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This page was generated on 2022-01-17 13:06:49 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 qrqc on tokay2


To the developers/maintainers of the qrqc package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qrqc.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.

raw results

Package 1501/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qrqc 1.48.0  (landing page)
Vince Buffalo
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/qrqc
git_branch: RELEASE_3_14
git_last_commit: 351c639
git_last_commit_date: 2021-10-26 11:58:43 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: qrqc
Version: 1.48.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qrqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings qrqc_1.48.0.tar.gz
StartedAt: 2022-01-17 01:59:16 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 02:07:17 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 481.4 seconds
RetCode: 0
Status:   OK  
CheckDir: qrqc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qrqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings qrqc_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/qrqc.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qrqc/DESCRIPTION' ... OK
* this is package 'qrqc' version '1.48.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'reshape', 'ggplot2', 'Biostrings', 'biovizBase', 'brew', 'xtable',
  'testthat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'qrqc' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'reshape' 'ggplot2' 'Biostrings' 'biovizBase'
A package should be listed in only one of these fields.
Versioned 'LinkingTo' value for 'Rhtslib' is only usable in R >= 3.0.2
* 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 ... NOTE
Packages in Depends field not imported from:
  'brew' 'testthat' 'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
binned2boxplot: no visible global function definition for 'quantile'
calcKL : kmerDist: no visible global function definition for
  'aggregate'
generateReads: no visible global function definition for 'DNAStringSet'
generateReads: no visible global function definition for
  'write.XStringSet'
makeReportDir: no visible global function definition for 'na.exclude'
basePlot,SequenceSummary: no visible binding for global variable 'base'
basePlot,list: no visible binding for global variable 'base'
gcPlot,SequenceSummary: no visible binding for global variable
  'position'
gcPlot,list: no visible binding for global variable 'position'
getBase,SequenceSummary: no visible global function definition for
  'aggregate'
getBase,SequenceSummary: no visible binding for global variable 'base'
getBaseProp,SequenceSummary: no visible global function definition for
  'aggregate'
getBaseProp,SequenceSummary: no visible binding for global variable
  'base'
getGC,SequenceSummary : <local>: no visible global function definition
  for 'aggregate'
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
  'position'
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
  'entropy'
kmerEntropyPlot,list: no visible binding for global variable 'position'
kmerEntropyPlot,list: no visible binding for global variable 'entropy'
kmerKLPlot,SequenceSummary: no visible binding for global variable
  'kmer'
kmerKLPlot,SequenceSummary: no visible binding for global variable
  'position'
kmerKLPlot,SequenceSummary: no visible binding for global variable 'kl'
kmerKLPlot,list : <anonymous>: no visible binding for global variable
  'kmer'
kmerKLPlot,list: no visible binding for global variable 'position'
kmerKLPlot,list: no visible binding for global variable 'kl'
kmerKLPlot,list: no visible binding for global variable 'kmer'
plotGC,SequenceSummary : <local>: no visible global function definition
  for 'aggregate'
qualPlot,FASTQSummary: no visible binding for global variable
  'position'
qualPlot,list: no visible binding for global variable 'position'
Undefined global functions or variables:
  DNAStringSet aggregate base entropy kl kmer na.exclude position
  quantile write.XStringSet
Consider adding
  importFrom("stats", "aggregate", "na.exclude", "quantile")
to your NAMESPACE file.
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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-3.14-bioc/R/library/qrqc/libs/i386/qrqc.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/qrqc/libs/x64/qrqc.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
kmerKLPlot 6.94   0.31    7.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
kmerKLPlot 5.39   0.05    5.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-functions.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-functions.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: 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/qrqc.Rcheck/00check.log'
for details.



Installation output

qrqc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/qrqc_1.48.0.tar.gz && rm -rf qrqc.buildbin-libdir && mkdir qrqc.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qrqc.buildbin-libdir qrqc_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL qrqc_1.48.0.zip && rm qrqc_1.48.0.tar.gz qrqc_1.48.0.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  347k  100  347k    0     0  1859k      0 --:--:-- --:--:-- --:--:-- 1868k

install for i386

* installing *source* package 'qrqc' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_io.c -o R_init_io.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c io.c -o io.o
In file included from io.c:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: warning: 'kseq_destroy' defined but not used [-Wunused-function]
  SCOPE void kseq_destroy(kseq_t *ks)         \
             ^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
  __KSEQ_BASIC(SCOPE, type_t)     \
  ^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^~~~~~~~~~
io.c:29:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(FILE_TYPE*, gzreadclone)
 ^~~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o qrqc.dll tmp.def R_init_io.o io.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/qrqc.buildbin-libdir/00LOCK-qrqc/00new/qrqc/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'qrqc'
    finding HTML links ... done
    FASTASummary-class                      html  
    FASTQSummary-class                      html  
    SequenceSummary-class                   html  
    basePlot-methods                        html  
    calcKL                                  html  
    gcPlot-methods                          html  
    geom_qlinerange                         html  
    getBase-methods                         html  
    getBaseProp-methods                     html  
    getGC-methods                           html  
    getKmer-methods                         html  
    getMCQual-methods                       html  
    getQual-methods                         html  
    getSeqlen-methods                       html  
    kmerEntropyPlot                         html  
    kmerKLPlot                              html  
    list2df                                 html  
    makeReport                              html  
    plotBases                               html  
    plotGC                                  html  
    plotQuals                               html  
    plotSeqLengths                          html  
    qualPlot-methods                        html  
    readSeqFile                             html  
    scale_color_dna                         html  
    scale_color_iupac                       html  
    seqlenPlot-methods                      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 'qrqc' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_io.c -o R_init_io.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c io.c -o io.o
In file included from io.c:12:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: warning: 'kseq_destroy' defined but not used [-Wunused-function]
  SCOPE void kseq_destroy(kseq_t *ks)         \
             ^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
  __KSEQ_BASIC(SCOPE, type_t)     \
  ^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^~~~~~~~~~
io.c:29:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(FILE_TYPE*, gzreadclone)
 ^~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o qrqc.dll tmp.def R_init_io.o io.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/qrqc.buildbin-libdir/qrqc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qrqc' as qrqc_1.48.0.zip
* DONE (qrqc)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'qrqc' successfully unpacked and MD5 sums checked

Tests output

qrqc.Rcheck/tests_i386/test-functions.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> ## test-functions.R - unit test some functions
> require(testthat)
Loading required package: testthat
> EPSILON <- 0.001
>   
> test_that(".trimRightCols", {
+   t1 <- matrix(c(2, 3, 4, 5, 0, 4, 0, 0), 2, 4)
+   expect_that(qrqc:::.trimRightCols(t1), is_equivalent_to(t1[, -4]))
+ })
Test passed 
> 
> test_that(".trimArray", {
+   t1 <- c(2, 3, 4, 5, 0, 4, 0, 0)
+   expect_that(qrqc:::.trimArray(t1), is_equivalent_to(t1[1:6]))
+ })
Test passed 
> 
> 
> test_that("length2weights", {
+   l <- c(0, 0, 0, 0, 10, 20, 30, 40)
+   expect_that(qrqc:::lengths2weights(l),
+               is_equivalent_to(c(100, 100, 100, 100, 100, 90, 70, 40)))
+ })
Test passed 
> 
> test_that("meanFromBins", {
+   m1 <- structure(list(`26` = c(2L, 0L, 0L, 2L, 3L, 0L, 0L, 0L, 1L, 0L),
+                        `27` = c(1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L),
+                        `28` = c(3L, 7L, 5L, 4L, 4L, 1L, 0L, 3L, 2L, 2L),
+                        `29` = c(1L, 0L, 1L, 1L, 1L, 3L, 0L, 4L, 1L, 1L),
+                        `30` = c(4L, 2L, 5L, 3L, 4L, 3L, 3L, 4L, 3L, 5L),
+                        `31` = c(0L, 0L, 2L, 0L, 1L, 1L, 1L, 1L, 1L, 3L), 
+                        `32` = c(3L, 8L, 3L, 2L, 7L, 5L, 0L, 4L, 8L, 4L),
+                        `33` = c(4L, 1L, 3L, 3L, 4L, 2L, 1L, 5L, 1L, 5L),
+                        `34` = c(2L, 6L, 3L, 1L, 3L, 2L, 12L, 4L, 4L, 1L),
+                        `35` = c(10L, 6L, 11L, 14L, 8L, 13L, 8L, 13L, 12L, 13L),
+                        `36` = c(14L, 13L, 16L, 15L, 14L, 18L, 21L, 15L, 20L, 16L)),
+                   .Names = c("26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36"),
+                   row.names = c(NA, 10L), class = "data.frame")
+   m1 <- cbind(position=1:nrow(m1), m1)
+   expect_that(qrqc:::meanFromBins(m1) - 33.60487 < EPSILON, is_true())
+ })
-- Warning (???): meanFromBins -------------------------------------------------
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...)
 2. testthat:::condition(object)

> 
> test_that("binned2quantilefunc", {
+   b <- c(0, 1, 2, 3, 4, 5, 6, 7, 6, 5, 4, 3, 2, 1, 0)
+   names(b) <- 1:length(b)
+   f <- qrqc:::binned2quantilefunc(b)
+   expect_that(f(0.25), is_equivalent_to(5.45))
+   expect_that(f(0.5), is_equivalent_to(7.5))
+   expect_that(f(0.75), is_equivalent_to(9.55))
+ })
Test passed 
> 
> test_that("binned2boxplot", {
+   b <- c(0, 1, 2, 3, 4, 5, 6, 7, 6, 5, 4, 3, 2, 1, 0)
+   names(b) <- 1:length(b)
+   f <- qrqc:::binned2quantilefunc(b)
+   ans <- structure(c(2, 3.63333333333333, 5.45, 7.5, 9.55, 11.3666666666667, 14),
+                    .Names = c("ymin", "alt.lower", "lower", "middle", "upper", "alt.upper", "ymax"))
+                                                   
+   expect_that(qrqc:::binned2boxplot(b), is_equivalent_to(ans))
+ })
Test passed 
> 
> 
> test_that("calcKL", {
+   ## Check that our sample spaces sum to 1
+   s.fastq <- qrqc:::readSeqFile(system.file('extdata', 'test.fastq',
+     package='qrqc'), hash.prop=1)
+ 
+   eps <- 1e-4
+   kld <- qrqc:::calcKL(s.fastq)
+   expect_that(all(with(kld, aggregate(p, list(position), sum))[, 2] - 1 < EPSILON), is_true())
+   expect_that(all(with(kld, aggregate(q, list(position), sum))[, 2] - 1 < EPSILON), is_true())
+ })
-- Warning (???): calcKL -------------------------------------------------------
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...)
 2. testthat:::condition(object)

-- Warning (???): calcKL -------------------------------------------------------
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...)
 2. testthat:::condition(object)

> 
> proc.time()
   user  system elapsed 
  14.93    1.92   16.86 

qrqc.Rcheck/tests_x64/test-functions.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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.

> ## test-functions.R - unit test some functions
> require(testthat)
Loading required package: testthat
> EPSILON <- 0.001
>   
> test_that(".trimRightCols", {
+   t1 <- matrix(c(2, 3, 4, 5, 0, 4, 0, 0), 2, 4)
+   expect_that(qrqc:::.trimRightCols(t1), is_equivalent_to(t1[, -4]))
+ })
Test passed 
> 
> test_that(".trimArray", {
+   t1 <- c(2, 3, 4, 5, 0, 4, 0, 0)
+   expect_that(qrqc:::.trimArray(t1), is_equivalent_to(t1[1:6]))
+ })
Test passed 
> 
> 
> test_that("length2weights", {
+   l <- c(0, 0, 0, 0, 10, 20, 30, 40)
+   expect_that(qrqc:::lengths2weights(l),
+               is_equivalent_to(c(100, 100, 100, 100, 100, 90, 70, 40)))
+ })
Test passed 
> 
> test_that("meanFromBins", {
+   m1 <- structure(list(`26` = c(2L, 0L, 0L, 2L, 3L, 0L, 0L, 0L, 1L, 0L),
+                        `27` = c(1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L),
+                        `28` = c(3L, 7L, 5L, 4L, 4L, 1L, 0L, 3L, 2L, 2L),
+                        `29` = c(1L, 0L, 1L, 1L, 1L, 3L, 0L, 4L, 1L, 1L),
+                        `30` = c(4L, 2L, 5L, 3L, 4L, 3L, 3L, 4L, 3L, 5L),
+                        `31` = c(0L, 0L, 2L, 0L, 1L, 1L, 1L, 1L, 1L, 3L), 
+                        `32` = c(3L, 8L, 3L, 2L, 7L, 5L, 0L, 4L, 8L, 4L),
+                        `33` = c(4L, 1L, 3L, 3L, 4L, 2L, 1L, 5L, 1L, 5L),
+                        `34` = c(2L, 6L, 3L, 1L, 3L, 2L, 12L, 4L, 4L, 1L),
+                        `35` = c(10L, 6L, 11L, 14L, 8L, 13L, 8L, 13L, 12L, 13L),
+                        `36` = c(14L, 13L, 16L, 15L, 14L, 18L, 21L, 15L, 20L, 16L)),
+                   .Names = c("26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36"),
+                   row.names = c(NA, 10L), class = "data.frame")
+   m1 <- cbind(position=1:nrow(m1), m1)
+   expect_that(qrqc:::meanFromBins(m1) - 33.60487 < EPSILON, is_true())
+ })
-- Warning (???): meanFromBins -------------------------------------------------
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...)
 2. testthat:::condition(object)

> 
> test_that("binned2quantilefunc", {
+   b <- c(0, 1, 2, 3, 4, 5, 6, 7, 6, 5, 4, 3, 2, 1, 0)
+   names(b) <- 1:length(b)
+   f <- qrqc:::binned2quantilefunc(b)
+   expect_that(f(0.25), is_equivalent_to(5.45))
+   expect_that(f(0.5), is_equivalent_to(7.5))
+   expect_that(f(0.75), is_equivalent_to(9.55))
+ })
Test passed 
> 
> test_that("binned2boxplot", {
+   b <- c(0, 1, 2, 3, 4, 5, 6, 7, 6, 5, 4, 3, 2, 1, 0)
+   names(b) <- 1:length(b)
+   f <- qrqc:::binned2quantilefunc(b)
+   ans <- structure(c(2, 3.63333333333333, 5.45, 7.5, 9.55, 11.3666666666667, 14),
+                    .Names = c("ymin", "alt.lower", "lower", "middle", "upper", "alt.upper", "ymax"))
+                                                   
+   expect_that(qrqc:::binned2boxplot(b), is_equivalent_to(ans))
+ })
Test passed 
> 
> 
> test_that("calcKL", {
+   ## Check that our sample spaces sum to 1
+   s.fastq <- qrqc:::readSeqFile(system.file('extdata', 'test.fastq',
+     package='qrqc'), hash.prop=1)
+ 
+   eps <- 1e-4
+   kld <- qrqc:::calcKL(s.fastq)
+   expect_that(all(with(kld, aggregate(p, list(position), sum))[, 2] - 1 < EPSILON), is_true())
+   expect_that(all(with(kld, aggregate(q, list(position), sum))[, 2] - 1 < EPSILON), is_true())
+ })
-- Warning (???): calcKL -------------------------------------------------------
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...)
 2. testthat:::condition(object)

-- Warning (???): calcKL -------------------------------------------------------
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...)
 2. testthat:::condition(object)

> 
> proc.time()
   user  system elapsed 
  16.43    0.82   17.25 

Example timings

qrqc.Rcheck/examples_i386/qrqc-Ex.timings

nameusersystemelapsed
FASTASummary-class000
FASTQSummary-class000
SequenceSummary-class000
basePlot-methods3.780.384.18
calcKL1.300.111.41
gcPlot-methods2.450.012.47
getBase-methods1.300.021.33
getBaseProp-methods1.300.011.31
getGC-methods1.120.021.14
getKmer-methods1.580.001.58
getMCQual-methods2.550.142.69
getQual-methods1.660.181.84
getSeqlen-methods1.230.321.55
kmerEntropyPlot2.720.122.84
kmerKLPlot6.940.317.25
list2df3.220.053.27
makeReport2.140.192.32
plotBases000
plotGC000
plotQuals000
plotSeqLengths000
qualPlot-methods3.950.124.08
readSeqFile0.960.000.97
scale_color_dna1.070.021.11
scale_color_iupac1.190.011.20
seqlenPlot-methods2.160.042.19

qrqc.Rcheck/examples_x64/qrqc-Ex.timings

nameusersystemelapsed
FASTASummary-class000
FASTQSummary-class0.000.020.02
SequenceSummary-class000
basePlot-methods4.200.194.39
calcKL1.230.011.25
gcPlot-methods2.320.032.34
getBase-methods1.290.021.32
getBaseProp-methods1.280.011.29
getGC-methods1.000.041.03
getKmer-methods1.520.011.53
getMCQual-methods2.140.102.24
getQual-methods1.120.001.12
getSeqlen-methods1.100.011.11
kmerEntropyPlot2.980.093.08
kmerKLPlot5.390.055.44
list2df4.120.024.15
makeReport2.520.062.57
plotBases000
plotGC000
plotQuals000
plotSeqLengths000
qualPlot-methods3.110.023.13
readSeqFile0.980.011.00
scale_color_dna1.140.001.14
scale_color_iupac1.240.021.25
seqlenPlot-methods2.280.032.31