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BioC 3.4: CHECK report for tweeDEseq on morelia

This page was generated on 2017-04-15 16:23:54 -0400 (Sat, 15 Apr 2017).

Package 1260/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tweeDEseq 1.20.0
Juan R Gonzalez
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/tweeDEseq
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: tweeDEseq
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tweeDEseq_1.20.0.tar.gz
StartedAt: 2017-04-15 09:06:07 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 09:06:55 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 48.3 seconds
RetCode: 0
Status:  OK 
CheckDir: tweeDEseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tweeDEseq_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/tweeDEseq.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 ‘tweeDEseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tweeDEseq’ version ‘1.20.0’
* 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 ‘tweeDEseq’ 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
* 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
Unexported object imported by a ':::' call: ‘stats:::format.perc’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AIC.glmPT: no visible global function definition for ‘logLik’
MAplot.tweeDE: no visible global function definition for ‘plot’
MAplot.tweeDE: no visible global function definition for ‘abline’
MAplot.tweeDE: no visible global function definition for ‘grey’
Vplot.tweeDE: no visible global function definition for ‘plot’
Vplot.tweeDE: no visible global function definition for ‘abline’
Vplot.tweeDE: no visible global function definition for ‘grey’
Vplot.tweeDE: no visible global function definition for ‘text’
anova.glmPT: no visible global function definition for ‘update’
anova.glmPT: no visible global function definition for ‘pchisq’
compareCountDist: no visible global function definition for ‘ecdf’
compareCountDist: no visible global function definition for ‘dnbinom’
compareCountDist: no visible global function definition for ‘dpois’
compareCountDist: no visible global function definition for ‘pchisq’
compareCountDist: no visible global function definition for ‘points’
compareCountDist: no visible global function definition for ‘lines’
compareCountDist: no visible global function definition for ‘legend’
confint.mlePT: no visible global function definition for ‘qnorm’
dPT: no visible global function definition for ‘dnbinom’
dPT: no visible global function definition for ‘dpois’
exactTestPT: no visible global function definition for ‘dpois’
glmPT: no visible global function definition for ‘model.response’
glmPT: no visible global function definition for ‘model.matrix’
glmPT: no visible binding for global variable ‘contrasts’
glmPT.fit: no visible global function definition for ‘optim’
loglikGlmPT: no visible global function definition for ‘dnbinom’
loglikGlmPT: no visible global function definition for ‘dpois’
loglikPoissonTweedie: no visible global function definition for
  ‘aggregate’
loglikPoissonTweedie: no visible global function definition for
  ‘dnbinom’
loglikPoissonTweedie: no visible global function definition for ‘dpois’
loglikPoissonTweedie2: no visible global function definition for
  ‘aggregate’
loglikPoissonTweedie2: no visible global function definition for
  ‘dnbinom’
loglikPoissonTweedie2: no visible global function definition for
  ‘dpois’
loglikPoissonTweedie3: no visible global function definition for
  ‘aggregate’
loglikPoissonTweedie3: no visible global function definition for
  ‘dnbinom’
loglikPoissonTweedie3: no visible global function definition for
  ‘dpois’
mlePoissonTweedie: no visible global function definition for
  ‘weighted.mean’
mlePoissonTweedie: no visible global function definition for ‘var’
mlePoissonTweedie: no visible global function definition for ‘optim’
momentEstimates: no visible global function definition for ‘var’
qqchisq: no visible global function definition for ‘qchisq’
qqchisq: no visible global function definition for ‘ppoints’
qqchisq: no visible global function definition for ‘qnorm’
qqchisq: no visible global function definition for ‘qqnorm’
qqchisq: no visible global function definition for ‘abline’
qqchisq: no visible global function definition for ‘plot’
qqchisq: no visible global function definition for ‘quantile’
qqchisq: no visible global function definition for ‘grey’
qqchisq: no visible global function definition for ‘axis’
rPT: no visible global function definition for ‘runif’
shapeTrend: no visible global function definition for ‘lowess’
shapeTrend: no visible global function definition for ‘approxfun’
summary.glmPT: no visible global function definition for ‘pnorm’
summary.glmPT: no visible global function definition for ‘symnum’
testPoissonTweedie: no visible global function definition for ‘pnorm’
testShapePT: no visible global function definition for ‘dnbinom’
testShapePT: no visible global function definition for ‘pchisq’
testShapePT: no visible global function definition for ‘pnorm’
tweeDE : test.i: no visible global function definition for
  ‘setTxtProgressBar’
tweeDE : test.i: no visible global function definition for ‘aggregate’
tweeDE : test.i.mc: no visible global function definition for
  ‘setTxtProgressBar’
tweeDE : test.i.mc: no visible global function definition for
  ‘aggregate’
tweeDE: no visible global function definition for ‘txtProgressBar’
tweeDE: no visible global function definition for ‘setTxtProgressBar’
tweeDE: no visible global function definition for ‘p.adjust’
tweeDEglm: no visible global function definition for ‘model.matrix’
tweeDEglm: no visible binding for global variable ‘contrasts’
tweeDEglm : test.i: no visible global function definition for
  ‘setTxtProgressBar’
tweeDEglm : test.i: no visible global function definition for ‘AIC’
tweeDEglm: no visible global function definition for ‘txtProgressBar’
tweeDEglm: no visible global function definition for
  ‘setTxtProgressBar’
tweeDEglm: no visible global function definition for ‘p.adjust’
tweeDExact : test.i: no visible global function definition for
  ‘setTxtProgressBar’
tweeDExact : test.i.mc: no visible global function definition for
  ‘setTxtProgressBar’
tweeDExact: no visible global function definition for ‘txtProgressBar’
tweeDExact: no visible global function definition for
  ‘setTxtProgressBar’
tweeDExact: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  AIC abline aggregate approxfun axis contrasts dnbinom dpois ecdf grey
  legend lines logLik lowess model.matrix model.response optim p.adjust
  pchisq plot pnorm points ppoints qchisq qnorm qqnorm quantile runif
  setTxtProgressBar symnum text txtProgressBar update var weighted.mean
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "points", "text")
  importFrom("stats", "AIC", "aggregate", "approxfun", "contrasts",
             "dnbinom", "dpois", "ecdf", "logLik", "lowess",
             "model.matrix", "model.response", "optim", "p.adjust",
             "pchisq", "pnorm", "ppoints", "qchisq", "qnorm", "qqnorm",
             "quantile", "runif", "symnum", "update", "var",
             "weighted.mean")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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 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 ... 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
Examples with CPU or elapsed time > 5s
       user system elapsed
glmPT 4.671  0.018   5.799
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/tweeDEseq.Rcheck/00check.log’
for details.


tweeDEseq.Rcheck/00install.out:

* installing *source* package ‘tweeDEseq’ ...
** 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 cov_wt_C.c -o cov_wt_C.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 init_tweeDEseq.c -o init_tweeDEseq.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 loglikGlm.c -o loglikGlm.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 logprobs.c -o logprobs.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 permtest.c -o permtest.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 probs.c -o probs.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 zhu2.c -o zhu2.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 zhu3.c -o zhu3.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 tweeDEseq.so cov_wt_C.o init_tweeDEseq.o loglikGlm.o logprobs.o permtest.o probs.o zhu2.o zhu3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/tweeDEseq.Rcheck/tweeDEseq/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 (tweeDEseq)

tweeDEseq.Rcheck/tweeDEseq-Ex.timings:

nameusersystemelapsed
compareCountDistributions0.1030.0040.166
distPoissonTweedie0.0030.0010.003
filterCounts0.0110.0010.012
glmPT4.6710.0185.799
gofTest0.5390.0060.545
mlePoissonTweedie0.1000.0030.104
normalizeCounts0.0710.0030.074
print.mlePT0.0930.0020.096
qqchisq0.5340.0050.539
seizure0.1880.0020.190
testShapePT0.1130.0020.116
tweeDE1.3980.0052.054
tweeDExact1.0310.0041.458