##############################################################################
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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_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/qrqc.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qrqc/DESCRIPTION’ ... OK
* this is package ‘qrqc’ version ‘1.46.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘qrqc’ can be installed ... WARNING
Found the following significant warnings:
  io.c:348:14: warning: incompatible pointer types initializing 'gzFile *' (aka 'struct gzFile_s **') with an expression of type 'gzFile' (aka 'struct gzFile_s *') [-Wincompatible-pointer-types]
  io.c:351:21: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  io.c:453:21: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  io.c:454:14: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/qrqc.Rcheck/00install.out’ for details.
* 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 ... 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
kmerKLPlot       9.000  0.109   9.113
qualPlot-methods 5.758  0.167   5.934
basePlot-methods 5.636  0.223   5.871
list2df          5.345  0.029   5.378
* 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: 1 WARNING, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/qrqc.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qrqc
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘qrqc’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_io.c -o R_init_io.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c io.c -o io.o
io.c:348:14: warning: incompatible pointer types initializing 'gzFile *' (aka 'struct gzFile_s **') with an expression of type 'gzFile' (aka 'struct gzFile_s *') [-Wincompatible-pointer-types]
  FILE_TYPE *fp = FILE_OPEN(CHAR(STRING_ELT(filename, 0)), "r");
             ^    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c:351:21: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  block = kseq_init(fp);
                    ^~
                    *
io.c:35:1: note: passing argument to parameter 'fd' here
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/4.1/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/4.1/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/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:170:33: note: expanded from macro '__KSEQ_BASIC'
        SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
                                       ^
io.c:453:21: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  block = kseq_init(fp);
                    ^~
                    *
io.c:35:1: note: passing argument to parameter 'fd' here
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/4.1/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/4.1/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/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:170:33: note: expanded from macro '__KSEQ_BASIC'
        SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
                                       ^
io.c:454:14: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  FILE_CLOSE(fp);
             ^~
             *
io.c:34:32: note: expanded from macro 'FILE_CLOSE'
#define FILE_CLOSE(x) (gzclose(x))
                               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/zlib.h:1644:43: note: passing argument to parameter 'file' here
ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                                          ^
io.c:35:1: warning: unused function 'kseq_destroy' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/4.1/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/4.1/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/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:176:13: note: expanded from macro '__KSEQ_BASIC'
        SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
                   ^
5 warnings generated.
clang -mmacosx-version-min=10.13 -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/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-qrqc/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (qrqc)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 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 
 21.217   0.959  22.170