Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-25 14:06:48 -0400 (Mon, 25 Oct 2021).

CHECK results for amplican on merida1

To the developers/maintainers of the amplican package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/amplican.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 51/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
amplican 1.15.6  (landing page)
Eivind Valen
Snapshot Date: 2021-10-24 14:50:04 -0400 (Sun, 24 Oct 2021)
git_url: https://git.bioconductor.org/packages/amplican
git_branch: master
git_last_commit: 0b45efe
git_last_commit_date: 2021-10-22 05:49:35 -0400 (Fri, 22 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: amplican
Version: 1.15.6
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:amplican.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings amplican_1.15.6.tar.gz
StartedAt: 2021-10-25 00:29:04 -0400 (Mon, 25 Oct 2021)
EndedAt: 2021-10-25 00:33:09 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 245.2 seconds
RetCode: 0
Status:   OK  
CheckDir: amplican.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:amplican.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings amplican_1.15.6.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/amplican.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.15.6’
* 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    10.129  0.996  11.141
amplicanPipeline  8.510  0.340   8.860
extractEvents     5.222  0.043   5.271
* 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-3.14-bioc/meat/amplican.Rcheck/00check.log’
for details.



Installation output

amplican.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL amplican
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘amplican’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bezier.cpp -o bezier.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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/4.1/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)

Tests output

amplican.Rcheck/tests/testthat.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

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 4 | SKIP 0 | PASS 57 ]
> 
> proc.time()
   user  system elapsed 
 36.285   1.913  38.183 

Example timings

amplican.Rcheck/amplican-Ex.timings

nameusersystemelapsed
AlignmentsExperimentSet-class1.8790.0821.964
amplicanAlign10.129 0.99611.141
amplicanConsensus0.1310.0020.134
amplicanFilter0.0330.0070.039
amplicanMap0.5500.0030.554
amplicanNormalize0.0520.0020.053
amplicanOverlap0.0300.0010.031
amplicanPipeline8.510.348.86
amplicanReport0.0180.0140.033
amplicanSummarize0.0230.0030.026
amplican_print_reads0.4520.0030.455
assignedCount0.0700.0010.072
barcodeData-set0.0400.0010.040
barcodeData0.0390.0010.040
comb_along0.0380.0030.042
experimentData-set0.0330.0000.033
experimentData0.0460.0010.046
extractEvents5.2220.0435.271
findEOP0.0050.0010.007
findLQR0.0060.0010.006
findPD0.0040.0010.005
fwdReads-set0.0350.0010.035
fwdReads0.7050.0020.708
fwdReadsType-set0.0350.0000.035
fwdReadsType0.0420.0000.043
geom_bezier0.4450.0090.454
lookupAlignment0.4330.0020.435
metaplot_deletions0.2930.0020.295
metaplot_insertions0.3770.0030.380
metaplot_mismatches0.3700.0030.374
plot_cuts0.3860.0060.393
plot_deletions0.3250.0050.331
plot_height0.0000.0010.001
plot_heterogeneity0.4160.0040.421
plot_insertions0.5610.0020.564
plot_mismatches0.6280.0030.632
plot_variants1.0700.0051.076
readCounts-set0.0410.0010.042
readCounts0.0330.0010.033
rveReads-set0.0380.0010.039
rveReads0.6690.0020.672
rveReadsType-set0.0400.0000.042
rveReadsType0.0330.0010.033
unassignedCount0.0330.0000.033
unassignedData-set0.0410.0010.042
unassignedData0.0390.0010.039
writeAlignments0.0740.0010.075