Dario Righelli
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/DEScan2 |
| Branch: RELEASE_3_12 |
| Last Commit: 7a7d1be |
| Last Changed Date: 2020-10-27 11:32:55 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:30:48 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the DEScan2 package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 463/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DEScan2 1.10.0 (landing page) Dario Righelli
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: DEScan2 |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEScan2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DEScan2_1.10.0.tar.gz |
| StartedAt: 2021-05-06 02:10:07 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:23:21 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 794.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DEScan2.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEScan2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DEScan2_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DEScan2.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEScan2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DEScan2' version '1.10.0'
* 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 'DEScan2' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpK6jlqK/R.INSTALL1cfc483b4d92/DEScan2/man/finalRegions.Rd:34: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpK6jlqK/R.INSTALL1cfc483b4d92/DEScan2/man/findPeaks.Rd:61: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DEScan2.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'constructBedRanges':
constructBedRanges
Code: function(filename, filetype = c("bam", "bed", "bed.zip",
"narrow", "broad"), genomeName = NULL, onlyStdChrs =
FALSE, arePeaks = FALSE, verbose = FALSE)
Docs: function(filename, filetype = c("bam", "bed", "bed.zip"),
genomeName = NULL, onlyStdChrs = FALSE, arePeaks =
FALSE, verbose = FALSE)
Mismatches in argument default values:
Name: 'filetype' Code: c("bam", "bed", "bed.zip", "narrow", "broad") Docs: c("bam", "bed", "bed.zip")
Codoc mismatches from documentation object 'readFilesAsGRangesList':
readFilesAsGRangesList
Code: function(filePath, fileType = c("bam", "bed", "bed.zip",
"narrow", "broad"), genomeName = NULL, onlyStdChrs =
TRUE, arePeaks = TRUE, verbose = TRUE)
Docs: function(filePath, fileType = c("bam", "bed", "bed.zip"),
genomeName = NULL, onlyStdChrs = TRUE, arePeaks =
TRUE, verbose = TRUE)
Mismatches in argument default values:
Name: 'fileType' Code: c("bam", "bed", "bed.zip", "narrow", "broad") Docs: c("bam", "bed", "bed.zip")
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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-3.12-bioc/R/library/DEScan2/libs/i386/DEScan2.dll':
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-3.12-bioc/R/library/DEScan2/libs/x64/DEScan2.dll':
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
findPeaks 21.41 2.04 23.46
finalRegions 19.23 0.05 19.28
binnedCoverage 12.29 1.53 14.00
findOverlapsOverSamples 10.45 0.00 10.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findPeaks 35.35 3.19 38.55
finalRegions 36.42 0.11 36.75
binnedCoverage 18.05 2.39 20.60
findOverlapsOverSamples 18.31 0.00 18.31
countFinalRegions 5.15 0.36 5.52
readFilesAsGRangesList 4.71 0.28 5.06
* 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: 2 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/DEScan2.Rcheck/00check.log'
for details.
DEScan2.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/DEScan2_1.10.0.tar.gz && rm -rf DEScan2.buildbin-libdir && mkdir DEScan2.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEScan2.buildbin-libdir DEScan2_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL DEScan2_1.10.0.zip && rm DEScan2_1.10.0.tar.gz DEScan2_1.10.0.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
100 2470k 100 2470k 0 0 39.7M 0 --:--:-- --:--:-- --:--:-- 40.2M
install for i386
* installing *source* package 'DEScan2' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpparma_max_win.cpp -o rcpparma_max_win.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o DEScan2.dll tmp.def RcppExports.o rcpparma_max_win.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/DEScan2.buildbin-libdir/00LOCK-DEScan2/00new/DEScan2/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DEScan2'
finding HTML links ... done
DEScan2 html
RleListToRleMatrix html
binToChrCoordMatRowNames html
binnedCovOnly html
binnedCoverage html
c_get_disjoint_max_win html
computeCoverageMovingWindowOnChr html
computeLambdaOnChr html
computeZ html
constructBedRanges html
countFinalRegions html
createGranges html
cutGRangesPerChromosome html
divideEachSampleByChromosomes html
evenRunMean html
evenRunSum html
finalRegions html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpK6jlqK/R.INSTALL1cfc483b4d92/DEScan2/man/finalRegions.Rd:34: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
findOverlapsOverSamples html
findPeaks html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpK6jlqK/R.INSTALL1cfc483b4d92/DEScan2/man/findPeaks.Rd:61: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
fromSamplesToChrsGRangesList html
generateDFofSamplesPerChromosomes html
get_disjoint_max_win html
giveUniqueNamesToPeaksOverSamples html
initMergedPeaksNames html
keepRelevantChrs html
rcpparma_get_disjoint_max_win html
readBamAsBed html
readBedFile html
readFilesAsGRangesList html
saveGRangesAsBed html
saveGRangesAsTsv html
setGRGenomeInfo 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 'DEScan2' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpparma_max_win.cpp -o rcpparma_max_win.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o DEScan2.dll tmp.def RcppExports.o rcpparma_max_win.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/DEScan2.buildbin-libdir/DEScan2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEScan2' as DEScan2_1.10.0.zip
* DONE (DEScan2)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'DEScan2' successfully unpacked and MD5 sums checked
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DEScan2.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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("DEScan2")
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
>
> test_check("DEScan2")
Maximizing with zthresh: 10 sigwin: 10
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
>
> proc.time()
user system elapsed
67.12 4.78 75.25
|
DEScan2.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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("DEScan2")
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
>
> test_check("DEScan2")
Maximizing with zthresh: 10 sigwin: 10
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
>
> proc.time()
user system elapsed
44.92 2.57 49.35
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DEScan2.Rcheck/examples_i386/DEScan2-Ex.timings
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DEScan2.Rcheck/examples_x64/DEScan2-Ex.timings
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