Juan R Gonzalez
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/tweeDEseq |
| git_branch: RELEASE_3_15 |
| git_last_commit: d74d181 |
| git_last_commit_date: 2022-04-26 11:09:40 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:22:27 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the tweeDEseq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tweeDEseq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2072/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| tweeDEseq 1.42.0 (landing page) Juan R Gonzalez
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: tweeDEseq |
| Version: 1.42.0 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tweeDEseq.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings tweeDEseq_1.42.0.tar.gz |
| StartedAt: 2022-10-19 05:01:23 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 05:02:15 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 51.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tweeDEseq.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tweeDEseq.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings tweeDEseq_1.42.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/tweeDEseq.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.42.0'
* 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 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 '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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/tweeDEseq/libs/x64/tweeDEseq.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
'F:/biocbuild/bbs-3.15-bioc/meat/tweeDEseq.Rcheck/00check.log'
for details.
tweeDEseq.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL tweeDEseq
###
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'tweeDEseq' ...
** using staged installation
** libs
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_tweeDEseq.c -o init_tweeDEseq.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c loglikGlm.c -o loglikGlm.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c logprobs.c -o logprobs.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c permtest.c -o permtest.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c probs.c -o probs.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c zhu2.c -o zhu2.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c zhu3.c -o zhu3.o
gcc -shared -s -static-libgcc -o tweeDEseq.dll tmp.def cov_wt_C.o init_tweeDEseq.o loglikGlm.o logprobs.o permtest.o probs.o zhu2.o zhu3.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-tweeDEseq/00new/tweeDEseq/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tweeDEseq)
tweeDEseq.Rcheck/tweeDEseq-Ex.timings
| name | user | system | elapsed | |
| compareCountDistributions | 0.07 | 0.00 | 0.07 | |
| distPoissonTweedie | 0 | 0 | 0 | |
| filterCounts | 0 | 0 | 0 | |
| glmPT | 2.45 | 0.04 | 2.50 | |
| gofTest | 0.46 | 0.00 | 0.45 | |
| mlePoissonTweedie | 0.06 | 0.00 | 0.06 | |
| normalizeCounts | 0.07 | 0.00 | 0.06 | |
| print.mlePT | 0.07 | 0.00 | 0.08 | |
| qqchisq | 0.46 | 0.02 | 0.47 | |
| seizure | 0.15 | 0.00 | 0.15 | |
| testShapePT | 0.16 | 0.00 | 0.16 | |
| tweeDE | 0.83 | 0.00 | 0.83 | |
| tweeDExact | 1.08 | 0.00 | 1.08 | |