Back to Multiple platform build/check report for BioC 3.16:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-03-20 11:05:20 -0400 (Mon, 20 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4516
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4295
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (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

CHECK results for amplican on palomino4


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.

raw results

Package 47/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
amplican 1.20.0  (landing page)
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)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.



Installation output

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)

Tests output

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 

Example timings

amplican.Rcheck/amplican-Ex.timings

nameusersystemelapsed
AlignmentsExperimentSet-class1.260.061.33
amplicanAlign5.920.306.22
amplicanConsensus0.110.000.11
amplicanFilter0.010.000.02
amplicanMap0.270.000.26
amplicanNormalize0.030.000.03
amplicanOverlap0.030.000.03
amplicanPipeline4.770.145.14
amplicanReport0.000.000.22
amplicanSummarize0.000.020.03
amplican_print_reads0.230.030.27
assignedCount0.030.000.03
barcodeData-set0.020.000.02
barcodeData0.010.000.02
comb_along0.040.000.03
experimentData-set0.010.000.01
experimentData0.030.000.04
extractEvents2.860.042.89
findEOP0.020.000.01
findLQR000
findPD000
fwdReads-set0.010.000.02
fwdReads0.320.000.32
fwdReadsType-set0.010.000.01
fwdReadsType0.030.000.03
geom_bezier0.320.030.35
lookupAlignment0.230.000.23
metaplot_deletions0.190.010.20
metaplot_insertions0.250.020.27
metaplot_mismatches0.220.030.25
plot_cuts0.290.030.33
plot_deletions0.210.000.20
plot_height000
plot_heterogeneity0.280.000.28
plot_insertions0.370.000.38
plot_mismatches0.420.000.42
plot_variants0.660.020.67
readCounts-set0.010.000.01
readCounts0.020.000.02
rveReads-set0.010.000.01
rveReads0.330.000.33
rveReadsType-set0.030.000.03
rveReadsType0.020.000.02
unassignedCount0.010.000.01
unassignedData-set0.020.000.02
unassignedData0.010.000.02
writeAlignments0.040.010.04