missing file link 'tolower' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyazJ2R/R.INSTALL3a24154e463e/scone/man/scone.Rd:101: missing file link 'bpparam' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/scone.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 ** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 sconeReport: no visible global function definition for 'visNetworkOutput' sconeReport: no visible global function definition for 'plotlyOutput' sconeReport : server: no visible global function definition for 'renderVisNetwork' sconeReport : server: no visible global function definition for '%>%' sconeReport : server: no visible global function definition for 'visNetwork' sconeReport : server: no visible global function definition for 'visHierarchicalLayout' sconeReport : server: no visible global function definition for 'visGroups' sconeReport : server: no visible global function definition for 'visEdges' sconeReport : server: no visible global function definition for 'visOptions' sconeReport : server: no visible global function definition for 'visLegend' sconeReport : server: no visible global function definition for 'visNetworkProxy' sconeReport : server: no visible global function definition for 'visSelectNodes' sconeReport : server: no visible global function definition for 'plot_ly' sconeReport : server: no visible global function definition for 'ggplot' sconeReport : server: no visible global function definition for 'aes' sconeReport : server: no visible global function definition for 'geom_bar' sconeReport : server: no visible global function definition for 'ylim' sconeReport : server: no visible global function definition for 'labs' sconeReport : server: no visible global function definition for 'theme' sconeReport : server: no visible global function definition for 'element_blank' sconeReport : server: no visible global function definition for 'ggplotly' sconeReport : server: no visible global function definition for 'geom_violin' sconeReport : server: no visible global function definition for 'coord_cartesian' sconeReport : server: no visible global function definition for 'scale_fill_manual' sconeReport : server: no visible global function definition for 'geom_point' sconeReport : server: no visible global function definition for 'guides' Undefined global functions or variables: %>% aes coord_cartesian element_blank geom_bar geom_point geom_violin ggplot ggplotly guides labs plot_ly plotlyOutput renderVisNetwork scale_fill_manual theme visEdges visGroups visHierarchicalLayout visLegend visNetwork visNetworkOutput visNetworkProxy visOptions visSelectNodes ylim * 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 ** running examples for arch 'x64' ... OK * 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, 1 NOTE See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/scone.Rcheck/00check.log' for details.
scone.Rcheck/00install.out
install for i386
* installing *source* package 'scone' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'scone'
finding HTML links ... done
CLR_FN html
DESEQ_FN html
FQ_FN html
SCRAN_FN html
SUM_FN html
SconeExperiment-class html
finding level-2 HTML links ... done
TMM_FN html
UQ_FN html
biplot_color html
biplot_interactive html
control_genes html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyazJ2R/R.INSTALL3a24154e463e/scone/man/control_genes.Rd:28: missing file link 'toupper'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyazJ2R/R.INSTALL3a24154e463e/scone/man/control_genes.Rd:29: missing file link 'tolower'
estimate_ziber html
factor_sample_filter html
fast_estimate_ziber html
get_bio html
get_design html
get_negconruv html
get_normalized html
get_params html
get_qc html
get_scores html
impute_expectation html
impute_null html
lm_adjust html
make_design html
metric_sample_filter html
scone html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyazJ2R/R.INSTALL3a24154e463e/scone/man/scone.Rd:101: missing file link 'bpparam'
sconeReport html
scone_easybake html
score_matrix html
select_methods html
simple_FNR_params html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'scone' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scone' as scone_1.2.0.zip
* DONE (scone)
In R CMD INSTALL
In R CMD INSTALL
|
scone.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.
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(scone)
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
>
> test_check("scone")
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:01)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:03)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:03)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:18)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:36 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
== testthat results ===========================================================
OK: 313 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
82.34 0.92 153.65
|
scone.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.
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(scone)
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
>
> test_check("scone")
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:03)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:04)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:05)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:29)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:36 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
== testthat results ===========================================================
OK: 313 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
113.04 0.85 189.54
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scone.Rcheck/examples_i386/scone-Ex.timings
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scone.Rcheck/examples_x64/scone-Ex.timings
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