Eivind Valen
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/amplican |
| git_branch: RELEASE_3_17 |
| git_last_commit: 1813c32 |
| git_last_commit_date: 2023-05-05 14:00:14 -0400 (Fri, 05 May 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:58 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 59/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| amplican 1.22.1 (landing page) Eivind Valen
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the amplican package: - 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: 1.22.1 |
| 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_1.22.1.tar.gz |
| StartedAt: 2023-10-17 02:05:29 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 02:10:01 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 272.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: amplican.Rcheck |
| Warnings: 0 |
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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_1.22.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/amplican.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘amplican/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘amplican’ version ‘1.22.1’
* 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 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 startup messages can be suppressed ... 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 7.666 0.267 12.147
amplicanPipeline 5.427 0.112 8.556
extractEvents 3.378 0.040 5.254
* 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-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/library’ * installing *source* package ‘amplican’ ... ** 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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bezier.cpp -o bezier.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 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: 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 1 | SKIP 0 | PASS 57 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 57 ]
>
> proc.time()
user system elapsed
26.739 1.009 42.646
amplican.Rcheck/amplican-Ex.timings
| name | user | system | elapsed | |
| AlignmentsExperimentSet-class | 1.195 | 0.032 | 1.885 | |
| amplicanAlign | 7.666 | 0.267 | 12.147 | |
| amplicanConsensus | 0.145 | 0.014 | 0.249 | |
| amplicanFilter | 0.027 | 0.008 | 0.066 | |
| amplicanMap | 0.367 | 0.033 | 0.632 | |
| amplicanNormalize | 0.037 | 0.004 | 0.066 | |
| amplicanOverlap | 0.023 | 0.002 | 0.037 | |
| amplicanPipeline | 5.427 | 0.112 | 8.556 | |
| amplicanReport | 0.017 | 0.021 | 0.057 | |
| amplicanSummarize | 0.018 | 0.002 | 0.031 | |
| amplican_print_reads | 0.356 | 0.006 | 0.560 | |
| assignedCount | 0.045 | 0.003 | 0.070 | |
| barcodeData-set | 0.025 | 0.001 | 0.038 | |
| barcodeData | 0.026 | 0.002 | 0.045 | |
| comb_along | 0.021 | 0.004 | 0.038 | |
| experimentData-set | 0.025 | 0.001 | 0.040 | |
| experimentData | 0.028 | 0.002 | 0.046 | |
| extractEvents | 3.378 | 0.040 | 5.254 | |
| findEOP | 0.005 | 0.002 | 0.013 | |
| findLQR | 0.005 | 0.001 | 0.009 | |
| findPD | 0.005 | 0.002 | 0.010 | |
| fwdReads-set | 0.025 | 0.001 | 0.042 | |
| fwdReads | 0.476 | 0.007 | 0.728 | |
| fwdReadsType-set | 0.025 | 0.001 | 0.036 | |
| fwdReadsType | 0.024 | 0.001 | 0.035 | |
| geom_bezier | 0.385 | 0.009 | 0.587 | |
| lookupAlignment | 0.321 | 0.004 | 0.501 | |
| metaplot_deletions | 0.222 | 0.007 | 0.355 | |
| metaplot_insertions | 0.362 | 0.009 | 0.584 | |
| metaplot_mismatches | 0.327 | 0.005 | 0.507 | |
| plot_cuts | 0.310 | 0.006 | 0.484 | |
| plot_deletions | 0.260 | 0.006 | 0.406 | |
| plot_height | 0.000 | 0.001 | 0.001 | |
| plot_heterogeneity | 0.431 | 0.009 | 0.676 | |
| plot_insertions | 0.490 | 0.008 | 0.769 | |
| plot_mismatches | 0.532 | 0.008 | 0.827 | |
| plot_variants | 1.482 | 0.018 | 2.298 | |
| readCounts-set | 0.025 | 0.001 | 0.041 | |
| readCounts | 0.023 | 0.001 | 0.039 | |
| rveReads-set | 0.025 | 0.002 | 0.041 | |
| rveReads | 0.443 | 0.007 | 0.693 | |
| rveReadsType-set | 0.024 | 0.001 | 0.038 | |
| rveReadsType | 0.024 | 0.001 | 0.039 | |
| unassignedCount | 0.023 | 0.002 | 0.037 | |
| unassignedData-set | 0.025 | 0.001 | 0.042 | |
| unassignedData | 0.026 | 0.002 | 0.043 | |
| writeAlignments | 0.043 | 0.003 | 0.068 | |