Aaron Taudt
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/chromstaR |
| git_branch: RELEASE_3_14 |
| git_last_commit: b8ef93b |
| git_last_commit_date: 2021-11-03 04:34:25 -0400 (Wed, 03 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:20 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 chromstaR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromstaR.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 314/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chromstaR 1.20.2 (landing page) Aaron Taudt
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: chromstaR |
| Version: 1.20.2 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chromstaR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings chromstaR_1.20.2.tar.gz |
| StartedAt: 2022-04-12 17:17:21 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 17:30:15 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 773.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chromstaR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chromstaR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings chromstaR_1.20.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/chromstaR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chromstaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chromstaR' version '1.20.2'
* 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 'chromstaR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
data 4.5Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Chromstar: multiple local function definitions for 'parallel.helper'
with different formal arguments
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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-3.14-bioc/R/library/chromstaR/libs/i386/chromstaR.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/chromstaR/libs/x64/chromstaR.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
combineMultivariates 34.20 0.45 34.97
enrichment_analysis 22.41 0.44 25.74
callPeaksMultivariate 14.64 0.18 15.39
callPeaksReplicates 12.93 0.25 13.55
combinatorialStates 10.02 0.08 10.09
unis2pseudomulti 10.00 0.09 10.09
changePostCutoff 8.97 0.15 9.12
plotExpression 8.05 0.06 10.75
plotGenomeBrowser 7.26 0.08 7.34
Chromstar 6.95 0.34 45.02
readCustomBedFile 6.42 0.04 6.47
plotHistogram 4.85 0.23 5.08
changeMaxPostCutoff 4.98 0.08 5.07
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
combineMultivariates 30.16 0.25 30.41
enrichment_analysis 18.56 0.35 29.31
callPeaksReplicates 13.07 0.13 13.19
callPeaksMultivariate 12.23 0.11 12.35
changePostCutoff 11.25 0.26 11.52
unis2pseudomulti 10.32 0.11 10.42
combinatorialStates 8.53 0.13 8.66
Chromstar 7.85 0.33 48.12
plotExpression 7.50 0.07 17.36
plotGenomeBrowser 7.33 0.03 7.36
changeMaxPostCutoff 5.87 0.10 5.97
readCustomBedFile 5.36 0.01 5.37
exportFiles 2.54 0.00 8.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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
'C:/Users/biocbuild/bbs-3.14-bioc/meat/chromstaR.Rcheck/00check.log'
for details.
chromstaR.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/chromstaR_1.20.2.tar.gz && rm -rf chromstaR.buildbin-libdir && mkdir chromstaR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromstaR.buildbin-libdir chromstaR_1.20.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL chromstaR_1.20.2.zip && rm chromstaR_1.20.2.tar.gz chromstaR_1.20.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
7 6684k 7 529k 0 0 593k 0 0:00:11 --:--:-- 0:00:11 593k
29 6684k 29 1961k 0 0 1038k 0 0:00:06 0:00:01 0:00:05 1038k
64 6684k 64 4295k 0 0 1489k 0 0:00:04 0:00:02 0:00:02 1489k
100 6684k 100 6684k 0 0 1843k 0 0:00:03 0:00:03 --:--:-- 1844k
install for i386
* installing *source* package 'chromstaR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_interface.cpp -o R_interface.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility.cpp -o utility.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o chromstaR.dll tmp.def R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/chromstaR.buildbin-libdir/00LOCK-chromstaR/00new/chromstaR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'chromstaR'
finding HTML links ... done
Chromstar html
binReads html
finding level-2 HTML links ... done
binned.data html
callPeaksMultivariate html
callPeaksReplicates html
callPeaksUnivariate html
callPeaksUnivariateAllChr html
changeMaxPostCutoff html
changePostCutoff html
chromstaR-objects html
chromstaR-package html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/chromstaR.buildbin-libdir/00LOCK-chromstaR/00new/chromstaR/help/chromstaR.html
collapseBins html
combinatorialStates html
combineMultivariates html
combinedMultiHMM html
conversion html
enrichmentAtAnnotation html
enrichment_analysis html
experiment.table html
exportFiles html
exportGRangesAsBedFile html
fixedWidthBins html
genes_rn4 html
genomicFrequencies html
getCombinations html
getDistinctColors html
getStateColors html
heatmapCombinations html
heatmapCountCorrelation html
heatmapTransitionProbs html
loadHmmsFromFiles html
mergeChroms html
model.combined html
model.multivariate html
model.univariate html
multiHMM html
multivariateSegmentation html
plotExpression html
plotGenomeBrowser html
plotHistogram html
plotHistograms html
plotting html
print.combinedMultiHMM html
print.multiHMM html
print.uniHMM html
readBamFileAsGRanges html
readBedFileAsGRanges html
readConfig html
readCustomBedFile html
removeCondition html
scanBinsizes html
scores html
simulateMultivariate html
simulateReadsFromCounts html
simulateUnivariate html
state.brewer html
stateBrewer html
subsample html
transitionFrequencies html
uniHMM html
unis2pseudomulti html
variableWidthBins html
writeConfig html
zinbinom html
** 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
install for x64
* installing *source* package 'chromstaR' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_interface.cpp -o R_interface.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility.cpp -o utility.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o chromstaR.dll tmp.def R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/chromstaR.buildbin-libdir/chromstaR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chromstaR' as chromstaR_1.20.2.zip
* DONE (chromstaR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'chromstaR' successfully unpacked and MD5 sums checked
|
chromstaR.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(chromstaR)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: chromstaRData
Please visit https://github.com/ataudt/chromstaR for the latest bugfixes and features.
>
> test_check("chromstaR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
>
> proc.time()
user system elapsed
16.95 0.93 17.87
|
chromstaR.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(chromstaR)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: chromstaRData
Please visit https://github.com/ataudt/chromstaR for the latest bugfixes and features.
>
> test_check("chromstaR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
>
> proc.time()
user system elapsed
16.98 0.82 17.79
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chromstaR.Rcheck/examples_i386/chromstaR-Ex.timings
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chromstaR.Rcheck/examples_x64/chromstaR-Ex.timings
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