Ting Gong
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DeconRNASeq |
| Branch: RELEASE_3_8 |
| Last Commit: 590bd50 |
| Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:23 -0400 (Sat, 13 Apr 2019).
| Package 379/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DeconRNASeq 1.24.0 Ting Gong
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DeconRNASeq |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:DeconRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DeconRNASeq_1.24.0.tar.gz |
| StartedAt: 2019-04-13 01:40:25 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:42:10 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 104.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DeconRNASeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:DeconRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DeconRNASeq_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DeconRNASeq.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.24.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'plot'
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 plot prep pushViewport rainbow t.test title viewport
xlab ylab
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "axis", "lines", "plot", "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-3.8-bioc/meat/DeconRNASeq.Rcheck/00check.log'
for details.
DeconRNASeq.Rcheck/00install.out
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch DeconRNASeq
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* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
* installing *source* package 'DeconRNASeq' ...
** 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
* DONE (DeconRNASeq)
Making 'packages.html' ... done
In R CMD INSTALL
DeconRNASeq.Rcheck/DeconRNASeq-Ex.timings
| name | user | system | elapsed | |
| DeconRNASeq | 0 | 0 | 0 | |
| all.datasets | 0.05 | 0.02 | 0.60 | |
| array.proportions | 0.08 | 0.00 | 0.08 | |
| array.signatures | 0.08 | 0.00 | 0.08 | |
| condplot | 0.08 | 0.00 | 0.08 | |
| datasets | 0.14 | 0.00 | 0.61 | |
| fraction | 0.42 | 0.01 | 0.56 | |
| liver_kidney | 0.15 | 0.00 | 0.14 | |
| multi_tissue | 0.39 | 0.03 | 0.42 | |
| multiplot | 0 | 0 | 0 | |
| proportions | 0.11 | 0.03 | 0.14 | |
| signatures | 0.09 | 0.00 | 0.10 | |
| x.data | 0.25 | 0.02 | 0.26 | |
| x.signature | 0.31 | 0.03 | 0.35 | |
| x.signature.filtered | 0.39 | 0.00 | 0.39 | |
| x.signature.filtered.optimal | 0.30 | 0.00 | 0.29 | |