Fabian Schmich
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/gespeR |
| Branch: RELEASE_3_11 |
| Last Commit: 93f31e1 |
| Last Changed Date: 2020-04-27 14:46:08 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:41 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE gespeR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 725/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gespeR 1.20.0 Fabian Schmich
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: gespeR |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gespeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gespeR_1.20.0.tar.gz |
| StartedAt: 2020-10-17 04:27:50 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:37:07 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 557.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: gespeR.Rcheck |
| Warnings: 1 |
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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:gespeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gespeR_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/gespeR.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 'gespeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gespeR' version '1.20.0'
* 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 'gespeR' 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
.gespeR.cv: no visible global function definition for 'coef'
.select.model: no visible global function definition for 'predict'
concordance: no visible global function definition for 'cor'
lasso.rand: no visible global function definition for 'runif'
plot.gespeR: no visible global function definition for 'hist'
stability.selection: no visible global function definition for 'lm'
Phenotypes,character: no visible global function definition for
'read.delim'
Undefined global functions or variables:
coef cor hist lm predict read.delim runif
Consider adding
importFrom("graphics", "hist")
importFrom("stats", "coef", "cor", "lm", "predict", "runif")
importFrom("utils", "read.delim")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'c,Phenotypes-method':
\S4method{c}{Phenotypes}
Code: function(x, ...)
Docs: function(x, ..., recursive = FALSE)
Argument names in docs not in code:
recursive
* 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
gespeR-package 6.70 0.51 65.72
gespeR-class 0.50 0.03 15.01
stability-methods 0.19 0.02 13.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
gespeR-package 6.58 0.25 66.45
gespeR-class 0.63 0.04 14.40
stability-methods 0.12 0.00 14.57
* 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 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/gespeR.Rcheck/00check.log'
for details.
gespeR.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/gespeR_1.20.0.tar.gz && rm -rf gespeR.buildbin-libdir && mkdir gespeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gespeR.buildbin-libdir gespeR_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL gespeR_1.20.0.zip && rm gespeR_1.20.0.tar.gz gespeR_1.20.0.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
3 24.1M 3 864k 0 0 11.6M 0 0:00:02 --:--:-- 0:00:02 12.7M
100 24.1M 100 24.1M 0 0 63.6M 0 --:--:-- --:--:-- --:--:-- 64.7M
install for i386
* installing *source* package 'gespeR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gespeR'
finding HTML links ... done
Phenotypes-class html
TargetRelations-class html
annotate.gsp-methods html
as.data.frame-Phenotypes-method html
as.data.frame.concordance html
c-Phenotypes-method html
concordance html
dim-Phenotypes-method html
gespeR-class html
finding level-2 HTML links ... done
gespeR-package html
gspssp-methods html
join-methods html
lasso.rand html
na.rem-methods html
path-methods html
plot.Phenotypes html
plot.concordance html
plot.gespeR html
rbo html
scores-methods html
simData html
stability-methods html
stability.selection html
stabilityfits html
sub-Phenotypes-ANY-ANY-ANY-method html
sub-TargetRelations-ANY-ANY-ANY-method
html
target-relations-methods html
trmatrix-methods html
values-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 'gespeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gespeR' as gespeR_1.20.0.zip
* DONE (gespeR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'gespeR' successfully unpacked and MD5 sums checked
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gespeR.Rcheck/examples_i386/gespeR-Ex.timings
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gespeR.Rcheck/examples_x64/gespeR-Ex.timings
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