J. Zhang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/cghMCR |
| Branch: RELEASE_3_7 |
| Last Commit: 7cec819 |
| Last Changed Date: 2018-04-30 10:35:04 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:32:49 -0400 (Wed, 17 Oct 2018).
| Package 215/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cghMCR 1.38.0 J. Zhang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: cghMCR |
| Version: 1.38.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cghMCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cghMCR_1.38.0.tar.gz |
| StartedAt: 2018-10-17 01:01:01 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:04:07 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 186.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cghMCR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cghMCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cghMCR_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/cghMCR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cghMCR/DESCRIPTION' ... OK
* this is package 'cghMCR' version '1.38.0'
* 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 'cghMCR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 98.1Mb
sub-directories of 1Mb or more:
sampleData 97.1Mb
* 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 ... NOTE
'library' or 'require' call to 'DNAcopy' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'CNTools' 'DNAcopy' 'limma' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'adjustSegments' 'alignGenes' 'drawSegs' 'getAdjustments'
'highlightChrom' 'markChrom'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SGOL: no visible global function definition for 'segBy'
SGOL: no visible global function definition for 'rs'
drawSegs : drawSegLine: no visible global function definition for
'lines'
dropGenes: no visible global function definition for 'approx'
getAlteredSegs: no visible global function definition for 'quantile'
getLineData: no visible global function definition for 'median'
getSegData: no visible global function definition for 'read.maimages'
getSegData: no visible global function definition for
'normalizeWithinArrays'
getSegData: no visible global function definition for
'backgroundCorrect'
getSegData: no visible global function definition for 'CNA'
getSegData: no visible global function definition for 'segment'
getSegData: no visible global function definition for 'smooth.CNA'
highlightChrom: no visible global function definition for 'polygon'
markChrom: no visible global function definition for 'polygon'
plot.DNAcopy: no visible global function definition for 'png'
plot.DNAcopy: no visible global function definition for 'par'
plot.DNAcopy: no visible global function definition for 'axis'
plot.DNAcopy: no visible global function definition for 'box'
plot.DNAcopy: no visible global function definition for 'points'
plot.DNAcopy: no visible global function definition for 'lines'
plot.DNAcopy: no visible global function definition for 'dev.off'
plot.MCR: no visible global function definition for 'png'
plot.MCR: no visible global function definition for 'par'
plot.MCR: no visible global function definition for 'dev.off'
plotSGOL: no visible global function definition for 'lines'
plotSGOL: no visible global function definition for 'axis'
plotSGOL: no visible global function definition for 'box'
showMCR : <anonymous>: no visible global function definition for
'median'
showMCR: no visible global function definition for 'lines'
showMCR: no visible global function definition for 'median'
showSegment : getMean: no visible global function definition for
'median'
topGenes: no visible global function definition for 'quantile'
Undefined global functions or variables:
CNA approx axis backgroundCorrect box dev.off lines median
normalizeWithinArrays par png points polygon quantile read.maimages
rs segBy segment smooth.CNA
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "axis", "box", "lines", "par", "points",
"polygon")
importFrom("stats", "approx", "median", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'SGOL,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mergeMCRProbes 5.8 0.01 5.82
* 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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/cghMCR.Rcheck/00check.log'
for details.
cghMCR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/cghMCR_1.38.0.tar.gz && rm -rf cghMCR.buildbin-libdir && mkdir cghMCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cghMCR.buildbin-libdir cghMCR_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL cghMCR_1.38.0.zip && rm cghMCR_1.38.0.tar.gz cghMCR_1.38.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
89 36.5M 89 32.8M 0 0 91.8M 0 --:--:-- --:--:-- --:--:-- 93.4M
100 36.5M 100 36.5M 0 0 90.6M 0 --:--:-- --:--:-- --:--:-- 92.1M
install for i386
* installing *source* package 'cghMCR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cghMCR'
finding HTML links ... done
SGOL-class html
cghMCR-class html
cghMCR html
mergeMCRProbes html
methods html
plot.DNAcopy html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'cghMCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cghMCR' as cghMCR_1.38.0.zip
* DONE (cghMCR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'cghMCR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
cghMCR.Rcheck/examples_i386/cghMCR-Ex.timings
|
cghMCR.Rcheck/examples_x64/cghMCR-Ex.timings
|