Juan R Gonzalez
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 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 2019-04-13 11:21:56 -0400 (Sat, 13 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 | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: tweeDEseq |
| Version: 1.28.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tweeDEseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings tweeDEseq_1.28.1.tar.gz |
| StartedAt: 2019-04-13 06:05:43 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 06:07:44 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 120.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: tweeDEseq.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tweeDEseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings tweeDEseq_1.28.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/tweeDEseq.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpA9RRSu/R.INSTALL1534190d2489/tweeDEseq/man/normalizeCounts.Rd:64: file link 'edgeR' in package 'edgeR' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/tweeDEseq.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/tweeDEseq/libs/i386/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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
glmPT 5.23 0 5.23
* 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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/tweeDEseq.Rcheck/00check.log'
for details.
tweeDEseq.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/tweeDEseq_1.28.1.tar.gz && rm -rf tweeDEseq.buildbin-libdir && mkdir tweeDEseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tweeDEseq.buildbin-libdir tweeDEseq_1.28.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL tweeDEseq_1.28.1.zip && rm tweeDEseq_1.28.1.tar.gz tweeDEseq_1.28.1.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 43733 100 43733 0 0 1181k 0 --:--:-- --:--:-- --:--:-- 1294k
install for i386
* installing *source* package 'tweeDEseq' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c init_tweeDEseq.c -o init_tweeDEseq.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c loglikGlm.c -o loglikGlm.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c logprobs.c -o logprobs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c permtest.c -o permtest.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c probs.c -o probs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c zhu2.c -o zhu2.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c zhu3.c -o zhu3.o
C:/Rtools/mingw_32/bin/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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/tweeDEseq.buildbin-libdir/tweeDEseq/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'tweeDEseq'
finding HTML links ... done
compareCountDistributions html
distPoissonTweedie html
filterCounts html
glmPT html
gofTest html
mlePoissonTweedie html
normalizeCounts html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpA9RRSu/R.INSTALL1534190d2489/tweeDEseq/man/normalizeCounts.Rd:64: file link 'edgeR' in package 'edgeR' does not exist and so has been treated as a topic
print.mlePT html
qqchisq html
finding level-2 HTML links ... done
seizure html
testShapePT html
tweeDE html
tweeDEseq-internal html
tweeDExact html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'tweeDEseq' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c init_tweeDEseq.c -o init_tweeDEseq.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c loglikGlm.c -o loglikGlm.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c logprobs.c -o logprobs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c permtest.c -o permtest.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c probs.c -o probs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c zhu2.c -o zhu2.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c zhu3.c -o zhu3.o
C:/Rtools/mingw_64/bin/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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/tweeDEseq.buildbin-libdir/tweeDEseq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tweeDEseq' as tweeDEseq_1.28.1.zip
* DONE (tweeDEseq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'tweeDEseq' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
tweeDEseq.Rcheck/examples_i386/tweeDEseq-Ex.timings
|
tweeDEseq.Rcheck/examples_x64/tweeDEseq-Ex.timings
|