Ting Gong
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/DeconRNASeq |
| Branch: RELEASE_3_11 |
| Last Commit: b462499 |
| Last Changed Date: 2020-04-27 14:31:20 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:25 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE DeconRNASeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 436/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DeconRNASeq 1.30.0 Ting Gong
| malbec2 | Linux (Ubuntu 18.04.4 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: DeconRNASeq |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:DeconRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DeconRNASeq_1.30.0.tar.gz |
| StartedAt: 2020-10-17 03:13:24 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:15:00 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 95.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DeconRNASeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:DeconRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DeconRNASeq_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DeconRNASeq.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 'DeconRNASeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeconRNASeq' version '1.30.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'DeconRNASeq' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
data 6.5Mb
* 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
* 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
'library' or 'require' call to 'grid' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'ggplot2' 'grid' 'pcaMethods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DeconRNASeq: no visible global function definition for 'prep'
DeconRNASeq: no visible global function definition for 'pca'
DeconRNASeq: no visible global function definition for 'R2cum'
DeconRNASeq: no visible global function definition for 'ggplot'
DeconRNASeq: no visible global function definition for 'aes'
DeconRNASeq: no visible global function definition for 'geom_point'
DeconRNASeq: no visible global function definition for 'labs'
DeconRNASeq: no visible global function definition for 'geom_abline'
DeconRNASeq: no visible global function definition for 'xlab'
DeconRNASeq: no visible global function definition for 'ylab'
condplot: no visible global function definition for 'rainbow'
condplot: no visible global function definition for 'lines'
condplot: no visible global function definition for 'axis'
condplot: no visible global function definition for 'title'
decon.bootstrap: no visible global function definition for 't.test'
multiplot: no visible global function definition for 'grid.newpage'
multiplot: no visible global function definition for 'pushViewport'
multiplot: no visible global function definition for 'viewport'
multiplot: no visible global function definition for 'grid.layout'
multiplot : vplayout: no visible global function definition for
'viewport'
Undefined global functions or variables:
R2cum aes axis geom_abline geom_point ggplot grid.layout grid.newpage
labs lines pca prep pushViewport rainbow t.test title viewport xlab
ylab
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "axis", "lines", "title")
importFrom("stats", "t.test")
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 ... 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 ... 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/DeconRNASeq.Rcheck/00check.log'
for details.
DeconRNASeq.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch DeconRNASeq
###
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* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
* installing *source* package 'DeconRNASeq' ...
** using staged installation
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DeconRNASeq'
finding HTML links ... done
DeconRNASeq-package html
DeconRNASeq html
all.datasets html
array.proportions html
array.signatures html
condplot html
datasets html
decon.bootstrap html
fraction html
liver_kidney html
multi_tissue html
multiplot html
proportions html
rmse html
signatures html
x.data html
x.signature html
x.signature.filtered html
x.signature.filtered.optimal 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
* DONE (DeconRNASeq)
Making 'packages.html' ... done
DeconRNASeq.Rcheck/DeconRNASeq-Ex.timings
| name | user | system | elapsed | |
| DeconRNASeq | 0 | 0 | 0 | |
| all.datasets | 0.08 | 0.00 | 0.08 | |
| array.proportions | 0.05 | 0.00 | 0.04 | |
| array.signatures | 0.05 | 0.01 | 0.07 | |
| condplot | 0.05 | 0.01 | 0.07 | |
| datasets | 0.08 | 0.02 | 0.10 | |
| fraction | 0.23 | 0.03 | 0.26 | |
| liver_kidney | 0.08 | 0.02 | 0.10 | |
| multi_tissue | 0.28 | 0.00 | 0.28 | |
| multiplot | 0 | 0 | 0 | |
| proportions | 0.10 | 0.00 | 0.09 | |
| signatures | 0.08 | 0.01 | 0.09 | |
| x.data | 0.23 | 0.02 | 0.25 | |
| x.signature | 0.23 | 0.01 | 0.25 | |
| x.signature.filtered | 0.29 | 0.00 | 0.29 | |
| x.signature.filtered.optimal | 0.25 | 0.02 | 0.26 | |