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BioC 3.4: CHECK report for DSS on morelia

This page was generated on 2017-04-15 16:24:10 -0400 (Sat, 15 Apr 2017).

Package 348/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DSS 2.14.0
Hao Wu
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/DSS
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 UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DSS
Version: 2.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DSS_2.14.0.tar.gz
StartedAt: 2017-04-15 01:19:22 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:22:03 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 161.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: DSS.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DSS_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/DSS.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DSS/DESCRIPTION’ ... OK
* this is package ‘DSS’ version ‘2.14.0’
* 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 ‘DSS’ 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 dependencies in R code ... NOTE
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.engine: no visible global function definition for
  ‘pnorm’
DMLtest.multiFactor.engine: 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’
find.factor: no visible global function definition for ‘terms’
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’
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 ... WARNING
Undocumented data sets:
  ‘RRBS’ ‘design’
All user-level objects in a package 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 ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* 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 ... 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: 2 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/DSS.Rcheck/00check.log’
for details.


DSS.Rcheck/00install.out:

* installing *source* package ‘DSS’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c compute_var_smooth.c -o compute_var_smooth.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c filter.c -o filter.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c nitem.c -o nitem.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DSS.so compute_var_smooth.o filter.o nitem.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/DSS.Rcheck/DSS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DSS)

DSS.Rcheck/DSS-Ex.timings:

nameusersystemelapsed
DMLfit.multiFactor1.3190.0331.389
DMLtest0.0010.0010.002
DMLtest.multiFactor1.1970.0121.210
DSS.DE0.2490.0040.253
SeqCountSet-class0.2940.0010.294
callDML0.0010.0000.002
callDMR000
dispersion0.2070.0140.221
estDispersion0.4160.0060.421
estNormFactors0.0170.0020.233
makeBSseqData1.3070.0361.344
normalizationFactor0.0040.0000.005
seqData0.0050.0010.150
showOneDMR0.0010.0000.001
waldTest0.1330.0020.135