copa 1.41.0
James W. MacDonald
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/copa | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings copa_1.41.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/copa.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘copa/DESCRIPTION’ ... OK
* this is package ‘copa’ version ‘1.41.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘copa’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘Biobase’ ‘methods’
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
copa: warning in matrix(1:dim(mat)[1], nc = dim(mat)[1], nr =
dim(mat)[1]): partial argument match of 'nr' to 'nrow'
copa: warning in matrix(1:dim(mat)[1], nc = dim(mat)[1], nr =
dim(mat)[1]): partial argument match of 'nc' to 'ncol'
pSum: warning in matrix(out, nc = length(a), nr = length(a)): partial
argument match of 'nr' to 'nrow'
pSum: warning in matrix(out, nc = length(a), nr = length(a)): partial
argument match of 'nc' to 'ncol'
plotCopa: warning in matrix(1:2, nc = 1): partial argument match of
'nc' to 'ncol'
copa: no visible binding for global variable ‘quantile’
do.copaFilter: no visible binding for global variable ‘median’
do.copaFilter: no visible binding for global variable ‘mad’
do.copaFilter: no visible global function definition for ‘quantile’
pSum: no visible binding for global variable ‘mat’
plotCopa: no visible global function definition for ‘par’
plotCopa: no visible global function definition for ‘layout’
plotCopa: no visible global function definition for ‘barplot’
scatterPlotCopa: no visible global function definition for ‘plot’
copaFilter,ExpressionSet: no visible global function definition for
‘exprs’
Undefined global functions or variables:
barplot exprs layout mad mat median par plot quantile
Consider adding
importFrom("graphics", "barplot", "layout", "par", "plot")
importFrom("stats", "mad", "median", "quantile")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/copa.Rcheck/00check.log’
for details.
* installing *source* package ‘copa’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c copa.c -o copa.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o copa.so copa.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/copa.Rcheck/copa/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (copa)