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CHECK report for amplican on tokay1

This page was generated on 2018-04-12 13:30:26 -0400 (Thu, 12 Apr 2018).

Package 40/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
amplican 1.0.0
Eivind Valen
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/amplican
Branch: RELEASE_3_6
Last Commit: cc2b529
Last Changed Date: 2017-10-30 12:41:46 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: amplican
Version: 1.0.0
Command: rm -rf amplican.buildbin-libdir amplican.Rcheck && mkdir amplican.buildbin-libdir amplican.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=amplican.buildbin-libdir amplican_1.0.0.tar.gz >amplican.Rcheck\00install.out 2>&1 && cp amplican.Rcheck\00install.out amplican-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=amplican.buildbin-libdir --install="check:amplican-install.out" --force-multiarch --no-vignettes --timings amplican_1.0.0.tar.gz
StartedAt: 2018-04-11 22:10:34 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:14:57 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 263.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: amplican.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf amplican.buildbin-libdir amplican.Rcheck && mkdir amplican.buildbin-libdir amplican.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=amplican.buildbin-libdir amplican_1.0.0.tar.gz >amplican.Rcheck\00install.out 2>&1 && cp amplican.Rcheck\00install.out amplican-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=amplican.buildbin-libdir --install="check:amplican-install.out" --force-multiarch --no-vignettes --timings amplican_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/amplican.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.0.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/AlignmentsExperimentSet-class.Rd:122: missing file link 'PairwiseAlignmentsSingleSubject'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/AlignmentsExperimentSet-class.Rd:154: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/amplicanAlign.Rd:37: missing file link 'nucleotideSubstitutionMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/amplicanPipeline.Rd:72: missing file link 'nucleotideSubstitutionMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/extractEvents.Rd:16: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/fwdReads-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/makeAlignment.Rd:25: missing file link 'nucleotideSubstitutionMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/readCounts-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/rveReads-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/unassignedData-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/amplican.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
Package unavailable to check Rd xrefs: 'CrispRVariants'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
amplicanAlign      4.81   1.16    7.56
amplicanPipeline   4.26   1.38    5.92
metaplot_deletions 5.25   0.31    5.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
amplicanAlign      6.40   1.53    8.19
metaplot_deletions 5.89   0.26    6.26
amplicanPipeline   4.53   1.30    6.41
* 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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/amplican.Rcheck/00check.log'
for details.



Installation output

amplican.Rcheck/00install.out


install for i386

* installing *source* package 'amplican' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'amplican'
    finding HTML links ... done
    AlignmentsExperimentSet-class           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/AlignmentsExperimentSet-class.Rd:122: missing file link 'PairwiseAlignmentsSingleSubject'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/AlignmentsExperimentSet-class.Rd:154: missing file link 'GRanges'
    alphabetQuality                         html  
    amplican                                html  
    amplicanAlign                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/amplicanAlign.Rd:37: missing file link 'nucleotideSubstitutionMatrix'
    amplicanConsensus                       html  
    amplicanFilter                          html  
    amplicanMap                             html  
    amplicanNormalize                       html  
    amplicanOverlap                         html  
    amplicanPipeline                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/amplicanPipeline.Rd:72: missing file link 'nucleotideSubstitutionMatrix'
    amplicanReport                          html  
    amplicanSummarize                       html  
    amplican_print_reads                    html  
    assignedCount                           html  
    barcodeData-set                         html  
    barcodeData                             html  
    checkConfigFile                         html  
    checkFileWriteAccess                    html  
    checkPrimers                            html  
    checkTarget                             html  
    comb_along                              html  
    cumsumw                                 html  
    decode                                  html  
    defGR                                   html  
    experimentData-set                      html  
    experimentData                          html  
    extractEvents                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/extractEvents.Rd:16: missing file link 'GRanges'
    findEOP                                 html  
    findLQR                                 html  
    findPD                                  html  
    flipRanges                              html  
    fwdReads-set                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/fwdReads-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
    fwdReads                                html  
    getEventInfo                            html  
    get_amplicon                            html  
    get_left_primer                         html  
    get_right_primer                        html  
    goodAvgQuality                          html  
    goodBaseQuality                         html  
    lookupAlignment                         html  
    makeAlignment                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/makeAlignment.Rd:25: missing file link 'nucleotideSubstitutionMatrix'
    metaplot_deletions                      html  
    metaplot_insertions                     html  
    metaplot_mismatches                     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  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/readCounts-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
    readCounts                              html  
    revComp                                 html  
    rveReads-set                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/rveReads-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
    rveReads                                html  
    unassignedCount                         html  
    unassignedData-set                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmIc8hm/R.INSTALLa605ab139a8/amplican/man/unassignedData-set.Rd:16: missing file link 'PairwiseAlignmentsSingleSubject'
    unassignedData                          html  
    upperGroups                             html  
    writeAlignments                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'amplican' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'amplican' as amplican_1.0.0.zip
* DONE (amplican)
In R CMD INSTALL
In R CMD INSTALL

Tests output

amplican.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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
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

> 
> test_check("amplican")
== testthat results  ===========================================================
OK: 74 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  24.17    2.25   27.17 

amplican.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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
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

> 
> test_check("amplican")
== testthat results  ===========================================================
OK: 74 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  27.84    2.01   30.31 

Example timings

amplican.Rcheck/examples_i386/amplican-Ex.timings

nameusersystemelapsed
AlignmentsExperimentSet-class1.610.021.83
amplicanAlign4.811.167.56
amplicanConsensus0.030.000.03
amplicanFilter0.060.000.06
amplicanMap0.810.010.96
amplicanNormalize0.170.030.20
amplicanOverlap0.050.000.05
amplicanPipeline4.261.385.92
amplicanReport0.100.010.11
amplicanSummarize0.040.000.05
amplican_print_reads0.410.000.59
assignedCount0.080.000.08
barcodeData-set000
barcodeData0.000.020.02
comb_along0.010.000.01
experimentData-set0.020.000.02
experimentData000
extractEvents2.050.002.05
findEOP0.010.000.01
findLQR000
findPD000
fwdReads-set0.020.000.02
fwdReads0.070.000.07
lookupAlignment0.40.00.4
metaplot_deletions5.250.315.68
metaplot_insertions0.50.00.5
metaplot_mismatches0.000.020.02
plot_cuts0.540.000.55
plot_deletions0.330.000.32
plot_height0.020.000.02
plot_heterogeneity0.560.000.56
plot_insertions0.310.000.31
plot_mismatches0.310.000.32
plot_variants0.710.010.72
readCounts-set000
readCounts000
rveReads-set000
rveReads0.110.000.11
unassignedCount000
unassignedData-set0.020.000.02
unassignedData000
writeAlignments0.030.000.03

amplican.Rcheck/examples_x64/amplican-Ex.timings

nameusersystemelapsed
AlignmentsExperimentSet-class2.080.032.33
amplicanAlign6.401.538.19
amplicanConsensus0.040.020.04
amplicanFilter0.100.000.11
amplicanMap1.080.001.08
amplicanNormalize0.240.000.23
amplicanOverlap0.080.000.08
amplicanPipeline4.531.306.41
amplicanReport0.070.000.08
amplicanSummarize0.050.000.05
amplican_print_reads0.420.000.42
assignedCount0.100.000.09
barcodeData-set000
barcodeData0.010.000.02
comb_along0.020.000.02
experimentData-set000
experimentData000
extractEvents2.240.002.24
findEOP000
findLQR000
findPD0.000.020.01
fwdReads-set000
fwdReads0.090.000.10
lookupAlignment0.460.000.45
metaplot_deletions5.890.266.26
metaplot_insertions0.620.000.63
metaplot_mismatches000
plot_cuts0.560.000.56
plot_deletions0.380.000.38
plot_height000
plot_heterogeneity0.690.000.68
plot_insertions0.320.020.35
plot_mismatches0.350.000.34
plot_variants0.860.000.86
readCounts-set000
readCounts000
rveReads-set000
rveReads0.140.000.14
unassignedCount0.020.000.01
unassignedData-set000
unassignedData0.010.000.02
writeAlignments0.020.000.01