Eivind Valen
| Snapshot Date: 2023-03-17 14:00:04 -0400 (Fri, 17 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/amplican |
| git_branch: RELEASE_3_16 |
| git_last_commit: eafd080 |
| git_last_commit_date: 2022-11-01 11:16:19 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-03-20 11:05:20 -0400 (Mon, 20 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.2 (2022-10-31) -- "Innocent and Trusting" | 4516 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" | 4295 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.2 (2022-10-31) -- "Innocent and Trusting" | 4324 |
| 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 | ||||
|
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. |
| Package 47/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| amplican 1.20.0 (landing page) Eivind Valen
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: amplican |
| Version: 1.20.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:amplican.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings amplican_1.20.0.tar.gz |
| StartedAt: 2023-03-17 22:50:51 -0400 (Fri, 17 Mar 2023) |
| EndedAt: 2023-03-17 22:53:42 -0400 (Fri, 17 Mar 2023) |
| EllapsedTime: 171.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: amplican.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:amplican.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings amplican_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/amplican.Rcheck'
* using R version 4.2.2 (2022-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.20.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/amplican/libs/x64/amplican.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
amplicanAlign 5.92 0.30 6.22
amplicanPipeline 4.77 0.14 5.14
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/amplican.Rcheck/00check.log'
for details.
amplican.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL amplican ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'amplican' ... ** using staged installation ** libs g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bezier.cpp -o bezier.o g++ -std=gnu++11 -shared -s -static-libgcc -o amplican.dll tmp.def RcppExports.o bezier.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-amplican/00new/amplican/libs/x64 ** 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 ** 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 4.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
21.15 0.98 23.85
amplican.Rcheck/amplican-Ex.timings
| name | user | system | elapsed | |
| AlignmentsExperimentSet-class | 1.26 | 0.06 | 1.33 | |
| amplicanAlign | 5.92 | 0.30 | 6.22 | |
| amplicanConsensus | 0.11 | 0.00 | 0.11 | |
| amplicanFilter | 0.01 | 0.00 | 0.02 | |
| amplicanMap | 0.27 | 0.00 | 0.26 | |
| amplicanNormalize | 0.03 | 0.00 | 0.03 | |
| amplicanOverlap | 0.03 | 0.00 | 0.03 | |
| amplicanPipeline | 4.77 | 0.14 | 5.14 | |
| amplicanReport | 0.00 | 0.00 | 0.22 | |
| amplicanSummarize | 0.00 | 0.02 | 0.03 | |
| amplican_print_reads | 0.23 | 0.03 | 0.27 | |
| assignedCount | 0.03 | 0.00 | 0.03 | |
| barcodeData-set | 0.02 | 0.00 | 0.02 | |
| barcodeData | 0.01 | 0.00 | 0.02 | |
| comb_along | 0.04 | 0.00 | 0.03 | |
| experimentData-set | 0.01 | 0.00 | 0.01 | |
| experimentData | 0.03 | 0.00 | 0.04 | |
| extractEvents | 2.86 | 0.04 | 2.89 | |
| findEOP | 0.02 | 0.00 | 0.01 | |
| findLQR | 0 | 0 | 0 | |
| findPD | 0 | 0 | 0 | |
| fwdReads-set | 0.01 | 0.00 | 0.02 | |
| fwdReads | 0.32 | 0.00 | 0.32 | |
| fwdReadsType-set | 0.01 | 0.00 | 0.01 | |
| fwdReadsType | 0.03 | 0.00 | 0.03 | |
| geom_bezier | 0.32 | 0.03 | 0.35 | |
| lookupAlignment | 0.23 | 0.00 | 0.23 | |
| metaplot_deletions | 0.19 | 0.01 | 0.20 | |
| metaplot_insertions | 0.25 | 0.02 | 0.27 | |
| metaplot_mismatches | 0.22 | 0.03 | 0.25 | |
| plot_cuts | 0.29 | 0.03 | 0.33 | |
| plot_deletions | 0.21 | 0.00 | 0.20 | |
| plot_height | 0 | 0 | 0 | |
| plot_heterogeneity | 0.28 | 0.00 | 0.28 | |
| plot_insertions | 0.37 | 0.00 | 0.38 | |
| plot_mismatches | 0.42 | 0.00 | 0.42 | |
| plot_variants | 0.66 | 0.02 | 0.67 | |
| readCounts-set | 0.01 | 0.00 | 0.01 | |
| readCounts | 0.02 | 0.00 | 0.02 | |
| rveReads-set | 0.01 | 0.00 | 0.01 | |
| rveReads | 0.33 | 0.00 | 0.33 | |
| rveReadsType-set | 0.03 | 0.00 | 0.03 | |
| rveReadsType | 0.02 | 0.00 | 0.02 | |
| unassignedCount | 0.01 | 0.00 | 0.01 | |
| unassignedData-set | 0.02 | 0.00 | 0.02 | |
| unassignedData | 0.01 | 0.00 | 0.02 | |
| writeAlignments | 0.04 | 0.01 | 0.04 | |