Eivind Valen
| Snapshot Date: 2025-09-09 13:45 -0400 (Tue, 09 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/amplican |
| git_branch: devel |
| git_last_commit: 48e5f7d |
| git_last_commit_date: 2025-07-11 08:07:29 -0400 (Fri, 11 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-10 12:05 -0400 (Wed, 10 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4617 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4564 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
| 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 | ||||
| Package 63/2322 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| amplican 1.31.2 (landing page) Eivind Valen
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the amplican package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: amplican |
| Version: 1.31.2 |
| 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_1.31.2.tar.gz |
| StartedAt: 2025-09-09 19:07:39 -0400 (Tue, 09 Sep 2025) |
| EndedAt: 2025-09-09 19:10:57 -0400 (Tue, 09 Sep 2025) |
| EllapsedTime: 198.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: amplican.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.31.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/amplican.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘amplican/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘amplican’ version ‘1.31.2’
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘get_seq’
* 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 ... NOTE
checkRd: (-1) amplicanAlign.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanAlign.Rd:65-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanAlign.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanAlign.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:60-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:107-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:60-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:107-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanSummarize.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanSummarize.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanSummarize.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanSummarize.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanSummarize.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeAlignment.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeAlignment.Rd:53-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeAlignment.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeAlignment.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_variants.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_variants.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_variants.Rd:77-78: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
AlignmentsExperimentSet-class.Rd: PairwiseAlignmentsSingleSubject,
GRanges
amplicanAlign.Rd: nucleotideSubstitutionMatrix
amplicanMap.Rd: GRanges
amplicanPipeline.Rd: nucleotideSubstitutionMatrix
amplicanPipelineConservative.Rd: nucleotideSubstitutionMatrix
cigarsToEvents.Rd: GRanges
cumsumw.Rd: IRanges
defGR.Rd: IRanges, GRanges
extractEvents.Rd: GRanges
findPD.Rd: GRanges
fwdReads-set.Rd: PairwiseAlignmentsSingleSubject
fwdReadsType-set.Rd: PairwiseAlignmentsSingleSubject
getEventInfo.Rd: PairwiseAlignmentsSingleSubject, GRanges
getEvents.Rd: pairwiseAlignment, GRanges
makeAlignment.Rd: nucleotideSubstitutionMatrix
pairToEvents.Rd: GRanges
readCounts-set.Rd: PairwiseAlignmentsSingleSubject
rveReads-set.Rd: PairwiseAlignmentsSingleSubject
rveReadsType-set.Rd: PairwiseAlignmentsSingleSubject
unassignedData-set.Rd: PairwiseAlignmentsSingleSubject
upperGroups.Rd: IRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'getEventInfo.Rd':
‘ampl_len’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 8.304 0.92 9.289
amplicanPipeline 5.717 0.54 6.303
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/amplican.Rcheck/00check.log’
for details.
amplican.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL amplican ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘amplican’ ... ** this is package ‘amplican’ version ‘1.31.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bezier.cpp -o bezier.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o amplican.so RcppExports.o bezier.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: Seqinfo
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: pwalign
Attaching package: 'pwalign'
The following objects are masked from 'package:Biostrings':
PairwiseAlignments, PairwiseAlignmentsSingleSubject, aligned,
alignedPattern, alignedSubject, compareStrings, deletion,
errorSubstitutionMatrices, indel, insertion, mismatchSummary,
mismatchTable, nedit, nindel, nucleotideSubstitutionMatrix,
pairwiseAlignment, pattern, pid, qualitySubstitutionMatrices,
stringDist, unaligned, writePairwiseAlignments
version: 1.31.2
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 0 | SKIP 0 | PASS 58 ]
>
> proc.time()
user system elapsed
27.215 1.918 29.315
amplican.Rcheck/amplican-Ex.timings
| name | user | system | elapsed | |
| AlignmentsExperimentSet-class | 1.457 | 0.060 | 1.527 | |
| amplicanAlign | 8.304 | 0.920 | 9.289 | |
| amplicanConsensus | 0.907 | 0.017 | 0.929 | |
| amplicanFilter | 0.029 | 0.010 | 0.040 | |
| amplicanMap | 0.314 | 0.004 | 0.322 | |
| amplicanNormalize | 0.038 | 0.002 | 0.040 | |
| amplicanOverlap | 0.022 | 0.002 | 0.025 | |
| amplicanPipeline | 5.717 | 0.540 | 6.303 | |
| amplicanReport | 0.015 | 0.021 | 0.037 | |
| amplicanSummarize | 0.019 | 0.003 | 0.024 | |
| amplican_print_reads | 0.300 | 0.004 | 0.305 | |
| assignedCount | 0.020 | 0.002 | 0.022 | |
| barcodeData-set | 0.004 | 0.001 | 0.005 | |
| barcodeData | 0.003 | 0.001 | 0.005 | |
| comb_along | 0.023 | 0.004 | 0.028 | |
| experimentData-set | 0.002 | 0.000 | 0.003 | |
| experimentData | 0.006 | 0.001 | 0.007 | |
| extractEvents | 3.121 | 0.022 | 3.155 | |
| findEOP | 0.005 | 0.002 | 0.007 | |
| findLQR | 0.004 | 0.001 | 0.005 | |
| findPD | 0.004 | 0.002 | 0.006 | |
| fwdReads-set | 0.005 | 0.001 | 0.005 | |
| fwdReads | 0.440 | 0.004 | 0.445 | |
| fwdReadsType-set | 0.005 | 0.001 | 0.005 | |
| fwdReadsType | 0.002 | 0.000 | 0.003 | |
| geom_bezier | 0.482 | 0.007 | 0.491 | |
| lookupAlignment | 0.289 | 0.003 | 0.294 | |
| metaplot_deletions | 0.234 | 0.004 | 0.239 | |
| metaplot_insertions | 0.387 | 0.005 | 0.394 | |
| metaplot_mismatches | 0.407 | 0.005 | 0.415 | |
| plot_cuts | 0.272 | 0.005 | 0.278 | |
| plot_deletions | 0.308 | 0.005 | 0.316 | |
| plot_height | 0 | 0 | 0 | |
| plot_heterogeneity | 0.319 | 0.004 | 0.325 | |
| plot_insertions | 0.544 | 0.005 | 0.554 | |
| plot_mismatches | 1.646 | 0.036 | 1.693 | |
| plot_variants | 0.991 | 0.009 | 1.004 | |
| readCounts-set | 0.004 | 0.001 | 0.005 | |
| readCounts | 0.003 | 0.001 | 0.004 | |
| rveReads-set | 0.004 | 0.001 | 0.005 | |
| rveReads | 0.439 | 0.005 | 0.447 | |
| rveReadsType-set | 0.004 | 0.001 | 0.005 | |
| rveReadsType | 0.002 | 0.000 | 0.004 | |
| unassignedCount | 0.003 | 0.001 | 0.003 | |
| unassignedData-set | 0.005 | 0.001 | 0.006 | |
| unassignedData | 0.005 | 0.001 | 0.006 | |
| writeAlignments | 0.023 | 0.002 | 0.024 | |