Dharmesh D. Bhuva
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/singscore |
| Branch: RELEASE_3_11 |
| Last Commit: 2001864 |
| Last Changed Date: 2020-04-27 15:16:32 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:49 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE singscore PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1675/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| singscore 1.8.0 Dharmesh D. Bhuva
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: singscore |
| Version: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singscore.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings singscore_1.8.0.tar.gz |
| StartedAt: 2020-10-17 08:22:20 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 08:28:03 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 343.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: singscore.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singscore.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings singscore_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/singscore.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'singscore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'singscore' version '1.8.0'
* 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 'singscore' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use 'given' instead of 'middle'.
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
plotDispersion: no visible binding for global variable 'Score'
plotDispersion: no visible binding for global variable 'Dispersion'
plotDispersion: no visible binding for global variable 'Class'
plotDispersion: no visible binding for global variable 'SampleText'
plotDispersion: no visible binding for global variable 'SampleLabel'
plotRankDensity_intl: no visible binding for global variable 'Ranks'
plotRankDensity_intl: no visible binding for global variable 'upDown'
plotRankDensity_intl: no visible binding for global variable
'..density..'
plotRankDensity_intl: no visible binding for global variable 'EntrezID'
plotScoreLandscape: no visible binding for global variable 'sc1'
plotScoreLandscape: no visible binding for global variable 'sc2'
projectScoreLandscape: no visible binding for global variable
'SampleText'
projectScoreLandscape: no visible binding for global variable 'Class'
projectScoreLandscape: no visible binding for global variable
'SampleLabel'
Undefined global functions or variables:
..density.. Class Dispersion EntrezID Ranks SampleLabel SampleText
Score sc1 sc2 upDown
* 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotDispersion 0.98 0.09 6.44
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/singscore.Rcheck/00check.log'
for details.
singscore.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/singscore_1.8.0.tar.gz && rm -rf singscore.buildbin-libdir && mkdir singscore.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=singscore.buildbin-libdir singscore_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL singscore_1.8.0.zip && rm singscore_1.8.0.tar.gz singscore_1.8.0.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
100 3753k 100 3753k 0 0 36.1M 0 --:--:-- --:--:-- --:--:-- 38.5M
install for i386
* installing *source* package 'singscore' ...
** using staged installation
It is recommended to use 'given' instead of 'middle'.
It is recommended to use 'given' instead of 'middle'.
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'singscore'
finding HTML links ... done
generateNull html
generateNull_intl html
getPvals html
getStableGenes html
multiScore html
finding level-2 HTML links ... done
plotDispersion html
plotNull html
plotRankDensity html
plotRankDensity_intl html
plotScoreLandscape html
projectScoreLandscape html
rankGenes html
scoredf_ccle_epi html
scoredf_ccle_mes html
scoredf_tcga_epi html
scoredf_tcga_mes html
simpleScore html
singscore html
tgfb_expr_10_se html
tgfb_gs_dn html
tgfb_gs_up html
toy_expr_se html
toy_gs_dn html
toy_gs_up html
*** copying figures
** 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 'singscore' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'singscore' as singscore_1.8.0.zip
* DONE (singscore)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'singscore' successfully unpacked and MD5 sums checked
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singscore.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(singscore)
>
> test_check("singscore")
== testthat results ===========================================================
[ OK: 138 | SKIPPED: 0 | WARNINGS: 40 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.43 0.95 21.12
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singscore.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(singscore)
>
> test_check("singscore")
== testthat results ===========================================================
[ OK: 138 | SKIPPED: 0 | WARNINGS: 40 | FAILED: 0 ]
>
> proc.time()
user system elapsed
15.07 0.62 19.92
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singscore.Rcheck/examples_i386/singscore-Ex.timings
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singscore.Rcheck/examples_x64/singscore-Ex.timings
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