Eivind Valen
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/amplican |
| Branch: RELEASE_3_6 |
| Last Commit: cc2b529 |
| Last Changed Date: 2017-10-30 12:41:46 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:30:26 -0400 (Thu, 12 Apr 2018).
| Package 40/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| amplican 1.0.0 Eivind Valen
| 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: amplican |
| Version: 1.0.0 |
| Command: rm -rf amplican.buildbin-libdir amplican.Rcheck && mkdir amplican.buildbin-libdir amplican.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=amplican.buildbin-libdir amplican_1.0.0.tar.gz >amplican.Rcheck\00install.out 2>&1 && cp amplican.Rcheck\00install.out amplican-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=amplican.buildbin-libdir --install="check:amplican-install.out" --force-multiarch --no-vignettes --timings amplican_1.0.0.tar.gz |
| StartedAt: 2018-04-11 22:10:34 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:14:57 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 263.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: amplican.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf amplican.buildbin-libdir amplican.Rcheck && mkdir amplican.buildbin-libdir amplican.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=amplican.buildbin-libdir amplican_1.0.0.tar.gz >amplican.Rcheck\00install.out 2>&1 && cp amplican.Rcheck\00install.out amplican-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=amplican.buildbin-libdir --install="check:amplican-install.out" --force-multiarch --no-vignettes --timings amplican_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/amplican.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 'amplican/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'amplican' version '1.0.0'
* 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 'amplican' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/AlignmentsExperimentSet-class.Rd:122: missing file link 'PairwiseAlignmentsSingleSubject'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/AlignmentsExperimentSet-class.Rd:154: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/amplicanAlign.Rd:37: missing file link 'nucleotideSubstitutionMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/amplicanPipeline.Rd:72: missing file link 'nucleotideSubstitutionMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/extractEvents.Rd:16: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/fwdReads-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/makeAlignment.Rd:25: missing file link 'nucleotideSubstitutionMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/readCounts-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/rveReads-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/unassignedData-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/amplican.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 10.8Mb
sub-directories of 1Mb or more:
doc 9.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
Package unavailable to check Rd xrefs: 'CrispRVariants'
* 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
amplicanAlign 4.81 1.16 7.56
amplicanPipeline 4.26 1.38 5.92
metaplot_deletions 5.25 0.31 5.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
amplicanAlign 6.40 1.53 8.19
metaplot_deletions 5.89 0.26 6.26
amplicanPipeline 4.53 1.30 6.41
* 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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/amplican.Rcheck/00check.log'
for details.
amplican.Rcheck/00install.out
install for i386
* installing *source* package 'amplican' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'amplican'
finding HTML links ... done
AlignmentsExperimentSet-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/AlignmentsExperimentSet-class.Rd:122: missing file link 'PairwiseAlignmentsSingleSubject'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/AlignmentsExperimentSet-class.Rd:154: missing file link 'GRanges'
alphabetQuality html
amplican html
amplicanAlign html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/amplicanAlign.Rd:37: missing file link 'nucleotideSubstitutionMatrix'
amplicanConsensus html
amplicanFilter html
amplicanMap html
amplicanNormalize html
amplicanOverlap html
amplicanPipeline html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/amplicanPipeline.Rd:72: missing file link 'nucleotideSubstitutionMatrix'
amplicanReport html
amplicanSummarize html
amplican_print_reads html
assignedCount html
barcodeData-set html
barcodeData html
checkConfigFile html
checkFileWriteAccess html
checkPrimers html
checkTarget html
comb_along html
cumsumw html
decode html
defGR html
experimentData-set html
experimentData html
extractEvents html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/extractEvents.Rd:16: missing file link 'GRanges'
findEOP html
findLQR html
findPD html
flipRanges html
fwdReads-set html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/fwdReads-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
fwdReads html
getEventInfo html
get_amplicon html
get_left_primer html
get_right_primer html
goodAvgQuality html
goodBaseQuality html
lookupAlignment html
makeAlignment html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/makeAlignment.Rd:25: missing file link 'nucleotideSubstitutionMatrix'
metaplot_deletions html
metaplot_insertions html
metaplot_mismatches html
plot_amplicon html
plot_cuts html
plot_deletions html
plot_height html
plot_heterogeneity html
plot_insertions html
plot_mismatches html
plot_variants html
readCounts-set html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/readCounts-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
readCounts html
revComp html
rveReads-set html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/rveReads-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
rveReads html
unassignedCount html
unassignedData-set html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/unassignedData-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
unassignedData html
upperGroups html
writeAlignments html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'amplican' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'amplican' as amplican_1.0.0.zip
* DONE (amplican)
In R CMD INSTALL
In R CMD INSTALL
|
amplican.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)
> library(amplican)
Loading required package: BiocGenerics
Loading required package: parallel
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
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:IRanges':
shift
The following objects are masked from 'package:S4Vectors':
first, second
>
> test_check("amplican")
== testthat results ===========================================================
OK: 74 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
24.17 2.25 27.17
|
amplican.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)
> library(amplican)
Loading required package: BiocGenerics
Loading required package: parallel
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
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:IRanges':
shift
The following objects are masked from 'package:S4Vectors':
first, second
>
> test_check("amplican")
== testthat results ===========================================================
OK: 74 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
27.84 2.01 30.31
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amplican.Rcheck/examples_i386/amplican-Ex.timings
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amplican.Rcheck/examples_x64/amplican-Ex.timings
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