Eivind Valen
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/amplican |
| Branch: RELEASE_3_12 |
| Last Commit: f593f59 |
| Last Changed Date: 2020-10-27 11:27:25 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:17 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the amplican package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 53/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| amplican 1.12.0 (landing page) Eivind Valen
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: amplican |
| Version: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2021-05-05 23:09:29 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 23:12:49 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 200.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: amplican.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/amplican.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.12.0’
* 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
amplicanAlign 9.747 0.833 10.597
amplicanPipeline 6.832 0.357 7.201
* 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-3.12-bioc/meat/amplican.Rcheck/00check.log’
for details.
amplican.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL amplican
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘amplican’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bezier.cpp -o bezier.o
In file included from bezier.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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 version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.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")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 56 ]
>
> proc.time()
user system elapsed
29.095 1.647 30.761
amplican.Rcheck/amplican-Ex.timings
| name | user | system | elapsed | |
| AlignmentsExperimentSet-class | 2.073 | 0.081 | 2.157 | |
| amplicanAlign | 9.747 | 0.833 | 10.597 | |
| amplicanConsensus | 0.103 | 0.002 | 0.106 | |
| amplicanFilter | 0.037 | 0.009 | 0.047 | |
| amplicanMap | 0.353 | 0.005 | 0.357 | |
| amplicanNormalize | 0.052 | 0.003 | 0.055 | |
| amplicanOverlap | 0.023 | 0.001 | 0.024 | |
| amplicanPipeline | 6.832 | 0.357 | 7.201 | |
| amplicanReport | 0.019 | 0.022 | 0.042 | |
| amplicanSummarize | 0.017 | 0.002 | 0.020 | |
| amplican_print_reads | 0.329 | 0.004 | 0.334 | |
| assignedCount | 0.067 | 0.002 | 0.070 | |
| barcodeData-set | 0.040 | 0.001 | 0.041 | |
| barcodeData | 0.039 | 0.001 | 0.041 | |
| comb_along | 0.032 | 0.004 | 0.037 | |
| experimentData-set | 0.035 | 0.001 | 0.036 | |
| experimentData | 0.041 | 0.002 | 0.044 | |
| extractEvents | 4.197 | 0.122 | 4.324 | |
| findEOP | 0.006 | 0.001 | 0.007 | |
| findLQR | 0.005 | 0.001 | 0.006 | |
| findPD | 0.005 | 0.002 | 0.007 | |
| fwdReads-set | 0.041 | 0.001 | 0.042 | |
| fwdReads | 0.606 | 0.003 | 0.609 | |
| fwdReadsType-set | 0.050 | 0.001 | 0.051 | |
| fwdReadsType | 0.041 | 0.001 | 0.041 | |
| geom_bezier | 0.380 | 0.007 | 0.386 | |
| lookupAlignment | 0.404 | 0.002 | 0.406 | |
| metaplot_deletions | 0.272 | 0.005 | 0.278 | |
| metaplot_insertions | 0.347 | 0.007 | 0.396 | |
| metaplot_mismatches | 0.246 | 0.003 | 0.249 | |
| plot_cuts | 0.319 | 0.004 | 0.323 | |
| plot_deletions | 0.255 | 0.002 | 0.258 | |
| plot_height | 0.001 | 0.000 | 0.001 | |
| plot_heterogeneity | 0.342 | 0.004 | 0.347 | |
| plot_insertions | 0.528 | 0.004 | 0.533 | |
| plot_mismatches | 0.488 | 0.003 | 0.492 | |
| plot_variants | 0.886 | 0.006 | 0.894 | |
| readCounts-set | 0.038 | 0.001 | 0.040 | |
| readCounts | 0.030 | 0.001 | 0.031 | |
| rveReads-set | 0.032 | 0.000 | 0.032 | |
| rveReads | 0.469 | 0.002 | 0.471 | |
| rveReadsType-set | 0.031 | 0.001 | 0.031 | |
| rveReadsType | 0.030 | 0.001 | 0.031 | |
| unassignedCount | 0.030 | 0.001 | 0.031 | |
| unassignedData-set | 0.032 | 0.001 | 0.033 | |
| unassignedData | 0.033 | 0.001 | 0.033 | |
| writeAlignments | 0.051 | 0.001 | 0.053 | |