Helen Lindsay
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/CrispRVariants |
| Branch: RELEASE_3_6 |
| Last Commit: 4c51a12 |
| Last Changed Date: 2017-10-30 12:41:11 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:27:16 -0400 (Thu, 12 Apr 2018).
| Package 310/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CrispRVariants 1.6.0 Helen Lindsay
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: CrispRVariants |
| Version: 1.6.0 |
| Command: rm -rf CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && mkdir CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CrispRVariants.buildbin-libdir CrispRVariants_1.6.0.tar.gz >CrispRVariants.Rcheck\00install.out 2>&1 && cp CrispRVariants.Rcheck\00install.out CrispRVariants-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CrispRVariants.buildbin-libdir --install="check:CrispRVariants-install.out" --force-multiarch --no-vignettes --timings CrispRVariants_1.6.0.tar.gz |
| StartedAt: 2018-04-11 23:16:21 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:22:38 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 377.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CrispRVariants.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && mkdir CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CrispRVariants.buildbin-libdir CrispRVariants_1.6.0.tar.gz >CrispRVariants.Rcheck\00install.out 2>&1 && cp CrispRVariants.Rcheck\00install.out CrispRVariants-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CrispRVariants.buildbin-libdir --install="check:CrispRVariants-install.out" --force-multiarch --no-vignettes --timings CrispRVariants_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CrispRVariants.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 'CrispRVariants/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CrispRVariants' version '1.6.0'
* 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 'CrispRVariants' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/CrisprRun-class.Rd:101: missing file link 'CrisprSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/CrisprSet-class.Rd:298: missing file link 'CrisprRun'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/addClipped.Rd:19: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/excludeFromBam.Rd:12: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/plotAlignments.Rd:127: missing file link 'CrisprSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsByPCRPrimer.Rd:32: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsByPCRPrimer.Rd:33: missing file link 'disjoin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsByPCRPrimer.Rd:43: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsByPCRPrimer.Rd:57: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsByPCRPrimer.Rd:57: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsToTarget.Rd:111: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsToTarget.Rd:114: missing file link 'bpparam'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CrispRVariants.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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... OK
* 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
plotVariants 6.38 0.11 6.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotVariants 9.14 0.08 9.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/CrispRVariants.Rcheck/00check.log'
for details.
CrispRVariants.Rcheck/00install.out
install for i386
* installing *source* package 'CrispRVariants' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'CrispRVariants'
finding HTML links ... done
CrisprRun-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/CrisprRun-class.Rd:101: missing file link 'CrisprSet'
CrisprSet-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/CrisprSet-class.Rd:298: missing file link 'CrisprRun'
abifToFastq html
addClipped html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/addClipped.Rd:19: missing file link 'GRanges'
addCodonFrame html
alns html
annotateGenePlot html
arrangePlots html
barplotAlleleFreqs html
collapsePairs html
consensusSeqs html
dispatchDots html
excludeFromBam html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/excludeFromBam.Rd:12: missing file link 'GRanges'
findChimeras html
findSNVs html
getChimeras html
gol_clutch1 html
indelCounts html
makeAlignmentTilePlot html
mergeChimeras html
mergeCrisprSets html
mutationEfficiency html
narrowAlignments html
plotAlignments html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/plotAlignments.Rd:127: missing file link 'CrisprSet'
plotChimeras html
plotFreqHeatmap html
plotVariants html
rcAlns html
readTargetBam html
readsByPCRPrimer html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsByPCRPrimer.Rd:32: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsByPCRPrimer.Rd:33: missing file link 'disjoin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsByPCRPrimer.Rd:43: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsByPCRPrimer.Rd:57: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsByPCRPrimer.Rd:57: missing file link 'GAlignments'
readsToTarget html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsToTarget.Rd:111: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqophj5/R.INSTALL172851f7547f/CrispRVariants/man/readsToTarget.Rd:114: missing file link 'bpparam'
refFromAlns html
reverseCigar html
rmMultiPCRChimera html
seqsToAln html
seqsToPartialAln html
setDNATileColours html
transformAlnsToLong html
variantCounts html
writeFastq html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'CrispRVariants' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CrispRVariants' as CrispRVariants_1.6.0.zip
* DONE (CrispRVariants)
In R CMD INSTALL
In R CMD INSTALL
|
CrispRVariants.Rcheck/tests_i386/testthat.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.
> library(testthat)
> test_check("CrispRVariants")
Loading required package: CrispRVariants
Loading required package: ggplot2
== testthat results ===========================================================
OK: 57 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
20.53 0.48 20.98
|
CrispRVariants.Rcheck/tests_x64/testthat.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.
> library(testthat)
> test_check("CrispRVariants")
Loading required package: CrispRVariants
Loading required package: ggplot2
== testthat results ===========================================================
OK: 57 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
27.42 0.25 27.65
|
|
CrispRVariants.Rcheck/examples_i386/CrispRVariants-Ex.timings
|
CrispRVariants.Rcheck/examples_x64/CrispRVariants-Ex.timings
|