Zachary Skidmore
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/GenVisR |
| git_branch: master |
| git_last_commit: 66e4001 |
| git_last_commit_date: 2022-02-01 15:15:37 -0400 (Tue, 01 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:37 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the GenVisR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenVisR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 764/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenVisR 1.27.1 (landing page) Zachary Skidmore
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GenVisR |
| Version: 1.27.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenVisR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenVisR_1.27.1.tar.gz |
| StartedAt: 2022-03-17 19:11:36 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:19:42 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 486.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenVisR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenVisR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenVisR_1.27.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GenVisR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.27.1'
* package encoding: UTF-8
* 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 ... 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
* 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
Namespace in Imports field not imported from: 'reshape2'
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
setTierTwo,data.table : a: no visible binding for global variable 'tmp'
toLolliplot,GMS: no visible binding for global variable 'missingINdex'
Undefined global functions or variables:
missingINdex tmp
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Lolliplot-class 26.33 1.32 37.84
lolliplot 10.57 0.11 18.86
genCov 6.60 0.56 7.16
geneViz 5.67 0.16 5.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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
'D:/biocbuild/bbs-3.15-bioc/meat/GenVisR.Rcheck/00check.log'
for details.
GenVisR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GenVisR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'GenVisR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GenVisR'
finding HTML links ... done
Clinical-class html
GMS-class html
GMS_Virtual-class html
GMS_v4-class html
GenVisR html
HCC1395_Germline html
HCC1395_N html
HCC1395_T html
Lolliplot-class html
LucCNseg html
MutSpectra-class html
MutationAnnotationFormat-class html
MutationAnnotationFormat_Virtual-class
html
MutationAnnotationFormat_v1.0-class html
MutationAnnotationFormat_v2.0-class html
MutationAnnotationFormat_v2.1-class html
MutationAnnotationFormat_v2.2-class html
MutationAnnotationFormat_v2.3-class html
MutationAnnotationFormat_v2.4-class html
PIK3CA html
Rainfall-class html
SNPloci html
TvTi html
VEP-class html
VEP_Virtual-class html
VEP_v88-class html
Waterfall-class html
brcaMAF html
cnFreq html
cnSpec html
cnView html
compIdent html
covBars html
cytoGeno html
drawPlot-methods html
genCov html
geneViz html
getData-methods html
getDescription-methods html
getGrob-methods html
getHeader-methods html
getMeta-methods html
getMutation-methods html
getPath-methods html
getPosition-methods html
getSample-methods html
getVersion-methods html
hg19chr html
ideoView html
lohSpec html
lohView html
lolliplot html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenVisR/00new/GenVisR/help/lolliplot.html
lolliplot_AA2sidechain html
lolliplot_buildMain html
waterfall html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenVisR/00new/GenVisR/help/waterfall.html
writeData-methods 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
* DONE (GenVisR)
Making 'packages.html' ... done
GenVisR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 18 | SKIP 54 | PASS 651 ]
== Skipped tests ===============================================================
* On Bioconductor (54)
[ FAIL 0 | WARN 18 | SKIP 54 | PASS 651 ]
>
> proc.time()
user system elapsed
110.40 7.92 163.70
GenVisR.Rcheck/GenVisR-Ex.timings
| name | user | system | elapsed | |
| Lolliplot-class | 26.33 | 1.32 | 37.84 | |
| TvTi | 1.20 | 0.02 | 1.22 | |
| Waterfall-class | 0.42 | 0.00 | 0.43 | |
| cnFreq | 4.24 | 0.00 | 4.23 | |
| cnSpec | 2.98 | 0.02 | 3.00 | |
| cnView | 1.61 | 0.01 | 1.62 | |
| compIdent | 1.53 | 0.22 | 1.75 | |
| covBars | 0.5 | 0.0 | 0.5 | |
| genCov | 6.60 | 0.56 | 7.16 | |
| geneViz | 5.67 | 0.16 | 5.83 | |
| ideoView | 1.36 | 0.00 | 1.36 | |
| lohSpec | 2.25 | 0.01 | 2.26 | |
| lohView | 1.51 | 0.00 | 1.52 | |
| lolliplot | 10.57 | 0.11 | 18.86 | |
| waterfall | 0.73 | 0.00 | 0.73 | |