Zachary Skidmore
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/GenVisR |
| Branch: RELEASE_3_12 |
| Last Commit: 2e30ead |
| Last Changed Date: 2020-12-25 19:00:29 -0400 (Fri, 25 Dec 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:31:29 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the GenVisR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 727/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenVisR 1.22.1 (landing page) Zachary Skidmore
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: GenVisR |
| Version: 1.22.1 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenVisR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GenVisR_1.22.1.tar.gz |
| StartedAt: 2021-05-06 03:07:38 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:28:01 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 1222.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenVisR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenVisR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GenVisR_1.22.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GenVisR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.22.1'
* 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
* 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 (user + system) or elapsed time > 5s
user system elapsed
Lolliplot-class 56.85 2.11 82.98
lolliplot 29.07 0.04 40.29
genCov 9.70 0.46 10.15
geneViz 8.47 0.12 8.60
cnFreq 6.78 0.20 6.98
cnSpec 5.33 0.00 5.33
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Lolliplot-class 44.12 1.12 63.23
lolliplot 15.57 0.08 36.50
genCov 9.26 0.64 9.91
cnFreq 9.80 0.02 9.81
geneViz 8.90 0.09 9.00
* 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-3.12-bioc/meat/GenVisR.Rcheck/00check.log'
for details.
GenVisR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GenVisR_1.22.1.tar.gz && rm -rf GenVisR.buildbin-libdir && mkdir GenVisR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenVisR.buildbin-libdir GenVisR_1.22.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GenVisR_1.22.1.zip && rm GenVisR_1.22.1.tar.gz GenVisR_1.22.1.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 2101k 100 2101k 0 0 53.2M 0 --:--:-- --:--:-- --:--:-- 55.4M
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_1.22.1.zip
* DONE (GenVisR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GenVisR' successfully unpacked and MD5 sums checked
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GenVisR.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
== Skipped tests ===============================================================
* On Bioconductor (54)
[ FAIL 0 | WARN 13 | SKIP 54 | PASS 651 ]
>
> proc.time()
user system elapsed
202.50 7.28 261.62
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GenVisR.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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")
== Skipped tests ===============================================================
* On Bioconductor (54)
[ FAIL 0 | WARN 13 | SKIP 54 | PASS 651 ]
>
> proc.time()
user system elapsed
141.53 4.23 200.25
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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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