Sarah Sheppard
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/cleanUpdTSeq |
| Branch: RELEASE_3_6 |
| Last Commit: 3e4e2d8 |
| Last Changed Date: 2017-10-30 12:40:04 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:23:00 -0400 (Thu, 12 Apr 2018).
| Package 238/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cleanUpdTSeq 1.16.0 Sarah Sheppard
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: cleanUpdTSeq |
| Version: 1.16.0 |
| Command: rm -rf cleanUpdTSeq.buildbin-libdir cleanUpdTSeq.Rcheck && mkdir cleanUpdTSeq.buildbin-libdir cleanUpdTSeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cleanUpdTSeq.buildbin-libdir cleanUpdTSeq_1.16.0.tar.gz >cleanUpdTSeq.Rcheck\00install.out 2>&1 && cp cleanUpdTSeq.Rcheck\00install.out cleanUpdTSeq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cleanUpdTSeq.buildbin-libdir --install="check:cleanUpdTSeq-install.out" --force-multiarch --no-vignettes --timings cleanUpdTSeq_1.16.0.tar.gz |
| StartedAt: 2018-04-11 22:56:37 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:04:29 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 471.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cleanUpdTSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### rm -rf cleanUpdTSeq.buildbin-libdir cleanUpdTSeq.Rcheck && mkdir cleanUpdTSeq.buildbin-libdir cleanUpdTSeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cleanUpdTSeq.buildbin-libdir cleanUpdTSeq_1.16.0.tar.gz >cleanUpdTSeq.Rcheck\00install.out 2>&1 && cp cleanUpdTSeq.Rcheck\00install.out cleanUpdTSeq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cleanUpdTSeq.buildbin-libdir --install="check:cleanUpdTSeq-install.out" --force-multiarch --no-vignettes --timings cleanUpdTSeq_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cleanUpdTSeq.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cleanUpdTSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cleanUpdTSeq' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics' 'BSgenome' 'BSgenome.Drerio.UCSC.danRer7'
'GenomicRanges' 'seqinr' 'e1071'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'cleanUpdTSeq' 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
* 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
BED2GRangesSeq: no visible global function definition for 'IRanges'
buildClassifier: no visible global function definition for 'as.formula'
getDownstreamSequence: no visible global function definition for
'IRanges'
getDownstreamSequence: no visible global function definition for
'seqlengths'
getUpstreamSequence: no visible global function definition for
'IRanges'
getUpstreamSequence: no visible global function definition for
'seqlengths'
predictTestSet: no visible global function definition for 'as.formula'
predictTestSet: no visible global function definition for 'predict'
predictTestSet: no visible global function definition for 'write.table'
Undefined global functions or variables:
IRanges as.formula predict seqlengths write.table
Consider adding
importFrom("stats", "as.formula", "predict")
importFrom("utils", "write.table")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
data.NaiveBayes 27.23 2.83 30.06
predictTestSet 23.61 0.62 24.23
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
data.NaiveBayes 41.00 0.44 41.44
predictTestSet 37.56 0.14 37.70
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/cleanUpdTSeq.Rcheck/00check.log'
for details.
cleanUpdTSeq.Rcheck/00install.out
install for i386
* installing *source* package 'cleanUpdTSeq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'cleanUpdTSeq'
finding HTML links ... done
BED2GRangesSeq html
PASclassifier-class html
buildClassifier html
buildFeatureVector html
classifier html
cleanUpdTSeq-package html
data.NaiveBayes html
featureVector-class html
getDownstreamSequence html
getUpstreamSequence html
modelInfo-class html
naiveBayes html
predictTestSet html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'cleanUpdTSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cleanUpdTSeq' as cleanUpdTSeq_1.16.0.zip
* DONE (cleanUpdTSeq)
In R CMD INSTALL
In R CMD INSTALL
|
cleanUpdTSeq.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.
> require("cleanUpdTSeq") || stop("unable to load Package:cleanUpdTSeq")
Loading required package: cleanUpdTSeq
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Loading required package: BSgenome.Drerio.UCSC.danRer7
Loading required package: seqinr
Attaching package: 'seqinr'
The following object is masked from 'package:Biostrings':
translate
Loading required package: e1071
[1] TRUE
> BiocGenerics:::testPackage("cleanUpdTSeq")
RUNIT TEST PROTOCOL -- Wed Apr 11 23:04:06 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
cleanUpdTSeq RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
17.90 0.43 18.32
|
cleanUpdTSeq.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.
> require("cleanUpdTSeq") || stop("unable to load Package:cleanUpdTSeq")
Loading required package: cleanUpdTSeq
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Loading required package: BSgenome.Drerio.UCSC.danRer7
Loading required package: seqinr
Attaching package: 'seqinr'
The following object is masked from 'package:Biostrings':
translate
Loading required package: e1071
[1] TRUE
> BiocGenerics:::testPackage("cleanUpdTSeq")
RUNIT TEST PROTOCOL -- Wed Apr 11 23:04:25 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
cleanUpdTSeq RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
17.87 0.18 18.04
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cleanUpdTSeq.Rcheck/examples_i386/cleanUpdTSeq-Ex.timings
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cleanUpdTSeq.Rcheck/examples_x64/cleanUpdTSeq-Ex.timings
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