Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:15 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the qrqc package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qrqc.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1566/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qrqc 1.52.0 (landing page) Vince Buffalo
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: qrqc |
Version: 1.52.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:qrqc.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings qrqc_1.52.0.tar.gz |
StartedAt: 2023-04-10 23:11:35 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 23:17:56 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 381.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: qrqc.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:qrqc.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings qrqc_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/qrqc.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘qrqc/DESCRIPTION’ ... OK * this is package ‘qrqc’ version ‘1.52.0’ * 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 of ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-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-3.16-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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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 ... ‘qrqc.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 6 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/qrqc.Rcheck/00check.log’ for details.
qrqc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL qrqc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘qrqc’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-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 of ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 33 | #define FILE_OPEN(x, m) (gzopen(x, m)) | ^ io.c:348:19: note: in expansion of macro ‘FILE_OPEN’ 348 | 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] 351 | block = kseq_init(fp); | ^~ | | | struct gzFile_s ** In file included from io.c:12: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:165:33: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 165 | SCOPE kseq_t *kseq_init(type_t fd) \ /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:237:2: note: in expansion of macro ‘__KSEQ_BASIC’ 237 | __KSEQ_BASIC(SCOPE, type_t) \ | ^~~~~~~~~~~~ /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’ 35 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ io.c:453:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types] 453 | block = kseq_init(fp); | ^~ | | | struct gzFile_s ** In file included from io.c:12: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:165:33: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 165 | SCOPE kseq_t *kseq_init(type_t fd) \ /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:237:2: note: in expansion of macro ‘__KSEQ_BASIC’ 237 | __KSEQ_BASIC(SCOPE, type_t) \ | ^~~~~~~~~~~~ /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’ 35 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ io.c:454:14: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 454 | FILE_CLOSE(fp); | ^~ | | | struct gzFile_s ** io.c:34:32: note: in definition of macro ‘FILE_CLOSE’ 34 | #define FILE_CLOSE(x) (gzclose(x)) | ^ In file included from /usr/include/zlib.h:34, from io.c:31: /usr/include/zlib.h:1631:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1631 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ In file included from io.c:12: At top level: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:171:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] 171 | SCOPE void kseq_destroy(kseq_t *ks) \ | ^~~~~~~~~~~~ /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:237:2: note: in expansion of macro ‘__KSEQ_BASIC’ 237 | __KSEQ_BASIC(SCOPE, type_t) \ | ^~~~~~~~~~~~ /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’ 35 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o qrqc.so R_init_io.o io.o /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 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 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 (local) 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 (local) condition(object) ── Warning (???): calcKL ─────────────────────────────────────────────────────── `is_true()` is deprecated. Please use `expect_true()` instead. Backtrace: 1. testthat::expect_that(...) 2. testthat (local) condition(object) > > proc.time() user system elapsed 16.023 0.844 16.855
qrqc.Rcheck/qrqc-Ex.timings
name | user | system | elapsed | |
FASTASummary-class | 0.001 | 0.000 | 0.002 | |
FASTQSummary-class | 0.000 | 0.000 | 0.001 | |
SequenceSummary-class | 0.001 | 0.000 | 0.001 | |
basePlot-methods | 4.210 | 0.207 | 4.419 | |
calcKL | 1.025 | 0.032 | 1.057 | |
gcPlot-methods | 1.894 | 0.056 | 1.951 | |
getBase-methods | 1.062 | 0.000 | 1.062 | |
getBaseProp-methods | 1.084 | 0.019 | 1.103 | |
getGC-methods | 0.917 | 0.008 | 0.925 | |
getKmer-methods | 1.547 | 0.004 | 1.552 | |
getMCQual-methods | 1.136 | 0.044 | 1.181 | |
getQual-methods | 2.027 | 0.068 | 2.096 | |
getSeqlen-methods | 0.852 | 0.012 | 0.864 | |
kmerEntropyPlot | 2.283 | 0.069 | 2.352 | |
kmerKLPlot | 4.884 | 0.108 | 4.992 | |
list2df | 2.562 | 0.048 | 2.611 | |
makeReport | 2.093 | 0.043 | 2.137 | |
plotBases | 0.001 | 0.001 | 0.000 | |
plotGC | 0 | 0 | 0 | |
plotQuals | 0 | 0 | 0 | |
plotSeqLengths | 0 | 0 | 0 | |
qualPlot-methods | 2.790 | 0.039 | 2.830 | |
readSeqFile | 0.865 | 0.020 | 0.885 | |
scale_color_dna | 1.011 | 0.012 | 1.023 | |
scale_color_iupac | 1.021 | 0.012 | 1.032 | |
seqlenPlot-methods | 1.919 | 0.024 | 1.943 | |