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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:tweeDEseq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings tweeDEseq_1.45.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/tweeDEseq.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘tweeDEseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tweeDEseq’ version ‘1.45.0’
* 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
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Missing object imported by a ':::' call: ‘stats:::format.perc’
* 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 ‘abline’
MAplot.tweeDE: no visible global function definition for ‘grey’
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 ‘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 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", "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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘tweeDEseq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Methods for objects of class 'mlePT'
> ### Title: Methods for objects of class 'mlePT'
> ### Aliases: print.mlePT logLik.mlePT confint.mlePT
> ### Keywords: methods
> 
> ### ** Examples
> 
> # Load and aggregate the 'seizure' database
> data(seizure)
> aggCounts <- aggregate(x = cbind(seizure$count, seizure$trx), by =
+ list(seizure$id), FUN = sum)
> 
> # Estimate the parameters
> mleSeizure <- mlePoissonTweedie(x = aggCounts[,2], a.ini = 0, D.ini =
+ 10)
> 
> # Print
> mleSeizure

Poisson-Tweedie parameter estimates (MLE)

   estimate  s.e.
mu     33.1  5.79
D      59.9 22.86
a       0.6  0.09
Skewness: 4.64

 Zhu parameterization 
    a     b     c 
0.602 4.533 0.993 

 Hougaard parameterization 
alpha delta theta 
0.602 4.514 0.007 

 log-likelihood: -259.6701
 number of iterations: 26
> 
> # Extract loglikelihood
> logLik(mleSeizure)
[1] -259.6701
> 
> # Compute confidence inerval
> confint(mleSeizure)
Error in confint.mlePT(mleSeizure) : object 'format.perc' not found
Calls: confint -> confint.mlePT
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘tweeDEseq.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/tweeDEseq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL tweeDEseq
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘tweeDEseq’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-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]
   79 |   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]
  154 |   free(y), free(moments), free(aux);
      |            ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c loglikGlm.c -o loglikGlm.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c logprobs.c -o logprobs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c permtest.c -o permtest.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c probs.c -o probs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c zhu2.c -o zhu2.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c zhu3.c -o zhu3.o
gcc -shared -L/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-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)