Aaron Lun
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/csaw |
| Branch: RELEASE_3_8 |
| Last Commit: 63ef4a6 |
| Last Changed Date: 2018-12-20 19:32:06 -0400 (Thu, 20 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:50:54 -0400 (Tue, 16 Apr 2019).
| Package 350/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| csaw 1.16.1 Aaron Lun
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: csaw |
| Version: 1.16.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings csaw_1.16.1.tar.gz |
| StartedAt: 2019-04-15 23:14:46 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:23:29 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 522.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: csaw.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings csaw_1.16.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/csaw.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘csaw/DESCRIPTION’ ... OK
* this is package ‘csaw’ version ‘1.16.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘csaw’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
libs 5.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
detailRanges 7.576 0.096 7.698
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/csaw.Rcheck/00check.log’
for details.
csaw.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL csaw
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘csaw’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c annotator.cpp -o annotator.o
annotator.cpp: In function ‘SEXPREC* annotate_overlaps(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
annotator.cpp:47:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (counter < nolaps && query[counter]==curreg) {
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c bam_utils.cpp -o bam_utils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c best_in_cluster.cpp -o best_in_cluster.o
best_in_cluster.cpp: In function ‘SEXPREC* best_in_cluster(SEXP, SEXP, SEXP)’:
best_in_cluster.cpp:11:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (nwin!=clustids.size() || nwin!=winweight.size()) {
^
best_in_cluster.cpp:11:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (nwin!=clustids.size() || nwin!=winweight.size()) {
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c check_bimodality.cpp -o check_bimodality.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c correlate_reads.cpp -o correlate_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c find_maxima.cpp -o find_maxima.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c get_cluster_stats.cpp -o get_cluster_stats.o
get_cluster_stats.cpp: In function ‘SEXPREC* get_cluster_stats(SEXP, SEXP, SEXP, SEXP, SEXP)’:
get_cluster_stats.cpp:17:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (nwin!=current.size()) {
^
get_cluster_stats.cpp:28:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (clustid.size()!=nwin) {
^
get_cluster_stats.cpp:33:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (nwin!=winweight.size()) {
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c get_profile.cpp -o get_profile.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c get_rle_counts.cpp -o get_rle_counts.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c merge_windows.cpp -o merge_windows.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c pair_reads.cpp -o pair_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c single_reads.cpp -o single_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o csaw.so annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o pair_reads.o single_reads.o utils.o -L/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/usrlib -Wl,-rpath,/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/csaw/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘csaw.Rnw’
** testing if installed package can be loaded
* DONE (csaw)
csaw.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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.
> library(testthat)
> library(csaw)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
>
> test_check("csaw")
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
══ testthat results ═══════════════════════════════════════════════════════════
OK: 2687 SKIPPED: 0 FAILED: 0
>
>
> proc.time()
user system elapsed
277.588 1.312 280.456
csaw.Rcheck/csaw-Ex.timings
| name | user | system | elapsed | |
| SEmethods | 0.284 | 0.004 | 0.302 | |
| calculateCPM | 0.808 | 0.004 | 0.811 | |
| checkBimodality | 0.300 | 0.012 | 0.311 | |
| clusterFDR | 0.852 | 0.076 | 0.929 | |
| clusterWindows | 2.124 | 0.000 | 2.134 | |
| combineTests | 0.160 | 0.000 | 0.162 | |
| consolidateClusters | 2.848 | 0.004 | 2.852 | |
| consolidateTests | 0.48 | 0.00 | 0.48 | |
| consolidateWindows | 0.380 | 0.000 | 0.379 | |
| correlateReads | 0.212 | 0.004 | 0.226 | |
| csawUsersGuide | 0.000 | 0.000 | 0.001 | |
| detailRanges | 7.576 | 0.096 | 7.698 | |
| empiricalFDR | 0.052 | 0.000 | 0.055 | |
| extractReads | 0.724 | 0.000 | 0.726 | |
| filterWindows | 0.752 | 0.000 | 0.752 | |
| findMaxima | 0.172 | 0.000 | 0.169 | |
| getBestTest | 0.076 | 0.000 | 0.079 | |
| getPESizes | 0.156 | 0.000 | 0.158 | |
| getWidths | 0.704 | 0.004 | 0.709 | |
| maximizeCcf | 0.000 | 0.000 | 0.002 | |
| mergeWindows | 0.068 | 0.000 | 0.068 | |
| mixedClusters | 0.072 | 0.000 | 0.071 | |
| normOffsets | 0.128 | 0.000 | 0.130 | |
| overlapStats | 0.500 | 0.000 | 0.501 | |
| profileSites | 0.632 | 0.004 | 0.643 | |
| readParam | 0.040 | 0.000 | 0.038 | |
| regionCounts | 0.360 | 0.004 | 0.365 | |
| scaledAverage | 0.492 | 0.000 | 0.495 | |
| strandedCounts | 1.872 | 0.012 | 1.884 | |
| upweightSummit | 0.008 | 0.000 | 0.007 | |
| windowCounts | 1.048 | 0.000 | 1.050 | |
| wwhm | 0.096 | 0.000 | 0.096 | |