CHECK report for DSS on tokay1
This page was generated on 2018-04-12 13:21:51 -0400 (Thu, 12 Apr 2018).
DSS 2.26.0 Hao Wu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
URL: https://git.bioconductor.org/packages/DSS |
Branch: RELEASE_3_6 |
Last Commit: 5bdf6cc |
Last Changed Date: 2017-10-30 12:39:43 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
Summary
Command output
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### Running command:
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### rm -rf DSS.buildbin-libdir DSS.Rcheck && mkdir DSS.buildbin-libdir DSS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DSS.buildbin-libdir DSS_2.26.0.tar.gz >DSS.Rcheck\00install.out 2>&1 && cp DSS.Rcheck\00install.out DSS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DSS.buildbin-libdir --install="check:DSS-install.out" --force-multiarch --no-vignettes --timings DSS_2.26.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DSS.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DSS/DESCRIPTION' ... OK
* this is package 'DSS' version '2.26.0'
* 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 'DSS' 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 ... NOTE
Namespaces in Imports field not imported from:
'graphics' 'stats'
All declared Imports should be used.
Package in Depends field not imported from: 'splines'
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
DMLfit.multiFactor: no visible global function definition for
'model.matrix'
DMLtest.multiFactor.Contrast: no visible global function definition for
'pnorm'
DMLtest.multiFactor.Contrast: no visible global function definition for
'p.adjust'
DMLtest.multiFactor.coef: no visible global function definition for
'pnorm'
DMLtest.multiFactor.coef: no visible global function definition for
'p.adjust'
callDML: no visible global function definition for 'pnorm'
callDMR: no visible global function definition for 'pnorm'
compute.baseSigma.notrend: no visible global function definition for
'IQR'
compute.baseSigma.trend: no visible global function definition for
'IQR'
compute.waldStat.Smooth: no visible global function definition for
'pnorm'
compute.waldStat.Smooth: no visible global function definition for
'p.adjust'
compute.waldStat.noSmooth: no visible global function definition for
'pnorm'
compute.waldStat.noSmooth: no visible global function definition for
'p.adjust'
dispersion.shrinkage.BSseq : plik.logN: no visible global function
definition for 'dnorm'
dispersion.shrinkage.BSseq: no visible global function definition for
'optimize'
est.phi0: no visible binding for global variable 'var'
est.prior.BSseq.logN: no visible global function definition for
'median'
est.prior.BSseq.logN: no visible global function definition for 'IQR'
est.trend: no visible global function definition for 'median'
est.trend: no visible global function definition for 'quantile'
est.trend: no visible binding for global variable 'median'
est.trend: no visible global function definition for 'isoreg'
est.trend: no visible global function definition for 'smooth.spline'
est.trend: no visible global function definition for 'predict'
estDispersion.multiFactor: no visible global function definition for
'median'
estDispersion.multiFactor: no visible global function definition for
'IQR'
estDispersion.multiFactor : get.phi : obj: no visible global function
definition for 'dnorm'
estDispersion.multiFactor : get.phi: no visible global function
definition for 'optimize'
estNormFactors.lr: no visible global function definition for 'quantile'
estNormFactors.lr: no visible global function definition for 'median'
estNormFactors.median: no visible binding for global variable 'median'
estNormFactors.quantile : <anonymous>: no visible global function
definition for 'quantile'
locfdr: no visible global function definition for 'median'
locfdr: no visible global function definition for 'quantile'
locfdr: no visible global function definition for 'hist'
locfdr: no visible global function definition for 'ns'
locfdr: no visible global function definition for 'glm'
locfdr: no visible binding for global variable 'poisson'
locfdr: no visible global function definition for 'poly'
locfdr: no visible global function definition for 'lm'
locfdr: no visible global function definition for 'qnorm'
locfdr: no visible global function definition for 'dnorm'
locfdr: no visible global function definition for 'approx'
locfdr: no visible global function definition for 'par'
locfdr: no visible global function definition for 'lines'
locfdr: no visible global function definition for 'title'
locfdr: no visible global function definition for 'points'
locfdr: no visible global function definition for 'matplot'
locfdr: no visible global function definition for 'abline'
locfdr: no visible global function definition for 'text'
locmle: no visible global function definition for 'median'
locmle: no visible global function definition for 'quantile'
locmle: no visible global function definition for 'qnorm'
locmle: no visible global function definition for 'pnorm'
locmle: no visible global function definition for 'dnorm'
lrTest: no visible global function definition for 'dnbinom'
lrTest: no visible global function definition for 'pchisq'
makeContrast: no visible global function definition for 'terms'
rnegbinom: no visible global function definition for 'rpois'
rnegbinom: no visible global function definition for 'rgamma'
scv: no visible global function definition for 'var'
showOneDMR: no visible global function definition for 'par'
showOneDMR: no visible global function definition for 'plot'
showOneDMR: no visible global function definition for 'box'
showOneDMR: no visible global function definition for 'axis'
showOneDMR: no visible global function definition for 'mtext'
showOneDMR: no visible global function definition for 'lines'
showOneDMR: no visible global function definition for 'rect'
shrink.dispersion.notrend: no visible global function definition for
'median'
shrink.dispersion.notrend: no visible global function definition for
'IQR'
shrink.dispersion.notrend : get.phi: no visible global function
definition for 'optimize'
shrink.dispersion.trend: no visible global function definition for
'IQR'
shrink.dispersion.trend : get.phi: no visible global function
definition for 'optimize'
waldTest: no visible global function definition for 'pnorm'
waldTest: no visible global function definition for 'median'
waldTest: no visible global function definition for 'IQR'
Undefined global functions or variables:
IQR abline approx axis box dnbinom dnorm glm hist isoreg lines lm
matplot median model.matrix mtext ns optimize p.adjust par pchisq
plot pnorm points poisson poly predict qnorm quantile rect rgamma
rpois smooth.spline terms text title var
Consider adding
importFrom("graphics", "abline", "axis", "box", "hist", "lines",
"matplot", "mtext", "par", "plot", "points", "rect", "text",
"title")
importFrom("stats", "IQR", "approx", "dnbinom", "dnorm", "glm",
"isoreg", "lm", "median", "model.matrix", "optimize",
"p.adjust", "pchisq", "pnorm", "poisson", "poly", "predict",
"qnorm", "quantile", "rgamma", "rpois", "smooth.spline",
"terms", "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 'callDML':
callDML
Code: function(DMLresult, delta = 0.1, p.threshold = 1e-05)
Docs: function(DMLresult, delta = 0, p.threshold = 1e-05)
Mismatches in argument default values:
Name: 'delta' Code: 0.1 Docs: 0
* 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 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-3.6-bioc/meat/DSS.buildbin-libdir/DSS/libs/i386/DSS.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 use Fortran I/O
nor system RNGs. 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'edgeR'
* 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, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/DSS.Rcheck/00check.log'
for details.
Installation output
DSS.Rcheck/00install.out
Tests output
Example timings
DSS.Rcheck/examples_i386/DSS-Ex.timings
|
DSS.Rcheck/examples_x64/DSS-Ex.timings
|