Vince Buffalo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/qrqc |
| Branch: RELEASE_3_9 |
| Last Commit: d6aef92 |
| Last Changed Date: 2019-05-02 11:53:24 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:59:45 -0400 (Wed, 16 Oct 2019).
| Package 1288/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| qrqc 1.38.0 Vince Buffalo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: qrqc |
| Version: 1.38.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:qrqc.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings qrqc_1.38.0.tar.gz |
| StartedAt: 2019-10-16 04:12:35 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:18:20 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 345.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: qrqc.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:qrqc.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings qrqc_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/qrqc.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘qrqc/DESCRIPTION’ ... OK * this is package ‘qrqc’ version ‘1.38.0’ * 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:33:25: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] io.c:351:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types] io.c:453:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types] io.c:454:14: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] See ‘/home/biocbuild/bbs-3.9-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 :: 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 : : 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 : : 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed kmerKLPlot 12.204 0.040 12.302 basePlot-methods 6.783 0.156 6.959 * 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, 5 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/qrqc.Rcheck/00check.log’ for details.
qrqc.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL qrqc
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘qrqc’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c R_init_io.c -o R_init_io.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c io.c -o io.o
io.c: In function ‘summarize_file’:
io.c:33:25: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
#define FILE_OPEN(x, m) (gzopen(x, m))
^
io.c:348:19: note: in expansion of macro ‘FILE_OPEN’
FILE_TYPE *fp = FILE_OPEN(CHAR(STRING_ELT(filename, 0)), "r");
^~~~~~~~~
io.c:351:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types]
block = kseq_init(fp);
^~
In file included from io.c:12:0:
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
SCOPE kseq_t *kseq_init(type_t fd) \
^
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’
__KSEQ_BASIC(SCOPE, type_t) \
^~~~~~~~~~~~
/home/biocbuild/bbs-3.9-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:35:1: note: in expansion of macro ‘KSEQ_INIT’
KSEQ_INIT(gzFile, gzread)
^~~~~~~~~
io.c:453:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types]
block = kseq_init(fp);
^~
In file included from io.c:12:0:
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
SCOPE kseq_t *kseq_init(type_t fd) \
^
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’
__KSEQ_BASIC(SCOPE, type_t) \
^~~~~~~~~~~~
/home/biocbuild/bbs-3.9-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:35:1: note: in expansion of macro ‘KSEQ_INIT’
KSEQ_INIT(gzFile, gzread)
^~~~~~~~~
io.c:454:14: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
FILE_CLOSE(fp);
^
io.c:34:32: note: in definition of macro ‘FILE_CLOSE’
#define FILE_CLOSE(x) (gzclose(x))
^
In file included from io.c:31:0:
/usr/include/zlib.h:1631:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
In file included from io.c:12:0:
At top level:
/home/biocbuild/bbs-3.9-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) \
^
/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’
__KSEQ_BASIC(SCOPE, type_t) \
^~~~~~~~~~~~
/home/biocbuild/bbs-3.9-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:35:1: note: in expansion of macro ‘KSEQ_INIT’
KSEQ_INIT(gzFile, gzread)
^~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o qrqc.so R_init_io.o io.o /home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/libhts.a -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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)
qrqc.Rcheck/tests/test-functions.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
17.633 0.610 18.327
qrqc.Rcheck/qrqc-Ex.timings
| name | user | system | elapsed | |
| FASTASummary-class | 0.002 | 0.000 | 0.003 | |
| FASTQSummary-class | 0.001 | 0.000 | 0.001 | |
| SequenceSummary-class | 0.001 | 0.000 | 0.001 | |
| basePlot-methods | 6.783 | 0.156 | 6.959 | |
| calcKL | 2.235 | 0.020 | 2.279 | |
| gcPlot-methods | 3.318 | 0.016 | 3.335 | |
| getBase-methods | 2.025 | 0.004 | 2.085 | |
| getBaseProp-methods | 1.978 | 0.000 | 1.995 | |
| getGC-methods | 1.691 | 0.000 | 1.707 | |
| getKmer-methods | 2.822 | 0.000 | 2.828 | |
| getMCQual-methods | 1.896 | 0.011 | 1.932 | |
| getQual-methods | 1.890 | 0.008 | 1.906 | |
| getSeqlen-methods | 1.559 | 0.000 | 1.570 | |
| kmerEntropyPlot | 4.410 | 0.000 | 4.445 | |
| kmerKLPlot | 12.204 | 0.040 | 12.302 | |
| list2df | 4.798 | 0.024 | 4.840 | |
| makeReport | 3.527 | 0.016 | 3.549 | |
| plotBases | 0 | 0 | 0 | |
| plotGC | 0.001 | 0.000 | 0.001 | |
| plotQuals | 0.001 | 0.000 | 0.000 | |
| plotSeqLengths | 0.001 | 0.000 | 0.001 | |
| qualPlot-methods | 4.370 | 0.008 | 4.389 | |
| readSeqFile | 1.349 | 0.012 | 1.370 | |
| scale_color_dna | 1.938 | 0.004 | 1.947 | |
| scale_color_iupac | 1.940 | 0.008 | 1.958 | |
| seqlenPlot-methods | 3.558 | 0.004 | 3.575 | |