Jonathon Hill
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/sangerseqR |
| Branch: RELEASE_3_9 |
| Last Commit: da60756 |
| Last Changed Date: 2019-05-02 11:53:47 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:03:57 -0400 (Wed, 16 Oct 2019).
| Package 1452/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sangerseqR 1.20.0 Jonathon Hill
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: sangerseqR |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:sangerseqR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings sangerseqR_1.20.0.tar.gz |
| StartedAt: 2019-10-16 04:47:14 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:49:20 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 125.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sangerseqR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:sangerseqR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings sangerseqR_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/sangerseqR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sangerseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sangerseqR’ version ‘1.20.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘sangerseqR’ 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
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
setAllelePhase 12.947 0.036 13.159
chromatogram 12.412 0.031 12.592
makeBaseCalls 12.147 0.016 12.260
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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 NOTE
See
‘/home/biocbuild/bbs-3.9-bioc/meat/sangerseqR.Rcheck/00check.log’
for details.
sangerseqR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL sangerseqR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘sangerseqR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (sangerseqR)
sangerseqR.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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, 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 -- Wed Oct 16 04:49:16 2019
***********************************************
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
3.153 0.149 4.199
sangerseqR.Rcheck/sangerseqR-Ex.timings
| name | user | system | elapsed | |
| PolyPeakParser | 0 | 0 | 0 | |
| abif-class | 0.181 | 0.021 | 0.214 | |
| chromatogram | 12.412 | 0.031 | 12.592 | |
| makeBaseCalls | 12.147 | 0.016 | 12.260 | |
| read.abif | 0.116 | 0.000 | 0.116 | |
| read.scf | 0.047 | 0.000 | 0.078 | |
| readsangerseq | 0.105 | 0.004 | 0.108 | |
| sangerseq-class | 0.116 | 0.000 | 0.116 | |
| sangerseqAccessors | 0.038 | 0.008 | 0.046 | |
| scf-class | 0.052 | 0.000 | 0.052 | |
| setAllelePhase | 12.947 | 0.036 | 13.159 | |