Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:36 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 51/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
amplican 1.16.0 (landing page) Eivind Valen
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: amplican |
Version: 1.16.0 |
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_1.16.0.tar.gz |
StartedAt: 2022-04-12 10:14:26 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 10:18:33 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 247.4 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_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/amplican.Rcheck’ * using R version 4.1.3 (2022-03-10) * 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 ‘1.16.0’ * 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 9.886 0.908 10.805 amplicanPipeline 9.484 0.429 9.925 extractEvents 5.629 0.049 5.680 * 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.
amplican.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL amplican ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)
amplican.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 57 ] > > proc.time() user system elapsed 38.944 2.084 41.031
amplican.Rcheck/amplican-Ex.timings
name | user | system | elapsed | |
AlignmentsExperimentSet-class | 1.998 | 0.097 | 2.095 | |
amplicanAlign | 9.886 | 0.908 | 10.805 | |
amplicanConsensus | 0.116 | 0.001 | 0.118 | |
amplicanFilter | 0.040 | 0.012 | 0.052 | |
amplicanMap | 0.626 | 0.004 | 0.630 | |
amplicanNormalize | 0.053 | 0.001 | 0.055 | |
amplicanOverlap | 0.030 | 0.002 | 0.032 | |
amplicanPipeline | 9.484 | 0.429 | 9.925 | |
amplicanReport | 0.021 | 0.028 | 0.049 | |
amplicanSummarize | 0.026 | 0.004 | 0.030 | |
amplican_print_reads | 0.458 | 0.003 | 0.462 | |
assignedCount | 0.068 | 0.002 | 0.070 | |
barcodeData-set | 0.046 | 0.001 | 0.046 | |
barcodeData | 0.039 | 0.001 | 0.040 | |
comb_along | 0.040 | 0.006 | 0.047 | |
experimentData-set | 0.036 | 0.001 | 0.036 | |
experimentData | 0.042 | 0.002 | 0.044 | |
extractEvents | 5.629 | 0.049 | 5.680 | |
findEOP | 0.003 | 0.001 | 0.005 | |
findLQR | 0.006 | 0.000 | 0.007 | |
findPD | 0.005 | 0.002 | 0.007 | |
fwdReads-set | 0.043 | 0.000 | 0.044 | |
fwdReads | 0.638 | 0.003 | 0.640 | |
fwdReadsType-set | 0.046 | 0.001 | 0.047 | |
fwdReadsType | 0.035 | 0.000 | 0.036 | |
geom_bezier | 0.498 | 0.007 | 0.505 | |
lookupAlignment | 0.469 | 0.002 | 0.471 | |
metaplot_deletions | 0.348 | 0.003 | 0.352 | |
metaplot_insertions | 0.425 | 0.005 | 0.431 | |
metaplot_mismatches | 0.419 | 0.004 | 0.422 | |
plot_cuts | 0.435 | 0.003 | 0.439 | |
plot_deletions | 0.275 | 0.002 | 0.278 | |
plot_height | 0.001 | 0.000 | 0.001 | |
plot_heterogeneity | 0.502 | 0.004 | 0.508 | |
plot_insertions | 0.617 | 0.005 | 0.623 | |
plot_mismatches | 0.608 | 0.006 | 0.614 | |
plot_variants | 1.031 | 0.005 | 1.037 | |
readCounts-set | 0.045 | 0.001 | 0.045 | |
readCounts | 0.043 | 0.001 | 0.045 | |
rveReads-set | 0.034 | 0.001 | 0.035 | |
rveReads | 0.642 | 0.003 | 0.646 | |
rveReadsType-set | 0.039 | 0.001 | 0.040 | |
rveReadsType | 0.045 | 0.001 | 0.045 | |
unassignedCount | 0.044 | 0.001 | 0.045 | |
unassignedData-set | 0.038 | 0.001 | 0.039 | |
unassignedData | 0.043 | 0.001 | 0.044 | |
writeAlignments | 0.153 | 0.026 | 0.179 | |