Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-12-07 11:05:15 -0500 (Wed, 07 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4423
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for amplican on nebbiolo1


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? 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 46/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
amplican 1.21.0  (landing page)
Eivind Valen
Snapshot Date: 2022-12-06 14:00:17 -0500 (Tue, 06 Dec 2022)
git_url: https://git.bioconductor.org/packages/amplican
git_branch: master
git_last_commit: 5b04ab5
git_last_commit_date: 2022-11-01 11:16:19 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'ShortRead' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'ShortRead' which is not available

Summary

Package: amplican
Version: 1.21.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:amplican.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings amplican_1.21.0.tar.gz
StartedAt: 2022-12-06 19:01:30 -0500 (Tue, 06 Dec 2022)
EndedAt: 2022-12-06 19:05:28 -0500 (Tue, 06 Dec 2022)
EllapsedTime: 237.7 seconds
RetCode: 0
Status:   OK  
CheckDir: amplican.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:amplican.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings amplican_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/amplican.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘amplican/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘amplican’ version ‘1.21.0’
* 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 6.07  0.392   6.464
* 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 ...
  ‘amplicanFAQ.Rmd’ using ‘UTF-8’... OK
  ‘amplicanOverview.Rmd’ using ‘UTF-8’... OK
  ‘example_amplicon_report.Rmd’ using ‘UTF-8’... OK
  ‘example_barcode_report.Rmd’ using ‘UTF-8’... OK
  ‘example_group_report.Rmd’ using ‘UTF-8’... OK
  ‘example_guide_report.Rmd’ using ‘UTF-8’... OK
  ‘example_id_report.Rmd’ using ‘UTF-8’... OK
  ‘example_index.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/amplican.Rcheck/00check.log’
for details.



Installation output

amplican.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL amplican
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘amplican’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c bezier.cpp -o bezier.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o amplican.so RcppExports.o bezier.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, aperm, 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

Please 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

> 
> test_check("amplican")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 57 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 57 ]
> 
> proc.time()
   user  system elapsed 
 21.718   0.839  22.508 

Example timings

amplican.Rcheck/amplican-Ex.timings

nameusersystemelapsed
AlignmentsExperimentSet-class1.1850.0561.241
amplicanAlign6.0700.3926.464
amplicanConsensus0.1030.0120.115
amplicanFilter0.0150.0120.028
amplicanMap0.2690.0120.282
amplicanNormalize0.0440.0000.031
amplicanOverlap0.0140.0040.018
amplicanPipeline4.0090.0694.061
amplicanReport0.0050.0080.012
amplicanSummarize0.0180.0040.016
amplican_print_reads0.2980.0200.316
assignedCount0.0370.0000.038
barcodeData-set0.0210.0000.021
barcodeData0.0220.0000.022
comb_along0.0170.0040.021
experimentData-set0.0200.0000.021
experimentData0.0200.0040.024
extractEvents2.6560.0762.732
findEOP0.0010.0040.005
findLQR0.0040.0000.004
findPD0.0040.0000.004
fwdReads-set0.0220.0000.022
fwdReads0.3810.0040.384
fwdReadsType-set0.0210.0000.021
fwdReadsType0.0220.0000.023
geom_bezier0.3080.0040.312
lookupAlignment0.2430.0040.247
metaplot_deletions0.1920.0120.204
metaplot_insertions0.2710.0000.265
metaplot_mismatches0.2710.0000.265
plot_cuts0.3870.0000.372
plot_deletions0.1970.0000.197
plot_height0.0000.0000.001
plot_heterogeneity0.2860.0000.276
plot_insertions0.3780.0040.377
plot_mismatches1.2430.0481.277
plot_variants0.6630.0160.668
readCounts-set0.020.000.02
readCounts0.0190.0000.019
rveReads-set0.0180.0010.020
rveReads0.3150.0030.317
rveReadsType-set0.0210.0000.020
rveReadsType0.0190.0000.019
unassignedCount0.0150.0040.019
unassignedData-set0.020.000.02
unassignedData0.0210.0000.021
writeAlignments0.0340.0040.037