Zachary Skidmore
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/GenVisR |
| Branch: RELEASE_3_10 |
| Last Commit: 827ef01 |
| Last Changed Date: 2019-10-30 10:24:24 -0400 (Wed, 30 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:26:02 -0400 (Wed, 15 Apr 2020).
| Package 693/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenVisR 1.18.1 Zachary Skidmore
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GenVisR |
| Version: 1.18.1 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenVisR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GenVisR_1.18.1.tar.gz |
| StartedAt: 2020-04-15 03:29:24 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:43:30 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 845.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenVisR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenVisR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GenVisR_1.18.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GenVisR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.18.1'
* 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 ... 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 ... 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 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
Lolliplot-class 29.61 2.39 49.61
genCov 12.50 0.30 13.17
cnFreq 7.43 0.00 7.43
cnSpec 5.19 0.03 5.22
lolliplot 3.29 0.03 18.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Lolliplot-class 25.91 0.98 33.50
genCov 10.42 0.36 10.78
cnFreq 8.71 0.00 8.70
cnSpec 7.00 0.01 7.02
lolliplot 3.61 0.01 7.28
* 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-3.10-bioc/meat/GenVisR.Rcheck/00check.log'
for details.
GenVisR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/GenVisR_1.18.1.tar.gz && rm -rf GenVisR.buildbin-libdir && mkdir GenVisR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenVisR.buildbin-libdir GenVisR_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GenVisR_1.18.1.zip && rm GenVisR_1.18.1.tar.gz GenVisR_1.18.1.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
100 2097k 100 2097k 0 0 12.5M 0 --:--:-- --:--:-- --:--:-- 12.8M
install for i386
* 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
lolliplot_AA2sidechain html
lolliplot_buildMain html
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
install for x64
* installing *source* package 'GenVisR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenVisR' as GenVisR_1.18.1.zip
* DONE (GenVisR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'GenVisR' successfully unpacked and MD5 sums checked
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GenVisR.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 651 | SKIPPED: 54 | WARNINGS: 11 | FAILED: 0 ]
>
> proc.time()
user system elapsed
121.46 7.65 149.04
|
GenVisR.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 651 | SKIPPED: 54 | WARNINGS: 11 | FAILED: 0 ]
>
> proc.time()
user system elapsed
113.06 4.82 133.12
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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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