Jonathon Hill
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/sangerseqR |
| Branch: RELEASE_3_6 |
| Last Commit: 8b87bbc |
| Last Changed Date: 2017-10-30 12:40:12 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:23:50 -0400 (Thu, 12 Apr 2018).
| Package 1245/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sangerseqR 1.14.0 Jonathon Hill
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: sangerseqR |
| Version: 1.14.0 |
| Command: rm -rf sangerseqR.buildbin-libdir sangerseqR.Rcheck && mkdir sangerseqR.buildbin-libdir sangerseqR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sangerseqR.buildbin-libdir sangerseqR_1.14.0.tar.gz >sangerseqR.Rcheck\00install.out 2>&1 && cp sangerseqR.Rcheck\00install.out sangerseqR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=sangerseqR.buildbin-libdir --install="check:sangerseqR-install.out" --force-multiarch --no-vignettes --timings sangerseqR_1.14.0.tar.gz |
| StartedAt: 2018-04-12 02:58:04 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:01:10 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 185.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: sangerseqR.Rcheck |
| Warnings: 1 |
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### Running command:
###
### rm -rf sangerseqR.buildbin-libdir sangerseqR.Rcheck && mkdir sangerseqR.buildbin-libdir sangerseqR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sangerseqR.buildbin-libdir sangerseqR_1.14.0.tar.gz >sangerseqR.Rcheck\00install.out 2>&1 && cp sangerseqR.Rcheck\00install.out sangerseqR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=sangerseqR.buildbin-libdir --install="check:sangerseqR-install.out" --force-multiarch --no-vignettes --timings sangerseqR_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/sangerseqR.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 'sangerseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sangerseqR' version '1.14.0'
* 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 'sangerseqR' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeQMogk/R.INSTALL3a7855544b7b/sangerseqR/man/sangerseq-class.Rd:36: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeQMogk/R.INSTALL3a7855544b7b/sangerseqR/man/sangerseq-class.Rd:39: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeQMogk/R.INSTALL3a7855544b7b/sangerseqR/man/scf-class.Rd:28: missing file link 'DNAString'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/sangerseqR.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 ... NOTE
chromatogram,sangerseq: no visible global function definition for 'par'
chromatogram,sangerseq: no visible global function definition for
'quantile'
chromatogram,sangerseq: no visible global function definition for 'IQR'
chromatogram,sangerseq: no visible global function definition for 'pdf'
chromatogram,sangerseq: no visible global function definition for
'plot'
chromatogram,sangerseq: no visible global function definition for
'rect'
chromatogram,sangerseq: no visible global function definition for
'lines'
chromatogram,sangerseq: no visible global function definition for
'mtext'
chromatogram,sangerseq: no visible global function definition for
'axis'
chromatogram,sangerseq: no visible global function definition for
'dev.off'
Undefined global functions or variables:
IQR axis dev.off lines mtext par pdf plot quantile rect
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "axis", "lines", "mtext", "par", "plot", "rect")
importFrom("stats", "IQR", "quantile")
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 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
setAllelePhase 11.91 0.06 11.97
chromatogram 10.41 0.03 10.74
makeBaseCalls 8.75 0.02 8.76
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
chromatogram 14.59 0.03 14.64
setAllelePhase 12.73 0.04 12.78
makeBaseCalls 10.38 0.01 10.39
* 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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/sangerseqR.Rcheck/00check.log'
for details.
sangerseqR.Rcheck/00install.out
install for i386
* installing *source* package 'sangerseqR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'sangerseqR'
finding HTML links ... done
PolyPeakParser html
abif-class html
chromatogram html
makeBaseCalls html
read.abif html
read.scf html
readsangerseq html
sangerseq-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeQMogk/R.INSTALL3a7855544b7b/sangerseqR/man/sangerseq-class.Rd:36: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeQMogk/R.INSTALL3a7855544b7b/sangerseqR/man/sangerseq-class.Rd:39: missing file link 'DNAString'
sangerseqAccessors html
finding level-2 HTML links ... done
sangerseqR-package html
scf-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeQMogk/R.INSTALL3a7855544b7b/sangerseqR/man/scf-class.Rd:28: missing file link 'DNAString'
setAllelePhase html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'sangerseqR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sangerseqR' as sangerseqR_1.14.0.zip
* DONE (sangerseqR)
In R CMD INSTALL
In R CMD INSTALL
|
sangerseqR.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.
> BiocGenerics:::testPackage("sangerseqR")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
RUNIT TEST PROTOCOL -- Thu Apr 12 03:00:59 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
sangerseqR 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
4.68 0.14 4.81
|
sangerseqR.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.
> BiocGenerics:::testPackage("sangerseqR")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
RUNIT TEST PROTOCOL -- Thu Apr 12 03:01:05 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
sangerseqR 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
5.07 0.17 5.23
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sangerseqR.Rcheck/examples_i386/sangerseqR-Ex.timings
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sangerseqR.Rcheck/examples_x64/sangerseqR-Ex.timings
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