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CHECK report for tweeDEseq on celaya2

This page was generated on 2019-04-09 13:03:03 -0400 (Tue, 09 Apr 2019).

Package 1653/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tweeDEseq 1.29.1
Juan R Gonzalez
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/tweeDEseq
Branch: master
Last Commit: 7d80bff
Last Changed Date: 2019-01-04 13:52:59 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: tweeDEseq
Version: 1.29.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tweeDEseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tweeDEseq_1.29.1.tar.gz
StartedAt: 2019-04-09 06:09:32 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:10:39 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 67.2 seconds
RetCode: 0
Status:  OK 
CheckDir: tweeDEseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tweeDEseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tweeDEseq_1.29.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/tweeDEseq.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.29.1’
* 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 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/tweeDEseq.Rcheck/00check.log’
for details.



Installation output

tweeDEseq.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tweeDEseq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘tweeDEseq’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -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  -fPIC  -Wall -g -O2  -c init_tweeDEseq.c -o init_tweeDEseq.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c loglikGlm.c -o loglikGlm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c logprobs.c -o logprobs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c permtest.c -o permtest.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c probs.c -o probs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c zhu2.c -o zhu2.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-tweeDEseq/00new/tweeDEseq/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tweeDEseq)

Tests output


Example timings

tweeDEseq.Rcheck/tweeDEseq-Ex.timings

nameusersystemelapsed
compareCountDistributions0.1270.0050.133
distPoissonTweedie0.0030.0020.004
filterCounts0.0060.0000.007
glmPT4.8560.0734.930
gofTest0.8700.0490.918
mlePoissonTweedie0.0930.0060.099
normalizeCounts0.0860.0090.096
print.mlePT0.1310.0100.141
qqchisq0.5870.0260.613
seizure0.2190.0030.221
testShapePT0.1680.0070.175
tweeDE1.7580.0141.801
tweeDExact1.2810.0151.296