sva 3.22.0
Jeffrey T. Leek , John D. Storey
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/sva | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf sva.buildbin-libdir sva.Rcheck && mkdir sva.buildbin-libdir sva.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sva.buildbin-libdir sva_3.22.0.tar.gz >sva.Rcheck\00install.out 2>&1 && cp sva.Rcheck\00install.out sva-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=sva.buildbin-libdir --install="check:sva-install.out" --force-multiarch --no-vignettes --timings sva_3.22.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/sva.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sva/DESCRIPTION' ... OK
* this is package 'sva' version '3.22.0'
* 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 'sva' 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
ComBat: no visible global function definition for 'model.matrix'
ComBat: no visible binding for global variable 'var'
ComBat: no visible global function definition for 'par'
ComBat: no visible global function definition for 'density'
ComBat: no visible global function definition for 'plot'
ComBat: no visible global function definition for 'lines'
ComBat: no visible global function definition for 'dnorm'
ComBat: no visible global function definition for 'qqnorm'
ComBat: no visible global function definition for 'qqline'
ComBat: no visible global function definition for 'rgamma'
ComBat: no visible global function definition for 'qqplot'
ComBat: no visible global function definition for 'title'
L: no visible global function definition for 'dnorm'
aprior: no visible global function definition for 'var'
bprior: no visible global function definition for 'var'
edge.lfdr: no visible global function definition for 'qnorm'
edge.lfdr: no visible global function definition for 'density'
edge.lfdr: no visible global function definition for 'smooth.spline'
edge.lfdr: no visible global function definition for 'predict'
edge.lfdr: no visible global function definition for 'dnorm'
f.pvalue: no visible global function definition for 'pf'
fsva: no visible global function definition for 'cor'
psva: no visible global function definition for 'lmFit'
sva.class2Model: no visible global function definition for
'model.matrix'
twostepsva.build: no visible global function definition for 'cor'
Undefined global functions or variables:
cor density dnorm lines lmFit model.matrix par pf plot predict qnorm
qqline qqnorm qqplot rgamma smooth.spline title var
Consider adding
importFrom("graphics", "lines", "par", "plot", "title")
importFrom("stats", "cor", "density", "dnorm", "model.matrix", "pf",
"predict", "qnorm", "qqline", "qqnorm", "qqplot", "rgamma",
"smooth.spline", "var")
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 'ComBat':
ComBat
Code: function(dat, batch, mod = NULL, par.prior = TRUE, prior.plots
= FALSE, mean.only = FALSE)
Docs: function(dat, batch, mod = NULL, par.prior = TRUE, prior.plots
= FALSE)
Argument names in code not in docs:
mean.only
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'ComBat':
'mean.only'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.4-bioc/meat/sva.buildbin-libdir/sva/libs/i386/sva.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/sva.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'sva' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sva.c -o sva.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o sva.dll tmp.def sva.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/sva.buildbin-libdir/sva/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'sva' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sva.c -o sva.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o sva.dll tmp.def sva.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/sva.buildbin-libdir/sva/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sva' as sva_3.22.0.zip
* DONE (sva)