Eivind Valen
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/amplican |
| git_branch: master |
| git_last_commit: 5b0baca |
| git_last_commit_date: 2021-11-19 04:13:23 -0400 (Fri, 19 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:06:55 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 48/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| amplican 1.17.1 (landing page) Eivind Valen
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: amplican |
| Version: 1.17.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:amplican.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings amplican_1.17.1.tar.gz |
| StartedAt: 2022-03-17 18:25:36 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:28:09 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 152.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: amplican.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:amplican.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings amplican_1.17.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/amplican.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'amplican/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'amplican' version '1.17.1'
* 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 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 'D:/biocbuild/bbs-3.15-bioc/R/library/amplican/libs/x64/amplican.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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 5.11 0.31 5.42
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/amplican.Rcheck/00check.log'
for details.
amplican.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL amplican
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'amplican' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c bezier.cpp -o bezier.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o amplican.dll tmp.def RcppExports.o bezier.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-amplican/00new/amplican/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'amplican'
finding HTML links ... done
AlignmentsExperimentSet-class html
finding level-2 HTML links ... done
alphabetQuality html
amplican html
amplicanAlign html
amplicanConsensus html
amplicanFilter html
amplicanMap html
amplicanNormalize html
amplicanOverlap html
amplicanPipeline html
amplicanPipelineConservative html
amplicanReport html
amplicanSummarize html
amplican_print_reads html
assignedCount html
barcodeData-set html
barcodeData html
checkConfigFile html
checkFileWriteAccess html
checkPrimers html
checkTarget html
cigarsToEvents html
comb_along html
cumsumw html
decode html
defGR html
experimentData-set html
experimentData html
extractEvents html
findEOP html
findLQR html
findPD html
flipRanges html
fwdReads-set html
fwdReads html
fwdReadsType-set html
fwdReadsType html
geom_bezier html
getEventInfo html
getEvents html
get_amplicon html
get_left_primer html
get_right_primer html
goodAvgQuality html
goodBaseQuality html
lookupAlignment html
makeAlignment html
metaplot_deletions html
metaplot_insertions html
metaplot_mismatches html
pairToEvents html
plot_amplicon html
plot_cuts html
plot_deletions html
plot_height html
plot_heterogeneity html
plot_insertions html
plot_mismatches html
plot_variants html
readCounts-set html
readCounts html
revComp html
rveReads-set html
rveReads html
rveReadsType-set html
rveReadsType html
unassignedCount html
unassignedData-set html
unassignedData html
upperGroups html
writeAlignments html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MouseFM' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'SMAD' is missing or broken
done
amplican.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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, 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 4 | SKIP 0 | PASS 57 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 57 ]
>
> proc.time()
user system elapsed
16.93 1.39 18.68
amplican.Rcheck/amplican-Ex.timings
| name | user | system | elapsed | |
| AlignmentsExperimentSet-class | 1.36 | 0.08 | 1.44 | |
| amplicanAlign | 5.11 | 0.31 | 5.42 | |
| amplicanConsensus | 0.07 | 0.00 | 0.08 | |
| amplicanFilter | 0.02 | 0.00 | 0.02 | |
| amplicanMap | 0.16 | 0.03 | 0.18 | |
| amplicanNormalize | 0.03 | 0.00 | 0.04 | |
| amplicanOverlap | 0.01 | 0.00 | 0.01 | |
| amplicanPipeline | 2.99 | 0.05 | 3.25 | |
| amplicanReport | 0.04 | 0.00 | 0.20 | |
| amplicanSummarize | 0.02 | 0.00 | 0.02 | |
| amplican_print_reads | 0.19 | 0.01 | 0.20 | |
| assignedCount | 0.03 | 0.00 | 0.03 | |
| barcodeData-set | 0 | 0 | 0 | |
| barcodeData | 0.02 | 0.00 | 0.02 | |
| comb_along | 0.01 | 0.00 | 0.01 | |
| experimentData-set | 0.02 | 0.00 | 0.02 | |
| experimentData | 0.02 | 0.00 | 0.01 | |
| extractEvents | 1.82 | 0.00 | 1.83 | |
| findEOP | 0 | 0 | 0 | |
| findLQR | 0.00 | 0.02 | 0.02 | |
| findPD | 0 | 0 | 0 | |
| fwdReads-set | 0.02 | 0.00 | 0.01 | |
| fwdReads | 0.25 | 0.00 | 0.25 | |
| fwdReadsType-set | 0.02 | 0.00 | 0.02 | |
| fwdReadsType | 0.01 | 0.00 | 0.01 | |
| geom_bezier | 0.20 | 0.00 | 0.21 | |
| lookupAlignment | 0.18 | 0.00 | 0.17 | |
| metaplot_deletions | 0.12 | 0.00 | 0.12 | |
| metaplot_insertions | 0.17 | 0.00 | 0.17 | |
| metaplot_mismatches | 0.17 | 0.00 | 0.18 | |
| plot_cuts | 0.18 | 0.00 | 0.17 | |
| plot_deletions | 0.14 | 0.00 | 0.14 | |
| plot_height | 0 | 0 | 0 | |
| plot_heterogeneity | 0.22 | 0.01 | 0.23 | |
| plot_insertions | 0.28 | 0.00 | 0.28 | |
| plot_mismatches | 0.33 | 0.00 | 0.33 | |
| plot_variants | 0.42 | 0.00 | 0.42 | |
| readCounts-set | 0.03 | 0.00 | 0.04 | |
| readCounts | 0.01 | 0.00 | 0.01 | |
| rveReads-set | 0.02 | 0.00 | 0.02 | |
| rveReads | 0.33 | 0.00 | 0.33 | |
| rveReadsType-set | 0.01 | 0.00 | 0.01 | |
| rveReadsType | 0.02 | 0.00 | 0.02 | |
| unassignedCount | 0.01 | 0.00 | 0.01 | |
| unassignedData-set | 0.02 | 0.00 | 0.02 | |
| unassignedData | 0.02 | 0.00 | 0.01 | |
| writeAlignments | 0.03 | 0.00 | 0.03 | |