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BioC 3.5: CHECK report for tweeDEseq on malbec2

This page was generated on 2017-08-16 13:14:16 -0400 (Wed, 16 Aug 2017).

Package 1344/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tweeDEseq 1.22.0
Juan R Gonzalez
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/tweeDEseq
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: tweeDEseq
Version: 1.22.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings tweeDEseq_1.22.0.tar.gz
StartedAt: 2017-08-16 02:48:20 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:49:00 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 39.9 seconds
RetCode: 0
Status:  OK 
CheckDir: tweeDEseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings tweeDEseq_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/tweeDEseq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.22.0’
* 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 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 installed files from ‘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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/tweeDEseq.Rcheck/00check.log’
for details.


tweeDEseq.Rcheck/00install.out:

* installing *source* package ‘tweeDEseq’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c cov_wt_C.c -o cov_wt_C.o
cov_wt_C.c: In function ‘cov_wt_C’:
cov_wt_C.c:79:14: warning: ‘wvar’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   free(aux), free(wvar), free(y);
              ^
cov_wt_C.c: In function ‘momentEstimates_wt_C’:
cov_wt_C.c:154:12: warning: ‘moments’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   free(y), free(moments), free(aux);
            ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init_tweeDEseq.c -o init_tweeDEseq.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c loglikGlm.c -o loglikGlm.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c logprobs.c -o logprobs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c permtest.c -o permtest.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c probs.c -o probs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c zhu2.c -o zhu2.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c zhu3.c -o zhu3.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/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 -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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
compareCountDistributions0.1440.0080.150
distPoissonTweedie0.0040.0000.002
filterCounts0.0080.0000.007
glmPT4.4520.0004.734
gofTest0.6080.0000.610
mlePoissonTweedie0.1160.0000.116
normalizeCounts0.2360.0000.240
print.mlePT0.0640.0040.069
qqchisq0.4840.0000.483
seizure0.1440.0040.148
testShapePT0.1160.0000.116
tweeDE1.0280.0041.031
tweeDExact0.9240.0000.928