Zachary Skidmore
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/GenVisR |
| Branch: RELEASE_3_6 |
| Last Commit: 17f22b8 |
| Last Changed Date: 2018-03-16 15:47:28 -0400 (Fri, 16 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:27:24 -0400 (Thu, 12 Apr 2018).
| Package 575/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenVisR 1.8.1 Zachary Skidmore
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: GenVisR |
| Version: 1.8.1 |
| Command: rm -rf GenVisR.buildbin-libdir GenVisR.Rcheck && mkdir GenVisR.buildbin-libdir GenVisR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenVisR.buildbin-libdir GenVisR_1.8.1.tar.gz >GenVisR.Rcheck\00install.out 2>&1 && cp GenVisR.Rcheck\00install.out GenVisR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenVisR.buildbin-libdir --install="check:GenVisR-install.out" --force-multiarch --no-vignettes --timings GenVisR_1.8.1.tar.gz |
| StartedAt: 2018-04-12 00:20:46 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:28:17 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 451.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenVisR.Rcheck |
| Warnings: 0 |
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###
### Running command:
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### rm -rf GenVisR.buildbin-libdir GenVisR.Rcheck && mkdir GenVisR.buildbin-libdir GenVisR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenVisR.buildbin-libdir GenVisR_1.8.1.tar.gz >GenVisR.Rcheck\00install.out 2>&1 && cp GenVisR.Rcheck\00install.out GenVisR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenVisR.buildbin-libdir --install="check:GenVisR-install.out" --force-multiarch --no-vignettes --timings GenVisR_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenVisR.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 'GenVisR/DESCRIPTION' ... OK
* this is package 'GenVisR' version '1.8.1'
* 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 'GenVisR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
doc 4.6Mb
* 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
waterfall: warning in waterfall_align(genes = gene_plot, heatmap =
heatmap, burden = burden_plot, clinical = clinical_plot, proportion =
proportions_plot, section_heights = section_heights): partial
argument match of 'proportion' to 'proportions'
waterfall: warning in waterfall_align(genes = gene_plot, heatmap =
heatmap, burden = burden_plot, proportion = proportions_plot,
section_heights = section_heights): partial argument match of
'proportion' to 'proportions'
* 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
genCov 5.49 0.33 5.81
cnFreq 5.49 0.06 5.54
lolliplot 2.41 0.01 11.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cnFreq 10.17 0.00 10.17
genCov 7.14 0.27 7.41
lolliplot 3.58 0.04 10.56
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenVisR.Rcheck/00check.log'
for details.
GenVisR.Rcheck/00install.out
install for i386
* installing *source* package 'GenVisR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'GenVisR'
finding HTML links ... done
GenVisR html
HCC1395_Germline html
HCC1395_N html
HCC1395_T html
LucCNseg html
SNPloci html
TvTi html
TvTi_alignPlot html
TvTi_annoTransTranv html
TvTi_buildMain html
TvTi_calcTransTranvFreq html
TvTi_convMAF html
TvTi_qual html
TvTi_rmIndel html
TvTi_rmMnuc html
brcaMAF html
cnFreq html
cnFreq_buildMain html
cnFreq_qual html
cnSpec html
cnSpec_buildMain html
cnSpec_qual html
cnView html
cnView_buildMain html
cnView_qual html
compIdent html
compIdent_bamRcnt html
compIdent_bamRcnt_qual html
compIdent_buildMain html
compIdent_format html
covBars html
covBars_buildMain html
covBars_qual html
cytoGeno html
genCov html
genCov_alignPlot html
genCov_assign_ggplotGrob_height html
genCov_assign_ggplotGrob_width html
genCov_buildCov html
genCov_buildTrack html
genCov_extr_ggplotGrob_height html
genCov_extr_ggplotGrob_width html
genCov_qual html
genCov_trackViz html
geneViz html
geneViz_Granges2dataframe html
geneViz_buildGene html
geneViz_calcGC html
geneViz_cdsFromTXID html
geneViz_extrCDS html
geneViz_extrUTR html
geneViz_formatCDS html
geneViz_formatUTR html
geneViz_mapCoordSpace html
geneViz_mapCovCoordSpace html
geneViz_mergeRegions html
geneViz_mergeTypeRegions html
geneViz_mergeTypes html
hg19chr html
ideoView html
ideoView_buildMain html
ideoView_formatCytobands html
ideoView_qual html
lohSpec html
lohSpec_buildMain html
lohSpec_fileGlob html
lohSpec_lohCalc html
lohSpec_qual html
lohSpec_slidingWindow html
lohSpec_stepCalc html
lohSpec_tileCalc html
lohSpec_tilePosition html
lohSpec_tileWindow html
lohSpec_windowPosition html
lohView html
lohView_buildMain html
lohView_qual html
lolliplot html
lolliplot_AA2sidechain html
lolliplot_Codon2AA html
lolliplot_DNAconv html
lolliplot_buildMain html
lolliplot_constructGene html
lolliplot_dodgeCoordX html
lolliplot_dodgeCoordY html
lolliplot_fetchDomain html
lolliplot_mutationObs html
lolliplot_qual html
lolliplot_reduceLolli html
lolliplot_transcriptID2codingSeq html
multi_align html
multi_buildClin html
multi_chrBound html
multi_cytobandRet html
multi_selectOut html
multi_subsetChr html
waterfall html
waterfall_Custom2anno html
waterfall_MAF2anno html
waterfall_MGI2anno html
waterfall_NA2gene html
waterfall_align html
waterfall_buildGenePrevelance html
waterfall_buildMain html
waterfall_buildMutBurden_A html
waterfall_buildMutBurden_B html
waterfall_build_proportions html
waterfall_calcMutFreq html
waterfall_geneAlt html
waterfall_geneRecurCutoff html
waterfall_geneSort html
waterfall_hierarchyTRV html
waterfall_palette_names html
waterfall_qual html
waterfall_rmvSilent html
waterfall_sampAlt html
waterfall_sampSort html
waterfall_select_palette html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'GenVisR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenVisR' as GenVisR_1.8.1.zip
* DONE (GenVisR)
In R CMD INSTALL
In R CMD INSTALL
|
GenVisR.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(GenVisR)
>
> test_check("GenVisR")
== testthat results ===========================================================
OK: 193 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
17.90 0.57 18.96
|
GenVisR.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(GenVisR)
>
> test_check("GenVisR")
== testthat results ===========================================================
OK: 193 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
19.96 0.39 20.84
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GenVisR.Rcheck/examples_i386/GenVisR-Ex.timings
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GenVisR.Rcheck/examples_x64/GenVisR-Ex.timings
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