li chen
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/traseR |
| Branch: RELEASE_3_7 |
| Last Commit: add29fb |
| Last Changed Date: 2018-04-30 10:35:37 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:40:52 -0400 (Wed, 17 Oct 2018).
| Package 1501/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| traseR 1.10.0 li chen
| 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: traseR |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:traseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings traseR_1.10.0.tar.gz |
| StartedAt: 2018-10-17 05:15:28 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 05:21:39 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 370.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: traseR.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:traseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings traseR_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/traseR.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 'traseR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'traseR' 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 'traseR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
data 6.0Mb
* 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
enrichTest: no visible global function definition for 'chisq.test'
enrichTest: no visible global function definition for 'binom.test'
enrichTest: no visible global function definition for 'phyper'
plotContext: no visible global function definition for 'subjectHits'
plotContext: no visible global function definition for 'pie'
plotContext: no visible global function definition for 'rainbow'
plotGene: no visible global function definition for 'plot'
plotGene: no visible global function definition for 'mtext'
plotGene: no visible global function definition for 'axis'
plotGene: no visible global function definition for 'box'
plotGene: no visible global function definition for 'points'
plotGene: no visible global function definition for 'text'
plotGene: no visible global function definition for 'arrows'
plotGene: no visible global function definition for 'segments'
plotInterval: no visible global function definition for 'subjectHits'
plotInterval: no visible global function definition for 'plot'
plotInterval: no visible global function definition for 'mtext'
plotInterval: no visible global function definition for 'axis'
plotInterval: no visible global function definition for 'box'
plotInterval: no visible global function definition for 'points'
plotInterval: no visible global function definition for 'text'
plotInterval: no visible global function definition for 'arrows'
plotInterval: no visible global function definition for 'segments'
plotPvalue: no visible global function definition for 'boxplot'
plotPvalue: no visible global function definition for 'density'
plotPvalue: no visible global function definition for 'plot'
plotPvalue: no visible global function definition for 'lines'
plotPvalue: no visible global function definition for 'legend'
plotPvalue: no visible global function definition for 'subjectHits'
plotSNP: no visible global function definition for 'plot'
plotSNP: no visible global function definition for 'mtext'
plotSNP: no visible global function definition for 'axis'
plotSNP: no visible global function definition for 'box'
plotSNP: no visible global function definition for 'points'
plotSNP: no visible global function definition for 'text'
plotSNP: no visible global function definition for 'arrows'
plotSNP: no visible global function definition for 'segments'
queryKeyword: no visible global function definition for 'subjectHits'
querySNP: no visible global function definition for 'subjectHits'
traseR: no visible global function definition for 'seqlengths'
traseR: no visible global function definition for 'subjectHits'
traseR: no visible global function definition for 'runif'
traseR: no visible global function definition for 'Rle'
traseR: no visible global function definition for 'queryHits'
traseR: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
Rle arrows axis binom.test box boxplot chisq.test density legend
lines mtext p.adjust phyper pie plot points queryHits rainbow runif
segments seqlengths subjectHits text
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "arrows", "axis", "box", "boxplot", "legend",
"lines", "mtext", "pie", "plot", "points", "segments",
"text")
importFrom("stats", "binom.test", "chisq.test", "density", "p.adjust",
"phyper", "runif")
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
print.traseR 6.29 0.51 6.92
traseR 4.95 0.11 5.07
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
traseR 7.44 0.08 7.51
print.traseR 5.91 0.16 6.06
querys 5.02 0.09 5.11
* 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/traseR.Rcheck/00check.log'
for details.
traseR.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/traseR_1.10.0.tar.gz && rm -rf traseR.buildbin-libdir && mkdir traseR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=traseR.buildbin-libdir traseR_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL traseR_1.10.0.zip && rm traseR_1.10.0.tar.gz traseR_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 6276k 100 6276k 0 0 32.2M 0 --:--:-- --:--:-- --:--:-- 33.3M
install for i386
* installing *source* package 'traseR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'traseR'
finding HTML links ... done
CEU html
Tcell html
plots html
print.traseR html
querys html
taSNP html
taSNPLD html
traseR-package html
traseR html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'traseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'traseR' as traseR_1.10.0.zip
* DONE (traseR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'traseR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
traseR.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.
> BiocGenerics:::testPackage("traseR")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
There are 128094211 bp in the query region, accounting for 0.0421875469310327 of the genome.
There are 573 traits in the analysis.
There are 33 trait class in the analysis.
100 traits have been tested!
200 traits have been tested!
300 traits have been tested!
400 traits have been tested!
500 traits have been tested!
10 trait class have been tested!
20 trait class have been tested!
30 trait class have been tested!
RUNIT TEST PROTOCOL -- Wed Oct 17 05:21:01 2018
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
traseR RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
34.96 1.65 37.28
|
traseR.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.
> BiocGenerics:::testPackage("traseR")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
There are 128094211 bp in the query region, accounting for 0.0421875469310327 of the genome.
There are 573 traits in the analysis.
There are 33 trait class in the analysis.
100 traits have been tested!
200 traits have been tested!
300 traits have been tested!
400 traits have been tested!
500 traits have been tested!
10 trait class have been tested!
20 trait class have been tested!
30 trait class have been tested!
RUNIT TEST PROTOCOL -- Wed Oct 17 05:21:33 2018
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
traseR RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
30.39 0.59 30.98
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traseR.Rcheck/examples_i386/traseR-Ex.timings
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traseR.Rcheck/examples_x64/traseR-Ex.timings
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