Juan R Gonzalez
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/tweeDEseq |
| Branch: RELEASE_3_8 |
| Last Commit: 95ffd20 |
| Last Changed Date: 2019-01-04 13:53:01 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:56:10 -0400 (Tue, 16 Apr 2019).
| Package 1601/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| tweeDEseq 1.28.1 Juan R Gonzalez
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: tweeDEseq |
| Version: 1.28.1 |
| 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_1.28.1.tar.gz |
| StartedAt: 2019-04-16 03:17:04 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:17:56 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 52.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tweeDEseq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.28.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/tweeDEseq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.28.1’
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
glmPT 5.38 0.044 6.854
* 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-3.8-bioc/meat/tweeDEseq.Rcheck/00check.log’
for details.
tweeDEseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tweeDEseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘tweeDEseq’ ... ** 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/3.5/Resources/library/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 * DONE (tweeDEseq)
tweeDEseq.Rcheck/tweeDEseq-Ex.timings
| name | user | system | elapsed | |
| compareCountDistributions | 0.160 | 0.004 | 0.165 | |
| distPoissonTweedie | 0.004 | 0.002 | 0.005 | |
| filterCounts | 0.011 | 0.002 | 0.012 | |
| glmPT | 5.380 | 0.044 | 6.854 | |
| gofTest | 0.660 | 0.018 | 0.684 | |
| mlePoissonTweedie | 0.102 | 0.003 | 0.105 | |
| normalizeCounts | 0.089 | 0.002 | 0.093 | |
| print.mlePT | 0.076 | 0.004 | 0.081 | |
| qqchisq | 0.604 | 0.009 | 0.615 | |
| seizure | 0.190 | 0.003 | 0.194 | |
| testShapePT | 0.126 | 0.002 | 0.129 | |
| tweeDE | 1.402 | 0.005 | 1.425 | |
| tweeDExact | 1.187 | 0.006 | 1.260 | |