Helen Lindsay
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CrispRVariants |
| Branch: RELEASE_3_9 |
| Last Commit: 52725a5 |
| Last Changed Date: 2019-05-02 11:53:59 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:34:40 -0400 (Wed, 16 Oct 2019).
| Package 365/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CrispRVariants 1.12.0 Helen Lindsay
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: CrispRVariants |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CrispRVariants.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CrispRVariants_1.12.0.tar.gz |
| StartedAt: 2019-10-16 02:59:21 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:06:05 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 404.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CrispRVariants.Rcheck |
| Warnings: 3 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CrispRVariants.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CrispRVariants_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CrispRVariants.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.12.0'
* 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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-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 ... WARNING
'::' or ':::' import not declared from: 'SummarizedExperiment'
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'indelLabels'
* 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 ... WARNING
Codoc mismatches from documentation object 'arrangePlots':
arrangePlots
Code: function(top.plot, left.plot, right.plot, fig.height = NULL,
col.wdth.ratio = c(2, 1), row.ht.ratio = c(1, 6),
left.plot.margin = grid::unit(c(0.1, 0.2, 3, 0.2),
"lines"))
Docs: function(top.plot, left.plot, right.plot, fig.height = NULL,
col.wdth.ratio = c(2, 1), row.ht.ratio = c(1, 6),
left.plot.margin = grid::unit(c(0.1, 0, 3, 0.2),
"lines"))
Mismatches in argument default values:
Name: 'left.plot.margin' Code: grid::unit(c(0.1, 0.2, 3, 0.2), "lines") Docs: grid::unit(c(0.1, 0, 3, 0.2), "lines")
Codoc mismatches from documentation object 'indelLabels':
indelLabels
Code: function(alns, rc = FALSE, genome.to.pos = NULL, keep.ops =
c("I", "D", "N"), regions = NULL, as.string = TRUE,
...)
Docs: function(alns, rc = FALSE, genome.to.pos = NULL, keep.ops =
c("I", "D", "N"), regions = NULL, ...)
Argument names in code not in docs:
as.string
Mismatches in argument names:
Position: 6 Code: as.string Docs: ...
* 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 8.71 1.03 10.96
mergeCrisprSets 5.42 0.02 5.44
readsToTarget 5.00 0.06 5.06
CrisprSet-class 4.53 0.07 9.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotVariants 6.55 0.05 6.6
* 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: 3 WARNINGs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/CrispRVariants.Rcheck/00check.log'
for details.
CrispRVariants.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CrispRVariants_1.12.0.tar.gz && rm -rf CrispRVariants.buildbin-libdir && mkdir CrispRVariants.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CrispRVariants.buildbin-libdir CrispRVariants_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CrispRVariants_1.12.0.zip && rm CrispRVariants_1.12.0.tar.gz CrispRVariants_1.12.0.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 1395k 100 1395k 0 0 12.9M 0 --:--:-- --:--:-- --:--:-- 13.9M
install for i386
* installing *source* package 'CrispRVariants' ...
** using staged installation
** 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
CrisprSet-class html
abifToFastq html
addClipped html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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-3.9-bioc/tmpdir/RtmpYBjD9y/R.INSTALL20c8407475c0/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CrispRVariants' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CrispRVariants' as CrispRVariants_1.12.0.zip
* DONE (CrispRVariants)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CrispRVariants' successfully unpacked and MD5 sums checked
|
CrispRVariants.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
18.18 1.51 19.68
|
CrispRVariants.Rcheck/tests_x64/testthat.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-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 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
29.45 0.70 30.21
|
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CrispRVariants.Rcheck/examples_i386/CrispRVariants-Ex.timings
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CrispRVariants.Rcheck/examples_x64/CrispRVariants-Ex.timings
|