Sarah Sheppard
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/cleanUpdTSeq |
| Branch: RELEASE_3_7 |
| Last Commit: 3fb69d7 |
| Last Changed Date: 2018-04-30 10:35:30 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:37:25 -0400 (Wed, 17 Oct 2018).
| Package 251/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cleanUpdTSeq 1.18.0 Sarah Sheppard
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: cleanUpdTSeq |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cleanUpdTSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cleanUpdTSeq_1.18.0.tar.gz |
| StartedAt: 2018-10-17 01:08:51 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:16:30 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 458.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cleanUpdTSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cleanUpdTSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cleanUpdTSeq_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/cleanUpdTSeq.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.18.0'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
data.NaiveBayes 27.14 3.87 31.13
predictTestSet 26.20 0.68 26.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
predictTestSet 36.11 0.25 36.36
data.NaiveBayes 30.17 0.44 30.61
* 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-3.7-bioc/meat/cleanUpdTSeq.Rcheck/00check.log'
for details.
cleanUpdTSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/cleanUpdTSeq_1.18.0.tar.gz && rm -rf cleanUpdTSeq.buildbin-libdir && mkdir cleanUpdTSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cleanUpdTSeq.buildbin-libdir cleanUpdTSeq_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL cleanUpdTSeq_1.18.0.zip && rm cleanUpdTSeq_1.18.0.tar.gz cleanUpdTSeq_1.18.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 3930k 100 3930k 0 0 38.4M 0 --:--:-- --:--:-- --:--:-- 41.2M
install for i386
* installing *source* package 'cleanUpdTSeq' ...
** R
** data
** inst
** byte-compile and prepare 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_1.18.0.zip
* DONE (cleanUpdTSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'cleanUpdTSeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
cleanUpdTSeq.Rcheck/tests_i386/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
dirname, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 Oct 17 01:16:04 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
19.78 0.75 20.92
|
cleanUpdTSeq.Rcheck/tests_x64/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
dirname, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 Oct 17 01:16:23 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
17.92 0.50 18.40
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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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