Dharmesh D. Bhuva
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/vissE |
| git_branch: RELEASE_3_13 |
| git_last_commit: 1a90b74 |
| git_last_commit_date: 2021-05-19 13:03:31 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:27 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the vissE package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/vissE.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 2009/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| vissE 1.0.0 (landing page) Dharmesh D. Bhuva
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: vissE |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vissE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings vissE_1.0.0.tar.gz |
| StartedAt: 2021-10-15 07:13:19 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 07:16:09 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 170.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: vissE.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vissE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings vissE_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/vissE.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'vissE/DESCRIPTION' ... OK
* this is package 'vissE' version '1.0.0'
* 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 'vissE' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotGeneStats: no visible binding for global variable 'Count'
plotGeneStats: no visible binding for global variable 'GeneStat'
plotGeneStats: no visible binding for global variable 'Gene'
plotMsigNetwork: no visible binding for global variable 'x_begin'
plotMsigNetwork: no visible binding for global variable 'y_begin'
plotMsigNetwork: no visible binding for global variable 'x_end'
plotMsigNetwork: no visible binding for global variable 'y_end'
plotMsigNetwork: no visible binding for global variable 'x'
plotMsigNetwork: no visible binding for global variable 'y'
plotMsigNetwork: no visible binding for global variable 'Size'
plotMsigNetwork: no visible binding for global variable 'Category'
plotMsigNetwork: no visible binding for global variable 'NodeGroup'
plotMsigWordcloud: no visible binding for global variable 'word'
plotMsigWordcloud: no visible binding for global variable 'freq'
plotMsigWordcloud: no visible binding for global variable 'angle'
Undefined global functions or variables:
Category Count Gene GeneStat NodeGroup Size angle freq word x x_begin
x_end y y_begin y_end
* 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 ... NOTE
'LazyDataCompression' is specified without 'LazyData'
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... 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
computeMsigNetwork 7.22 0.55 8.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
computeMsigNetwork 6.77 0.45 7.89
characteriseGeneset 5.31 0.22 5.54
* 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-3.13-bioc/meat/vissE.Rcheck/00check.log'
for details.
vissE.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/vissE_1.0.0.tar.gz && rm -rf vissE.buildbin-libdir && mkdir vissE.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=vissE.buildbin-libdir vissE_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL vissE_1.0.0.zip && rm vissE_1.0.0.tar.gz vissE_1.0.0.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
1 3269k 1 45685 0 0 290k 0 0:00:11 --:--:-- 0:00:11 289k
52 3269k 52 1716k 0 0 1482k 0 0:00:02 0:00:01 0:00:01 1482k
79 3269k 79 2599k 0 0 1218k 0 0:00:02 0:00:02 --:--:-- 1218k
100 3269k 100 3269k 0 0 1305k 0 0:00:02 0:00:02 --:--:-- 1304k
install for i386
* installing *source* package 'vissE' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'vissE'
finding HTML links ... done
bhuvad_theme html
characteriseGeneset html
computeMsigNetwork html
computeMsigOverlap html
computeMsigWordFreq html
getMsigBlacklist html
hgsc html
mem_mat_hs html
mem_mat_mm html
plotGeneStats html
plotMsigNetwork html
plotMsigWordcloud html
vissE-package 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 'vissE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'vissE' as vissE_1.0.0.zip
* DONE (vissE)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'vissE' successfully unpacked and MD5 sums checked
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vissE.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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(vissE)
>
> test_check("vissE")
[ FAIL 0 | WARN 133 | SKIP 0 | PASS 67 ]
>
> proc.time()
user system elapsed
20.23 1.23 22.10
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vissE.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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(vissE)
>
> test_check("vissE")
[ FAIL 0 | WARN 133 | SKIP 0 | PASS 67 ]
>
> proc.time()
user system elapsed
20.46 1.15 22.26
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vissE.Rcheck/examples_i386/vissE-Ex.timings
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vissE.Rcheck/examples_x64/vissE-Ex.timings
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