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CHECK report for qrqc on merida2

This page was generated on 2019-04-09 13:25:48 -0400 (Tue, 09 Apr 2019).

Package 1262/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qrqc 1.37.1
Vince Buffalo
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/qrqc
Branch: master
Last Commit: b11d69f
Last Changed Date: 2019-03-20 15:09:11 -0400 (Wed, 20 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: qrqc
Version: 1.37.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qrqc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qrqc_1.37.1.tar.gz
StartedAt: 2019-04-09 03:06:15 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:12:47 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 391.6 seconds
RetCode: 0
Status:  OK 
CheckDir: qrqc.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qrqc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qrqc_1.37.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/qrqc.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qrqc/DESCRIPTION’ ... OK
* this is package ‘qrqc’ version ‘1.37.1’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
kmerKLPlot       14.805  0.306  15.176
list2df           6.809  0.083   6.909
basePlot-methods  6.393  0.165   6.640
qualPlot-methods  5.688  0.097   5.814
makeReport        5.003  0.189   5.365
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/qrqc.Rcheck/00check.log’
for details.



Installation output

qrqc.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qrqc
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘qrqc’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_io.c -o R_init_io.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c io.c -o io.o
io.c:35:1: warning: unused function 'kseq_destroy' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib/kseq.h:176:13: note: expanded from macro '__KSEQ_BASIC'
        SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
                   ^
1 warning generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o qrqc.so R_init_io.o io.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/qrqc/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qrqc)

Tests output

qrqc.Rcheck/tests/test-functions.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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_that(".trimArray", {
+   t1 <- c(2, 3, 4, 5, 0, 4, 0, 0)
+   expect_that(qrqc:::.trimArray(t1), is_equivalent_to(t1[1:6]))
+ })
> 
> 
> 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_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())
+ })
> 
> 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_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_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())
+ })
> 
> proc.time()
   user  system elapsed 
 15.722   0.803  16.611 

Example timings

qrqc.Rcheck/qrqc-Ex.timings

nameusersystemelapsed
FASTASummary-class0.0010.0000.002
FASTQSummary-class0.0010.0000.001
SequenceSummary-class0.0010.0000.001
basePlot-methods6.3930.1656.640
calcKL2.5200.0392.592
gcPlot-methods3.6780.0263.733
getBase-methods2.1530.0092.173
getBaseProp-methods2.8350.0102.879
getGC-methods1.7520.0141.777
getKmer-methods2.8320.0112.864
getMCQual-methods1.6210.0281.655
getQual-methods1.8880.0141.912
getSeqlen-methods1.4560.0121.476
kmerEntropyPlot4.0450.0544.122
kmerKLPlot14.805 0.30615.176
list2df6.8090.0836.909
makeReport5.0030.1895.365
plotBases0.0000.0000.001
plotGC0.0000.0010.000
plotQuals0.0000.0000.001
plotSeqLengths000
qualPlot-methods5.6880.0975.814
readSeqFile1.9270.0191.979
scale_color_dna2.2120.0172.245
scale_color_iupac1.9560.0061.983
seqlenPlot-methods3.5500.0113.582