Eivind Valen
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/amplican |
| Branch: master |
| Last Commit: 041cf8c |
| Last Changed Date: 2019-12-10 08:04:29 -0500 (Tue, 10 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:49:00 -0500 (Thu, 16 Jan 2020).
| Package 51/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| amplican 1.9.2 Eivind Valen
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: amplican |
| Version: 1.9.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:amplican.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings amplican_1.9.2.tar.gz |
| StartedAt: 2020-01-16 01:39:08 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 01:43:27 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 259.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: amplican.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:amplican.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings amplican_1.9.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/amplican.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘amplican/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘amplican’ version ‘1.9.2’
* package encoding: UTF-8
* 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 ‘amplican’ 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
amplicanPipeline 11.393 1.136 9.226
amplicanAlign 11.278 0.946 12.229
extractEvents 5.149 0.086 5.236
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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 NOTE
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/amplican.Rcheck/00check.log’
for details.
amplican.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL amplican ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘amplican’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c bezier.cpp -o bezier.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o amplican.so RcppExports.o bezier.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-amplican/00new/amplican/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (amplican)
amplican.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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
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
Pease consider supporting this software by citing:
Labun et al. 2019
Accurate analysis of genuine CRISPR editing events with ampliCan.
Genome Res. 2019 Mar 8
doi: 10.1101/gr.244293.118
Without appreciation scientific software is usually abandoned and eventually deprecated, but you can easily support authors by citations.
>
> test_check("amplican")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 56 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
>
> proc.time()
user system elapsed
45.536 6.407 44.405
amplican.Rcheck/amplican-Ex.timings
| name | user | system | elapsed | |
| AlignmentsExperimentSet-class | 2.680 | 0.261 | 2.941 | |
| amplicanAlign | 11.278 | 0.946 | 12.229 | |
| amplicanConsensus | 0.455 | 0.273 | 0.186 | |
| amplicanFilter | 0.252 | 0.182 | 0.099 | |
| amplicanMap | 0.990 | 0.404 | 0.807 | |
| amplicanNormalize | 0.245 | 0.159 | 0.098 | |
| amplicanOverlap | 0.116 | 0.073 | 0.046 | |
| amplicanPipeline | 11.393 | 1.136 | 9.226 | |
| amplicanReport | 0.102 | 0.091 | 0.055 | |
| amplicanSummarize | 0.157 | 0.094 | 0.067 | |
| amplican_print_reads | 0.755 | 0.323 | 0.432 | |
| assignedCount | 0.049 | 0.001 | 0.053 | |
| barcodeData-set | 0.011 | 0.001 | 0.012 | |
| barcodeData | 0.012 | 0.002 | 0.014 | |
| comb_along | 0.053 | 0.009 | 0.062 | |
| experimentData-set | 0.006 | 0.001 | 0.007 | |
| experimentData | 0.016 | 0.002 | 0.017 | |
| extractEvents | 5.149 | 0.086 | 5.236 | |
| findEOP | 0.007 | 0.002 | 0.008 | |
| findLQR | 0.019 | 0.010 | 0.011 | |
| findPD | 0.023 | 0.017 | 0.009 | |
| fwdReads-set | 0.032 | 0.020 | 0.012 | |
| fwdReads | 1.177 | 0.267 | 0.863 | |
| fwdReadsType-set | 0.011 | 0.001 | 0.011 | |
| fwdReadsType | 0.010 | 0.001 | 0.010 | |
| geom_bezier | 0.637 | 0.007 | 0.644 | |
| lookupAlignment | 0.552 | 0.003 | 0.555 | |
| metaplot_deletions | 0.910 | 0.415 | 0.493 | |
| metaplot_insertions | 1.561 | 0.225 | 0.590 | |
| metaplot_mismatches | 0.941 | 0.347 | 0.599 | |
| plot_cuts | 0.993 | 0.336 | 0.649 | |
| plot_deletions | 1.235 | 0.346 | 0.529 | |
| plot_height | 0.001 | 0.000 | 0.002 | |
| plot_heterogeneity | 1.045 | 0.397 | 0.635 | |
| plot_insertions | 1.246 | 0.338 | 0.896 | |
| plot_mismatches | 1.173 | 0.342 | 0.823 | |
| plot_variants | 1.743 | 0.431 | 1.311 | |
| readCounts-set | 0.007 | 0.001 | 0.007 | |
| readCounts | 0.005 | 0.000 | 0.006 | |
| rveReads-set | 0.007 | 0.000 | 0.007 | |
| rveReads | 0.562 | 0.002 | 0.564 | |
| rveReadsType-set | 0.007 | 0.000 | 0.006 | |
| rveReadsType | 0.005 | 0.000 | 0.006 | |
| unassignedCount | 0.005 | 0.000 | 0.006 | |
| unassignedData-set | 0.006 | 0.001 | 0.007 | |
| unassignedData | 0.008 | 0.001 | 0.008 | |
| writeAlignments | 0.028 | 0.001 | 0.029 | |