Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:09:31 -0400 (Thu, 12 Apr 2018).
Package 1098/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
qrqc 1.32.0 Vince Buffalo
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: qrqc |
Version: 1.32.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings qrqc_1.32.0.tar.gz |
StartedAt: 2018-04-12 02:03:17 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 02:07:42 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 265.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: qrqc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings qrqc_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/qrqc.Rcheck’ * using R version 3.4.4 (2018-03-15) * 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 ‘1.32.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: ‘reshape’ ‘ggplot2’ ‘Biostrings’ ‘biovizBase’ ‘brew’ ‘xtable’ ‘Rsamtools’ ‘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. * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: 'Rsamtools' '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 ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed kmerKLPlot 7.204 0.06 7.269 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.6-bioc/meat/qrqc.Rcheck/00check.log’ for details.
qrqc.Rcheck/00install.out
* installing *source* package ‘qrqc’ ... ** libs gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c R_init_io.c -o R_init_io.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c io.c -o io.o io.c: In function ‘summarize_file’: io.c:32:25: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] #define FILE_OPEN(x, m) (gzopen(x, m)) ^ io.c:347:19: note: in expansion of macro ‘FILE_OPEN’ FILE_TYPE *fp = FILE_OPEN(CHAR(STRING_ELT(filename, 0)), "r"); ^ io.c:350:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types] block = kseq_init(fp); ^ In file included from io.c:11:0: /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include/samtools/kseq.h:152:16: 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-3.6-bioc/R/library/Rsamtools/include/samtools/kseq.h:223:2: note: in expansion of macro ‘__KSEQ_BASIC’ __KSEQ_BASIC(SCOPE, type_t) \ ^ /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include/samtools/kseq.h:226:35: note: in expansion of macro ‘KSEQ_INIT2’ #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ io.c:34:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^ io.c:452:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types] block = kseq_init(fp); ^ In file included from io.c:11:0: /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include/samtools/kseq.h:152:16: 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-3.6-bioc/R/library/Rsamtools/include/samtools/kseq.h:223:2: note: in expansion of macro ‘__KSEQ_BASIC’ __KSEQ_BASIC(SCOPE, type_t) \ ^ /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include/samtools/kseq.h:226:35: note: in expansion of macro ‘KSEQ_INIT2’ #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ io.c:34:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^ io.c:453:14: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] FILE_CLOSE(fp); ^ io.c:33:32: note: in definition of macro ‘FILE_CLOSE’ #define FILE_CLOSE(x) (gzclose(x)) ^ In file included from io.c:30:0: /usr/include/zlib.h:1511:24: 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:11:0: io.c: At top level: /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include/samtools/kseq.h:158:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] SCOPE void kseq_destroy(kseq_t *ks) \ ^ /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include/samtools/kseq.h:223:2: note: in expansion of macro ‘__KSEQ_BASIC’ __KSEQ_BASIC(SCOPE, type_t) \ ^ /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include/samtools/kseq.h:226:35: note: in expansion of macro ‘KSEQ_INIT2’ #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ io.c:34:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^ g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o qrqc.so R_init_io.o io.o /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.6-bioc/meat/qrqc.Rcheck/qrqc/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (qrqc)
qrqc.Rcheck/tests/test-functions.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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 10.780 0.216 11.604
qrqc.Rcheck/qrqc-Ex.timings
name | user | system | elapsed | |
FASTASummary-class | 0.004 | 0.000 | 0.003 | |
FASTQSummary-class | 0.000 | 0.000 | 0.001 | |
SequenceSummary-class | 0.000 | 0.000 | 0.001 | |
basePlot-methods | 4.476 | 0.020 | 4.497 | |
calcKL | 0.624 | 0.008 | 0.633 | |
gcPlot-methods | 1.100 | 0.000 | 1.101 | |
getBase-methods | 0.584 | 0.000 | 0.584 | |
getBaseProp-methods | 0.800 | 0.000 | 0.797 | |
getGC-methods | 0.368 | 0.008 | 0.375 | |
getKmer-methods | 0.696 | 0.008 | 0.703 | |
getMCQual-methods | 0.508 | 0.008 | 0.519 | |
getQual-methods | 0.680 | 0.004 | 0.687 | |
getSeqlen-methods | 0.400 | 0.000 | 0.402 | |
kmerEntropyPlot | 1.964 | 0.044 | 2.010 | |
kmerKLPlot | 7.204 | 0.060 | 7.269 | |
list2df | 1.140 | 0.036 | 1.177 | |
makeReport | 1.664 | 0.016 | 1.681 | |
plotBases | 0.000 | 0.000 | 0.001 | |
plotGC | 0 | 0 | 0 | |
plotQuals | 0.000 | 0.000 | 0.001 | |
plotSeqLengths | 0.000 | 0.000 | 0.001 | |
qualPlot-methods | 1.372 | 0.012 | 1.385 | |
readSeqFile | 0.204 | 0.016 | 0.220 | |
scale_color_dna | 0.348 | 0.000 | 0.350 | |
scale_color_iupac | 0.372 | 0.012 | 0.388 | |
seqlenPlot-methods | 0.788 | 0.016 | 0.807 | |