Vince Buffalo
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/qrqc |
| Branch: RELEASE_3_12 |
| Last Commit: b90bb78 |
| Last Changed Date: 2020-10-27 10:41:07 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:00 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the qrqc package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1428/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qrqc 1.44.0 (landing page) Vince Buffalo
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: qrqc |
| Version: 1.44.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qrqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings qrqc_1.44.0.tar.gz |
| StartedAt: 2021-05-06 05:53:56 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:03:56 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 599.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qrqc.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qrqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings qrqc_1.44.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/qrqc.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.44.0'
* 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-3.12-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-3.12-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
basePlot-methods 6.92 0.87 7.79
kmerKLPlot 5.67 0.27 5.94
qualPlot-methods 5.45 0.03 5.49
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
kmerKLPlot 8.81 0.12 8.93
basePlot-methods 4.95 0.06 5.02
* 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-3.12-bioc/meat/qrqc.Rcheck/00check.log'
for details.
qrqc.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/qrqc_1.44.0.tar.gz && rm -rf qrqc.buildbin-libdir && mkdir qrqc.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qrqc.buildbin-libdir qrqc_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL qrqc_1.44.0.zip && rm qrqc_1.44.0.tar.gz qrqc_1.44.0.zip
###
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% 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 353k 100 353k 0 0 21.9M 0 --:--:-- --:--:-- --:--:-- 23.0M
install for i386
* installing *source* package 'qrqc' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-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-3.12-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-3.12-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-3.12-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-3.12-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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-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-3.12-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-3.12-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-3.12-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-3.12-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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/qrqc.buildbin-libdir/qrqc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qrqc' as qrqc_1.44.0.zip
* DONE (qrqc)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'qrqc' successfully unpacked and MD5 sums checked
|
qrqc.Rcheck/tests_i386/test-functions.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
14.40 2.15 18.07
|
qrqc.Rcheck/tests_x64/test-functions.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
16.26 0.60 18.39
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qrqc.Rcheck/examples_i386/qrqc-Ex.timings
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qrqc.Rcheck/examples_x64/qrqc-Ex.timings
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