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CHECK report for amplican on tokay1

This page was generated on 2020-08-11 11:45:45 -0400 (Tue, 11 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE amplican PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 50/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
amplican 1.11.1
Eivind Valen
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/amplican
Branch: master
Last Commit: ccd6e2a
Last Changed Date: 2020-07-03 10:24:14 -0400 (Fri, 03 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: amplican
Version: 1.11.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:amplican.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings amplican_1.11.1.tar.gz
StartedAt: 2020-08-11 04:11:43 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 04:16:48 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 305.1 seconds
RetCode: 0
Status:  OK  
CheckDir: amplican.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:amplican.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings amplican_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/amplican.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.11.1'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/amplican/libs/i386/amplican.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
amplicanAlign    10.08   2.68   12.76
amplicanPipeline  5.25   1.51    6.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
amplicanAlign    8.98   1.61   10.59
amplicanPipeline 6.87   1.53    8.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/amplican.Rcheck/00check.log'
for details.



Installation output

amplican.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/amplican_1.11.1.tar.gz && rm -rf amplican.buildbin-libdir && mkdir amplican.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=amplican.buildbin-libdir amplican_1.11.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL amplican_1.11.1.zip && rm amplican_1.11.1.tar.gz amplican_1.11.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2133k  100 2133k    0     0  30.5M      0 --:--:-- --:--:-- --:--:-- 32.5M

install for i386

* installing *source* package 'amplican' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c bezier.cpp -o bezier.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o amplican.dll tmp.def RcppExports.o bezier.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/amplican.buildbin-libdir/00LOCK-amplican/00new/amplican/libs/i386
** 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

install for x64

* installing *source* package 'amplican' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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 -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/amplican.buildbin-libdir/amplican/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'amplican' as amplican_1.11.1.zip
* DONE (amplican)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'amplican' successfully unpacked and MD5 sums checked

Tests output

amplican.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector

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")
== testthat results  ===========================================================
[ OK: 56 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  28.46    3.68   32.23 

amplican.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector

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")
== testthat results  ===========================================================
[ OK: 56 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  31.56    2.46   34.04 

Example timings

amplican.Rcheck/examples_i386/amplican-Ex.timings

nameusersystemelapsed
AlignmentsExperimentSet-class2.080.072.16
amplicanAlign10.08 2.6812.76
amplicanConsensus0.100.080.18
amplicanFilter0.030.020.04
amplicanMap0.400.000.41
amplicanNormalize0.070.000.06
amplicanOverlap0.030.000.03
amplicanPipeline5.251.516.78
amplicanReport0.010.000.04
amplicanSummarize0.030.000.03
amplican_print_reads0.430.030.45
assignedCount0.060.020.08
barcodeData-set0.030.010.04
barcodeData0.050.000.05
comb_along0.040.000.05
experimentData-set0.050.020.06
experimentData0.050.000.05
extractEvents4.470.024.48
findEOP0.010.000.02
findLQR000
findPD0.020.000.01
fwdReads-set0.040.000.05
fwdReads0.640.000.64
fwdReadsType-set0.050.000.05
fwdReadsType0.030.000.03
geom_bezier0.440.000.44
lookupAlignment0.440.000.43
metaplot_deletions0.260.000.27
metaplot_insertions0.350.060.41
metaplot_mismatches0.370.080.45
plot_cuts0.330.000.33
plot_deletions0.170.000.17
plot_height000
plot_heterogeneity0.340.010.35
plot_insertions0.560.000.56
plot_mismatches0.580.000.58
plot_variants0.920.000.92
readCounts-set0.050.000.05
readCounts0.030.000.03
rveReads-set0.050.000.05
rveReads0.610.000.61
rveReadsType-set0.030.000.03
rveReadsType0.040.000.03
unassignedCount0.040.000.05
unassignedData-set0.030.000.03
unassignedData0.030.000.03
writeAlignments0.080.000.08

amplican.Rcheck/examples_x64/amplican-Ex.timings

nameusersystemelapsed
AlignmentsExperimentSet-class1.800.021.82
amplicanAlign 8.98 1.6110.59
amplicanConsensus0.110.000.11
amplicanFilter0.030.000.03
amplicanMap0.230.080.32
amplicanNormalize0.050.000.04
amplicanOverlap0.020.000.02
amplicanPipeline6.871.538.44
amplicanReport0.020.020.03
amplicanSummarize0.030.000.05
amplican_print_reads0.450.020.47
assignedCount0.060.000.06
barcodeData-set0.040.000.03
barcodeData0.040.020.06
comb_along0.050.000.05
experimentData-set0.050.000.05
experimentData0.040.000.04
extractEvents4.830.014.85
findEOP000
findLQR000
findPD000
fwdReads-set0.030.000.03
fwdReads0.570.000.56
fwdReadsType-set0.010.000.02
fwdReadsType0.010.000.02
geom_bezier0.410.000.41
lookupAlignment0.310.000.31
metaplot_deletions0.190.000.19
metaplot_insertions0.410.000.40
metaplot_mismatches0.400.000.41
plot_cuts0.420.000.42
plot_deletions0.440.000.44
plot_height000
plot_heterogeneity0.270.000.26
plot_insertions0.640.000.64
plot_mismatches0.400.000.41
plot_variants2.000.012.01
readCounts-set0.050.000.05
readCounts0.030.000.03
rveReads-set0.050.000.05
rveReads0.660.000.65
rveReadsType-set0.030.000.03
rveReadsType0.040.000.05
unassignedCount0.030.000.03
unassignedData-set0.050.000.05
unassignedData0.030.000.03
writeAlignments0.050.000.05