Helen Lindsay
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CrispRVariants |
| Branch: RELEASE_3_7 |
| Last Commit: c9f0422 |
| Last Changed Date: 2018-04-30 10:35:39 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:41:30 -0400 (Wed, 17 Oct 2018).
| Package 323/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CrispRVariants 1.8.0 Helen Lindsay
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CrispRVariants |
| Version: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CrispRVariants.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CrispRVariants_1.8.0.tar.gz |
| StartedAt: 2018-10-17 01:23:20 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:29:27 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 366.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CrispRVariants.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CrispRVariants.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CrispRVariants_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CrispRVariants.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 'CrispRVariants/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CrispRVariants' version '1.8.0'
* 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-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/CrisprRun-class.Rd:105: file link 'CrisprSet' in package 'CrispRVariants' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/CrisprSet-class.Rd:293: file link 'CrisprRun' in package 'CrispRVariants' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/addClipped.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/excludeFromBam.Rd:12: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/plotAlignments.Rd:131: file link 'CrisprSet' in package 'CrispRVariants' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:32: file link 'findOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:33: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:43: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:57: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:57: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsToTarget.Rd:111: file link 'findOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsToTarget.Rd:114: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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
* 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 ... 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 8.97 0.08 9.06
CrisprSet-class 5.71 0.42 6.32
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotVariants 7.47 0.04 7.50
readsToTarget 5.05 0.00 5.04
* 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-3.7-bioc/meat/CrispRVariants.Rcheck/00check.log'
for details.
CrispRVariants.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/CrispRVariants_1.8.0.tar.gz && rm -rf CrispRVariants.buildbin-libdir && mkdir CrispRVariants.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CrispRVariants.buildbin-libdir CrispRVariants_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CrispRVariants_1.8.0.zip && rm CrispRVariants_1.8.0.tar.gz CrispRVariants_1.8.0.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 1394k 100 1394k 0 0 22.4M 0 --:--:-- --:--:-- --:--:-- 23.8M
install for i386
* installing *source* package 'CrispRVariants' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/CrisprRun-class.Rd:105: file link 'CrisprSet' in package 'CrispRVariants' does not exist and so has been treated as a topic
CrisprSet-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/CrisprSet-class.Rd:293: file link 'CrisprRun' in package 'CrispRVariants' does not exist and so has been treated as a topic
abifToFastq html
addClipped html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/addClipped.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
addCodonFrame html
alleleLabelsHelpers html
alleles html
alns html
annotateGenePlot html
arrangePlots html
barplotAlleleFreqs html
collapsePairs html
consensusSeqs html
dispatchDots html
excludeFromBam html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/excludeFromBam.Rd:12: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
explodeCigarOpCombs html
findChimeras html
findSNVs html
getAxisCoords html
getChimeras html
getInsertionsTable html
gol_clutch1 html
indelCounts html
indelLabels html
intersperse html
makeAlignmentTilePlot html
mergeChimeras html
mergeCrisprSets html
mismatchLabels html
mutationEfficiency html
narrowAlignments html
plotAlignments html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/plotAlignments.Rd:131: file link 'CrisprSet' in package 'CrispRVariants' does not exist and so has been treated as a topic
plotChimeras html
plotFreqHeatmap html
plotVariants html
rcAlns html
readTargetBam html
readsByPCRPrimer html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:32: file link 'findOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:33: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:43: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:57: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:57: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
readsToTarget html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsToTarget.Rd:111: file link 'findOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsToTarget.Rd:114: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
refFromAlns html
reverseCigar html
rmMultiPCRChimera html
selectAlnRegionsHelpers html
selectOps html
seqsToAln html
setDNATileColours html
setMismatchTileColours 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_1.8.0.zip
* DONE (CrispRVariants)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CrispRVariants' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
CrispRVariants.Rcheck/tests_i386/testthat.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.
> library(testthat)
> test_check("CrispRVariants")
Loading required package: CrispRVariants
Loading required package: ggplot2
== testthat results ===========================================================
OK: 75 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
25.85 1.50 27.37
|
CrispRVariants.Rcheck/tests_x64/testthat.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.
> library(testthat)
> test_check("CrispRVariants")
Loading required package: CrispRVariants
Loading required package: ggplot2
== testthat results ===========================================================
OK: 75 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
24.60 0.48 25.07
|
|
CrispRVariants.Rcheck/examples_i386/CrispRVariants-Ex.timings
|
CrispRVariants.Rcheck/examples_x64/CrispRVariants-Ex.timings
|